What a beautiful crystal structure is reported by Yasufumi Umena of Osaka City University and colleagues in Nature (473, 55; 2011 – paper here). They have revealed the entire photosystem II complex at 1.9 Å resolution, showing the hydration structure of the core Mn4CaO5 cluster along with the locations of 1,300 water molecules in a hydration shell that seems to offer several hydrogen-bonded channels for protons, water molecules for photolysis, or oxygen molecules. The latter are probably formed by oxidation of some of the four waters bound to the Mn cluster. I don’t recall ever seeing before such a complex, orchestrated and carefully rationalized example of a multifunctional hydration structure.
Collagen is generally considered a structural protein, but particular collagen motifs are also recognized as substrates by collagen binding proteins such as adhesins in some human pathogens. On the basis of MD simulations and comparison with crystal structures, Luigi Vitagliano at the Consiglio Nazionale delle Ricerce in Naples and colleagues say that the regions of collagen-binding adhesin CNA involved in binding to hydrophobic parts of the collagen triple helix are inherently prone to dewetting, making them primed to bind their target by reducing the desolvation penalty (Vitagliano et al., Biophys. J. 100, 2253-2261; 2011 – paper here). Moreover, besides these hydrophobic contacts the interaction between CNA and collagen is mediated by an intricate network of 13 water molecules.
Local water densities around biological systems can be calculated fairly accurately with a computationally cheap interaction-site model (based on the Ornstein-Zernicke integral equation), rather than with a full MD simulation, according to a new study by Vijay Pande at Stanford and colleagues, who compare the two for the hydration of GroEL (M. C. Stumpe et al., J. Phys. Chem. B 115, 319; 2011 – paper here).
In drug design, the surfaces of target proteins are often mapped out to look for ‘hot spots’ where it is particularly advantageous to place functional groups in the ligand complementary to those on the protein. This process often identifies many such local minima in a rugged potential-energy surface. But that’s in vacuo for a rigid surface. One might expect that including the protein’s conformational flexibility and interactions with water will smooth out this rugged landscape. But Katrina Lexa and Heather Carlson at the University of Michigan say that it doesn’t, unless the protein is allowed its full flexibility (JACS 133, 200; 2011 – paper here). In other words, there are no short cuts: if the molecule is semi-rigid, spurious hot spots remain.
Structured water molecules bound within cytochrome c have been suspected for some time of participating in the enzyme’s electron-transfer and oxygen reduction reactions, but it hasn’t been clear exactly how. Amandine Maréchal and Peter Rich at University College London have used FTIR spectroscopy to investigate the issue (PNAS pnas.1019419108 – paper here). They find that rearrangements of up to 8 water molecules are associated with the photolysis reaction, probably forming transient hydrogen-bonded pathways for proton conduction and gating.
More roles for water in protein-ligand binding are revealed by Michelle Sahai and Philip Biggin at Oxford (J. Phys. Chem. B 10.1021/jp200776t – paper here). They consider how the GluA2 ionotropic glutamate receptor binds both glutamate and the related compound AMPA, and find two quite distinct modes of binding. The difference seems to be in the location of a single water molecule in the binding cleft. They use density functional theory to figure out why it is more favourable for the water to sit in different positions in the two different cases. That they don’t seem yet to have fully settled that question (they cannot consider entropic contributions) seems to underline how tricky it might be to use bound waters in rational drug design.
Joe Dzubiella in Berlin has an interesting preprint on the thermodynamics of hydrophobic association which claims that the curvature of the interface is important. He points out how there seems to be a crossover at small size scales (about 1 nm) between enthalpy-driven hydrophobic association at larger scales and entropy-driven at smaller scales. But for concave binding cavities this does not seem to apply: enthalpy continues to dominate even at very small scales. Joe explains this on the basis that the surface-area-based models used to describe large-scale interactions on the basis of solvent-accessible area and surface tension remain applicable at small scales so long as “the antagonistic effects on concave vs. convex bending on water interface thermodynamics are properly taken into account”. The paper will appear in a forthcoming special issue of J. Stat. Phys. dedicated to water.
There’s a nice potted summary of current understanding of antifreeze protein ice-binding mechanisms by Kim Sharp of the University of Pennsylvania in PNAS (pnas.1104618108 – paper here). It is a commentary on a new study by Garnham et al. (PNAS pnas.1100429108), which I haven’t yet got hold of. They report the crystal structure of the AFP of an Antarctic bacterium, Marinomonas primoryensis, which has a new binding motif, a parallel beta-helix. This structure has the ice-binding surface fully solvent-exposed in the crystalline state, and so is likely to be “free from crystal-packing artifacts.” Much of this surface is hydrophobic (although anchored at the edges by H-bonds), and the claim is that this induces a clathrate-like structure in the first hydration layer that is close to the structure of ice – in other words, the AFP “brings its own ‘ice’ with it”.
With an eye on the Lum/Chandler/Weeks model of hydrophobic attraction, Pablo Debenedetti and colleagues have calculated the evaporation length scale – the separation of solvophobic plates at which capillary evaporation occurs – for water and a range of organic liquids (C. A. Cerdeiriña et al., J. Phys. Chem. Lett. 2, 1000; 2011 – paper here). There’s nothing conceptually new here, but the numbers are somewhat surprising: for water they find a length scale of about 1.5 microns at atmospheric pressure, which is much larger than I’d have expected. However, this applies for purely repulsive surfaces (contact angle of 180 degrees), which is of course rarely found, and never for protein surfaces. The length is also large for the organics, such as benzene, heptane and cyclohexane, but about a factor of 3 less so – water is (somewhat) anomalous here because of its large surface tension.
Hydration seems to respond to the flexibility of alicyclic systems, according to Annalisa Boscaino and Kevin Naidoo of the University of Cape Town in South Africa (J. Phys. Chem. B 10.1021/jp110248j – paper here). They find from MD simulations that molecules with a cyclopyranose framework, such as glucose, have a significantly higher hydration number than those based on a cyclohexane framework with hydroxyls, such as cyclohexanol. This seems to result from the greater rigidity of the former, enabling the formation of longer-lived hydrogen bonds to the surrounding water.
It’s generally thought that rearrangements of the hydrogen-bond network in bulk water must have a collective character. Andrei Tokmakoff at MIT and colleagues now provide evidence of that (R. A. Nicodemus et al., J. Phys. Chem. B 115, 5604; 2011 – paper here). They have used ultrafast IR spectroscopy of HOD in pure water to measure the energy barriers to spectral diffusion and reorientational relaxation, and find that the slow-decay component is consistent with collective reorganization.
Marcus Weinwurm and Christoph Dellago have calculated the vibrational spectra of single-file water molecules in narrow pores, enabling them to distinguish it from the stacked-ring structure in wider pores (J. Phys. Chem. B 115, 5268; 2011 – paper here).
Tuesday, May 24, 2011
Thursday, April 28, 2011
Water as glue
There is a very nice crop of papers to draw on for this post, many of which speak to very central questions in this field. First up is a paper in Nature Communications from Volkhard Helms and colleagues at Saarbrücken, which looks at the detailed role of interfacial water in the association of hydrophilic protein surfaces (M. Ahmad et al., Nat. Commun. 2, 261; 2011 – paper here). Whereas hydrophobic association has been the focus of a lot of recent attention, especially with a view to the possibility of a dewetting-induced process, hydrophilic surfaces have received less attention. That’s an important lacuna, since as the authors point out, around 70% of interfacial residues are hydrophilic. The common approach is to assume direct electrostatic interaction mediated by a continuum solvent. But the water network has a more complex role. As shown in these MD simulations of the barnase-barstar complex, water molecules mediate and stabilize the interactions between native contacts. Moreover, for electrostatic interactions to be important, the interfacial water’s dielectric constant needs to be reduced to reduce screening. This happens as a consequence of changes in the structure of the interfacial layers (the dielectric permittivity is less than 50% of the bulk value for interfacial separations of less than 1.2 nm), and it preferentially promotes electrostatic interactions normal to the surfaces. In other words, you could say that (once again, though arguably to put the cart before the horse) water does exactly what is required of it.
Jeremy England, now at Princeton, has a paper in press with Structure which shows that it is possible to estimate low-energy conformational changes in a protein, such as those involved in allosteric effects, on the basis simply of residue-by-residue hydrophobic effects. Specifically, he develops a method for determining the most energetically favourable way of burying hydrophobic residues, given a particular amino-acid sequence. This amounts to identifying the particular ‘burial modes’ of any given sequence. Thus, although the stabilities of conformations are doubtless multifactorial, hydrophobicity seems to be the major governing factor.
Calculating the surface free energies of heterogeneous surfaces exposed to water (such as protein surfaces) is tough. The approach of the Cassie equation is additive, but as Alenka Luzar and colleagues point out, that doesn’t always work (J. Wang et al., PNAS 108, 6374-6379; 2011 – paper here). They show that deviations from linear additivity result when parts of a surface are unevenly exposed to solvent. In particular, it seems that polar patches exert an inordinately strong influence, being able to ‘pin’ a droplet so that it might remain closely attached to adjacent hydrophobic patches. They examine these effects with reference to water droplets first on a functionalized graphene surface and then on the surface of melittin.
Daryl Eggers at San José State University presents an interesting approach to the energetics of reactions in aqueous solution, geared especially to biochemical equilibria, that treats the water as a reactant and product, thereby subsuming the local changes in water structure that inevitably accompany the reaction (Biochemistry 50, 2004-2012; 2011 – paper here). Here the free energy of bulk water is treated as a variable, allowing for the effects of all solutes including those that may not participate directly in the reaction (such as dissolved salts). As I understand it, this offers a means of accommodating the effects of such solutes (for example, in salting in/out) that does not make any assumptions about global changes in ‘water structure’, but represents only the global average of localized changes. Also jettisoned in that process is any insistence on putative structure-makers and structure-breakers; rather, solvation effects need be discussed only in what seems like relatively uncontentious terms of subpopulations of water with differing free energies. I haven’t yet quite figured out how one gets at these free energies in experimental terms, but I like the principle, not least because it explicitly acknowledges the role of water as a participant.
Yingkai Zhang at New York University and coworkers have used ab initio MD simulations to study the mechanism of action of histone deacetylase (HDAC) enzymes, which remove acetyl groups from histone residues and have been identified as a target for anti-cancer drugs (R. Wu et al., JACS 133, 6110-6113; 2011 – paper here). They suggest that some HDACs function via a mechanism involving a modulation of water access (a hydrogen-bonded chain of waters) to the binding pocket, in which a zinc ion in the metalloenzyme binds to its substrate. The presence or absence of water alters the dielectric constant in the binding pocket and thereby affects the strength of zinc binding.
Transitions of DNA between A, B and Z forms are thought to be associated with and perhaps driven by transitions in the nature of hydration. Karim Fahmy and colleagues at the Institute of Radiochemistry in Dresden now suggest that the same applies to the more subtle sub-transitions between the BI and BII states of the B-form (H. Khesbak et al., JACS 133, 5834-5842; 2011 – paper here). Specifically, there are two sub-populations of water molecules – one bound to phosphates, the other not – that contribute to stabilizing the two conformations via entropic effects. These water rearrangements can also be involved in interactions with DNA-binding ligands, such as the antimicrobial peptide indolicidin, by a water-mediated induced fit.
The structures of amyloid fibrillar assemblies are still far from well understood. The hydration state of the peptides is a particularly important issue in determining their stability and perhaps their mode of formation. Beat Meier at ETH and colleagues report some tricks that enable this question to be probed by NMR (Van Melckebeke et al., J. Mol. Biol. 405, 765; 2011 – paper here). For a particular prion domain called HET-s(218-289) they show that, although these protofibrils have a hydrophobic core and a semi-hydrophobic pocket, they do not engage in ‘dry’ interfibril contacts but are each surrounded by water.
The behaviour of water close to and between lipid bilayers has been much studied, but there doesn’t seem to have been much consideration of how that behaviour might feature in biological membrane processes such as fusion. This issue is investigated by Vijay Pande at Stanford and colleagues using simulations (P. M. Kasson, E. Lindahl & V. S. Pande, JACS 133, 3812-3815; 2011 – paper here). They look at the water trapped between the faces of two approaching membranes – that is, in hydrophilic confinement – and find that the dynamics are altered significantly. Specifically, the trapped water has reduced rotational entropy, and it helps the two membranes to adhere. However, the slower dynamics also retards the process of fusion itself – the formation of the ‘stalk’ that bridges the lipid membranes.
Mafumi Hishida and Koichiro Tanaka at Kyoto have also looked at the hydration of phospholipid bilayers, here experimentally using terahertz spectroscopy and SAXS (Phys. Rev. Lett. 106, 158102; 2011 – paper here). They conclude that water structure is perturbed up to 4-5 layers from the surface, over a distance of at least 1 nm, and that the average density in this hydration layer is slightly greater than that in the bulk.
Meanwhile, Joshua Layfield and Diego Troya at Virginia Tech have considered a water droplet confined between hydrophobic surfaces of self-assembled monolayers (J. Phys. Chem. B 115, 4662-4670; 2011 – paper here). Here the water motions (lateral translational diffusion) are accelerated by confinement, and this effect seems to operate over distances of more than 1 nm from the surfaces. Structural effects (preferential orientation of the water molecules) aren’t evident beyond 1 nm, however – but while the authors consider this to be a relatively short-ranged effect, I’d have been surprised to see anything structural with a longer reach.
Daniela Russo at the ILL and colleagues have used inelastic neutron scattering to probe the low-frequency densities of states of water hydrating small ‘model peptides’ (N-acetyl-leucine-methylamide, NALMA, and N-acetyl-glycine-methylamide, NAGMA) at low temperatures (Russo et al., JACS 133, 4882-4888; 2011 – paper here). At 200K they find that the hydration water for the hydrophilic NAGMA is similar to high-density amorphous ice, while that of the hydrophobic NALMA is more like low-density amorphous ice. Something similar has been reported at 100 K by Paciaroni et al. (Phys. Rev. Lett. 101, 148104; 2008), but was in that case attributed to curvature of the biomolecular surface – which is evidently not the case for these small molecules.
Aquaporins seem to play a crucial role in water regulation in arid periods during the life cycle of the major malaria vector mosquito Anopheles gambiae, according to Kun Liu of the Johns Hopkins Malaria Research Institute in Baltimore and colleagues (K. Liu et al., PNAS 108, 6062-6066; 2011 – paper here). The authors don’t say whether this makes these AQPs a potential target for controlling the spread of malaria, though I suppose that is a possible implication.
There’s still more to be understood about what hydrogen bonds are, as evidenced by a recent IUPAC working group set up to redefine them (see here). Angelos Michaelides at UCL (who I have to thank for my water-crested football shirt) and colleagues have now refined the quantum picture of the H-bond, showing how quantum nuclear effects due to the anharmonicity of the bond and the small proton mass can alter the bond strength, weakening weak H-bonds (like those in water) and strengthening strong ones (X.-Z. Li et al., PNAS 108, 6369-6373; 2011 – paper here).
There are one or two other papers I’ve still to get to, including some that folks have kindly sent to me. Apologies for that – more soon, I hope.
Jeremy England, now at Princeton, has a paper in press with Structure which shows that it is possible to estimate low-energy conformational changes in a protein, such as those involved in allosteric effects, on the basis simply of residue-by-residue hydrophobic effects. Specifically, he develops a method for determining the most energetically favourable way of burying hydrophobic residues, given a particular amino-acid sequence. This amounts to identifying the particular ‘burial modes’ of any given sequence. Thus, although the stabilities of conformations are doubtless multifactorial, hydrophobicity seems to be the major governing factor.
Calculating the surface free energies of heterogeneous surfaces exposed to water (such as protein surfaces) is tough. The approach of the Cassie equation is additive, but as Alenka Luzar and colleagues point out, that doesn’t always work (J. Wang et al., PNAS 108, 6374-6379; 2011 – paper here). They show that deviations from linear additivity result when parts of a surface are unevenly exposed to solvent. In particular, it seems that polar patches exert an inordinately strong influence, being able to ‘pin’ a droplet so that it might remain closely attached to adjacent hydrophobic patches. They examine these effects with reference to water droplets first on a functionalized graphene surface and then on the surface of melittin.
Daryl Eggers at San José State University presents an interesting approach to the energetics of reactions in aqueous solution, geared especially to biochemical equilibria, that treats the water as a reactant and product, thereby subsuming the local changes in water structure that inevitably accompany the reaction (Biochemistry 50, 2004-2012; 2011 – paper here). Here the free energy of bulk water is treated as a variable, allowing for the effects of all solutes including those that may not participate directly in the reaction (such as dissolved salts). As I understand it, this offers a means of accommodating the effects of such solutes (for example, in salting in/out) that does not make any assumptions about global changes in ‘water structure’, but represents only the global average of localized changes. Also jettisoned in that process is any insistence on putative structure-makers and structure-breakers; rather, solvation effects need be discussed only in what seems like relatively uncontentious terms of subpopulations of water with differing free energies. I haven’t yet quite figured out how one gets at these free energies in experimental terms, but I like the principle, not least because it explicitly acknowledges the role of water as a participant.
Yingkai Zhang at New York University and coworkers have used ab initio MD simulations to study the mechanism of action of histone deacetylase (HDAC) enzymes, which remove acetyl groups from histone residues and have been identified as a target for anti-cancer drugs (R. Wu et al., JACS 133, 6110-6113; 2011 – paper here). They suggest that some HDACs function via a mechanism involving a modulation of water access (a hydrogen-bonded chain of waters) to the binding pocket, in which a zinc ion in the metalloenzyme binds to its substrate. The presence or absence of water alters the dielectric constant in the binding pocket and thereby affects the strength of zinc binding.
Transitions of DNA between A, B and Z forms are thought to be associated with and perhaps driven by transitions in the nature of hydration. Karim Fahmy and colleagues at the Institute of Radiochemistry in Dresden now suggest that the same applies to the more subtle sub-transitions between the BI and BII states of the B-form (H. Khesbak et al., JACS 133, 5834-5842; 2011 – paper here). Specifically, there are two sub-populations of water molecules – one bound to phosphates, the other not – that contribute to stabilizing the two conformations via entropic effects. These water rearrangements can also be involved in interactions with DNA-binding ligands, such as the antimicrobial peptide indolicidin, by a water-mediated induced fit.
The structures of amyloid fibrillar assemblies are still far from well understood. The hydration state of the peptides is a particularly important issue in determining their stability and perhaps their mode of formation. Beat Meier at ETH and colleagues report some tricks that enable this question to be probed by NMR (Van Melckebeke et al., J. Mol. Biol. 405, 765; 2011 – paper here). For a particular prion domain called HET-s(218-289) they show that, although these protofibrils have a hydrophobic core and a semi-hydrophobic pocket, they do not engage in ‘dry’ interfibril contacts but are each surrounded by water.
The behaviour of water close to and between lipid bilayers has been much studied, but there doesn’t seem to have been much consideration of how that behaviour might feature in biological membrane processes such as fusion. This issue is investigated by Vijay Pande at Stanford and colleagues using simulations (P. M. Kasson, E. Lindahl & V. S. Pande, JACS 133, 3812-3815; 2011 – paper here). They look at the water trapped between the faces of two approaching membranes – that is, in hydrophilic confinement – and find that the dynamics are altered significantly. Specifically, the trapped water has reduced rotational entropy, and it helps the two membranes to adhere. However, the slower dynamics also retards the process of fusion itself – the formation of the ‘stalk’ that bridges the lipid membranes.
Mafumi Hishida and Koichiro Tanaka at Kyoto have also looked at the hydration of phospholipid bilayers, here experimentally using terahertz spectroscopy and SAXS (Phys. Rev. Lett. 106, 158102; 2011 – paper here). They conclude that water structure is perturbed up to 4-5 layers from the surface, over a distance of at least 1 nm, and that the average density in this hydration layer is slightly greater than that in the bulk.
Meanwhile, Joshua Layfield and Diego Troya at Virginia Tech have considered a water droplet confined between hydrophobic surfaces of self-assembled monolayers (J. Phys. Chem. B 115, 4662-4670; 2011 – paper here). Here the water motions (lateral translational diffusion) are accelerated by confinement, and this effect seems to operate over distances of more than 1 nm from the surfaces. Structural effects (preferential orientation of the water molecules) aren’t evident beyond 1 nm, however – but while the authors consider this to be a relatively short-ranged effect, I’d have been surprised to see anything structural with a longer reach.
Daniela Russo at the ILL and colleagues have used inelastic neutron scattering to probe the low-frequency densities of states of water hydrating small ‘model peptides’ (N-acetyl-leucine-methylamide, NALMA, and N-acetyl-glycine-methylamide, NAGMA) at low temperatures (Russo et al., JACS 133, 4882-4888; 2011 – paper here). At 200K they find that the hydration water for the hydrophilic NAGMA is similar to high-density amorphous ice, while that of the hydrophobic NALMA is more like low-density amorphous ice. Something similar has been reported at 100 K by Paciaroni et al. (Phys. Rev. Lett. 101, 148104; 2008), but was in that case attributed to curvature of the biomolecular surface – which is evidently not the case for these small molecules.
Aquaporins seem to play a crucial role in water regulation in arid periods during the life cycle of the major malaria vector mosquito Anopheles gambiae, according to Kun Liu of the Johns Hopkins Malaria Research Institute in Baltimore and colleagues (K. Liu et al., PNAS 108, 6062-6066; 2011 – paper here). The authors don’t say whether this makes these AQPs a potential target for controlling the spread of malaria, though I suppose that is a possible implication.
There’s still more to be understood about what hydrogen bonds are, as evidenced by a recent IUPAC working group set up to redefine them (see here). Angelos Michaelides at UCL (who I have to thank for my water-crested football shirt) and colleagues have now refined the quantum picture of the H-bond, showing how quantum nuclear effects due to the anharmonicity of the bond and the small proton mass can alter the bond strength, weakening weak H-bonds (like those in water) and strengthening strong ones (X.-Z. Li et al., PNAS 108, 6369-6373; 2011 – paper here).
There are one or two other papers I’ve still to get to, including some that folks have kindly sent to me. Apologies for that – more soon, I hope.
Thursday, February 24, 2011
Coarse-grained models
More on the mechanisms of urea-induced protein denaturation, this time from Ruhong Zhou at IBM and his colleagues in Beijing (M. Gao et al., J. Phys. Chem. B 114, 15687; 2010 – paper here). In simulations, they look at the populations of water and urea molecules around each residue in hen egg-white lysozyme, and find that some of the hydrophobic core residues stay virtually dry as unfolding proceeds in 8M urea. Moreover, the urea molecules are bound preferentially to uncharged rather than to charged residues. So the picture is that the protein swells to a molten globule state while keeping largely dry inside, because it is the urea rather than water that penetrates. this may not be a wholly general order of events, however – depending on the detailed shape and structure of the protein, water might sometimes penetrate first, as found for example by Bennion and Daggett (PNAS 100, 5142; 2003).
John Klassen and colleagues at the University of Alberta present an interesting comparison of protein-ligand dissociation constants in the hydrated and dehydrated states (L. Liu et al., JACS 132, 17658; 2010 – paper here). The latter are obtained from gas-phase measurements at 25-66 C. The kinetic stability of the associated state is significantly reduced in the hydrated phase: water stabilizes the dissociative transition state and might thereby be considered a kind of lubricant that facilitates the departure of the ligand.
David Beauchamp and Mazdak Khajehpour predicate their study of water-water interactions on enzyme activity with the supposition that the hydrogen-bond distribution in pure water is bimodal, with bonds that are high- and low-angle (J. Phys. Chem. B 10/1021/jp107556s – paper here). They say this is supported by some simulations, and that it is consistent with the (contentious) two-state model of the liquid. They also say that salts have the ability to perturb this distribution. OK… so given these assumptions, they see what added salts do to the activity of ribonuclease t1, and say that their spectroscopic and kinetic results are consistent with the notion that salts that promote the high-angle bonds stabilize the more compact and less active forms of the enzyme. Interesting ideas, but it seems a big leap from the data to the microscopic interpretation.
I recently described work by Martin Gruebele, Martina Havenith and colleagues on the mechanism of antifreeze glycoproteins, in which they argued that the biomolecules can effect long-range changes in water dynamics to inhibit freezing (S. Ebbinghaus et al., JACS 132, 12210; 2010). The authors now report similar findings for a 37-residue alpha-helical antifreeze protein from winter flounder (S. Ebbinghaus et al., Biophys. J. Biophys. Lett. in press). The find using CD and FRET on native and mutant versions that the antifreeze activity seems to be connected to a kinking of the helix, and that this is coupled to a suppression of bulk-like dynamics in the solvation water over a range of at least 3 nm, as indicated by THz spectroscopy.
Years ago, Royer et al. showed that a group of water molecules at the interface between the subunits of the dimeric haemoglobin of Scapharca clams seem implicated in the molecule’s allosteric cooperativity (Royer et al., PNAS 93, 14526; 1996). David Leitner and colleagues at the University of Nevada at Reno now look in detail at the dynamics of this cluster of waters using MD simulations based on the crystal structures (R. Gnanasekaran et al., J. Phys. Chem. B 114, 16989; 2010 – paper here). They find that those in the oxy form (11 molecules) exhibit slower relaxation than those (17) in the deoxy form, and that the water cluster, although rather static on ps timescales, can enhance energy transport across the interface of the subunits via vibrations.
The close and reciprocal interactions of water and protein dynamics, especially at low temperatures, seems to be echoed in the case of hydrated lipid bilayers, according to Peter Berntsen and colleagues at Chalmers University in Göteborg (J. Phys. Chem. B 10.1021/jp110899j – paper here). They have used dielectric rexlaxation measurements below 250 K to show that at low temperatures the water dynamics becomes increasingly dominated by the movements of the lipids, and is super-Arrhenius-like at low hydration levels.
Fast proton transport along peptide backbones can be assisted by water bridges, according to ab initio calculations by Po-Tuan Chen of the National Taiwan University of Science and Technology and colleagues (J. Phys. Chem. B 10.1021/jp107219r – paper here). They say that a two-molecule water bridge can make the transport between two adjacent carbonyl oxygens almost barrierless.
In a preprint (not sure where it is destined, but it looks like JCP format), David Chandler and his coworkers present a coarse-grained lattice model to implement the Lum-Chandler-Weeks dewetting theory of hydrophobic interactions (P. Varilly et al., arxiv: 1010.5750 – paper here). The model captures the essential features of the model at far less computational cost than full MD simulations, in particular modelling the solvent fluctuations that are essential for the dewetting mechanism.
With much the same objective of computational cheapness, Ken Dill at UCSF and colleagues present a new solvation model that they call semi-explicit self-assembly (C. J. Fennell et al., PNAS 108, 3234; 2011 – paper here). They basically construct a solute’s solvation shell as some combination of pre-computed solvation shells for simple spheres in explicit TIP3P water. They have so far only tested it here on simple small molecules such as sugars.
And Valeria Molinero and colleagues at the University of Utah have a coarse-grained model of DNA solvation with explicit water and ions (R. C. DeMille et al., J. Phys. Chem. B 115, 132; 2011 – paper here). It reproduces base-pair specificity and is computationally faster by two orders of magnitude than atomistic simulations.
There is a curious paper in Nature Structural and Molecular Biology by Nathaniel Nucci and colleagues at the University of Pennsylvania (NSMB 18, 245; 2011 – paper here) on an NMR technique to identify residence times of specific clusters of water molecules around proteins. I say curious, because these useful results are presented, particularly in a News & Views article in Nature (V. J. Hilser, Nature 469, 166; 2011 – paper here), as “challenging current dogma about protein hydration”. It seems this challenge comes from the fact that the results show that not all ‘bound’ water exchanges slowly with the surrounding solvent. But a wide range of exchange times is surely already well established, especially from simulations – the old crystallographic picture in which ‘hydration water’ is all securely bound and long-lived seemed long dead. Still, it is interesting that Nucci et al., whose method relies on confining the proteins (here ubiquitin) within reverse micelles to slow the hydration dynamics, found that water molecules with similar residence times seem to cluster on the protein surface, so that the molecules in each cluster form independent networks which exhibit intra-cluster cooperativity.
In another preprint, Giancarlo Franzese and colleagues at the University of Barcelona offer something of a mini-review of hydration structure and dynamics at protein surfaces, along with some Monte Carlo simulations that investigate cooperativity and dynamical transitions of a water monolayer hydrating a protein surface at low temperatures (arxiv preprint 1010.4984; paper here).
On the still-evolving picture of pure liquid water: Alessandro Cunsolo at Brookhaven and his colleagues study it using QENS to look at single-particle diffusion rates at 200 MPa as a function of temperature, and find that their results point to the proposed existence of a second critical point at about 220 K, and of the Widom line which ends at this point (J. Phys. Chem. B 114, 16713; 2010 – paper here).
Meanwhile, Richard Henchman and Sheeba Jem Irudayam of Manchester University in the UK propose a ‘topological’ definition of hydrogen bonding in water that offers a new description of water structure and dynamics (investigated in simulations using TIP4P/2005 water) based on the character of the H-bond network (J. Phys. Chem. B 10.1021/jp105381s – paper here). They say that in this description almost all the water molecules are H-bonded and that there are an appreciable number of ‘defects’ in which molecules are acceptors for one (trigonal) and three (trigonal bipyramidal) hydrogens rather than two.
John Klassen and colleagues at the University of Alberta present an interesting comparison of protein-ligand dissociation constants in the hydrated and dehydrated states (L. Liu et al., JACS 132, 17658; 2010 – paper here). The latter are obtained from gas-phase measurements at 25-66 C. The kinetic stability of the associated state is significantly reduced in the hydrated phase: water stabilizes the dissociative transition state and might thereby be considered a kind of lubricant that facilitates the departure of the ligand.
David Beauchamp and Mazdak Khajehpour predicate their study of water-water interactions on enzyme activity with the supposition that the hydrogen-bond distribution in pure water is bimodal, with bonds that are high- and low-angle (J. Phys. Chem. B 10/1021/jp107556s – paper here). They say this is supported by some simulations, and that it is consistent with the (contentious) two-state model of the liquid. They also say that salts have the ability to perturb this distribution. OK… so given these assumptions, they see what added salts do to the activity of ribonuclease t1, and say that their spectroscopic and kinetic results are consistent with the notion that salts that promote the high-angle bonds stabilize the more compact and less active forms of the enzyme. Interesting ideas, but it seems a big leap from the data to the microscopic interpretation.
I recently described work by Martin Gruebele, Martina Havenith and colleagues on the mechanism of antifreeze glycoproteins, in which they argued that the biomolecules can effect long-range changes in water dynamics to inhibit freezing (S. Ebbinghaus et al., JACS 132, 12210; 2010). The authors now report similar findings for a 37-residue alpha-helical antifreeze protein from winter flounder (S. Ebbinghaus et al., Biophys. J. Biophys. Lett. in press). The find using CD and FRET on native and mutant versions that the antifreeze activity seems to be connected to a kinking of the helix, and that this is coupled to a suppression of bulk-like dynamics in the solvation water over a range of at least 3 nm, as indicated by THz spectroscopy.
Years ago, Royer et al. showed that a group of water molecules at the interface between the subunits of the dimeric haemoglobin of Scapharca clams seem implicated in the molecule’s allosteric cooperativity (Royer et al., PNAS 93, 14526; 1996). David Leitner and colleagues at the University of Nevada at Reno now look in detail at the dynamics of this cluster of waters using MD simulations based on the crystal structures (R. Gnanasekaran et al., J. Phys. Chem. B 114, 16989; 2010 – paper here). They find that those in the oxy form (11 molecules) exhibit slower relaxation than those (17) in the deoxy form, and that the water cluster, although rather static on ps timescales, can enhance energy transport across the interface of the subunits via vibrations.
The close and reciprocal interactions of water and protein dynamics, especially at low temperatures, seems to be echoed in the case of hydrated lipid bilayers, according to Peter Berntsen and colleagues at Chalmers University in Göteborg (J. Phys. Chem. B 10.1021/jp110899j – paper here). They have used dielectric rexlaxation measurements below 250 K to show that at low temperatures the water dynamics becomes increasingly dominated by the movements of the lipids, and is super-Arrhenius-like at low hydration levels.
Fast proton transport along peptide backbones can be assisted by water bridges, according to ab initio calculations by Po-Tuan Chen of the National Taiwan University of Science and Technology and colleagues (J. Phys. Chem. B 10.1021/jp107219r – paper here). They say that a two-molecule water bridge can make the transport between two adjacent carbonyl oxygens almost barrierless.
In a preprint (not sure where it is destined, but it looks like JCP format), David Chandler and his coworkers present a coarse-grained lattice model to implement the Lum-Chandler-Weeks dewetting theory of hydrophobic interactions (P. Varilly et al., arxiv: 1010.5750 – paper here). The model captures the essential features of the model at far less computational cost than full MD simulations, in particular modelling the solvent fluctuations that are essential for the dewetting mechanism.
With much the same objective of computational cheapness, Ken Dill at UCSF and colleagues present a new solvation model that they call semi-explicit self-assembly (C. J. Fennell et al., PNAS 108, 3234; 2011 – paper here). They basically construct a solute’s solvation shell as some combination of pre-computed solvation shells for simple spheres in explicit TIP3P water. They have so far only tested it here on simple small molecules such as sugars.
And Valeria Molinero and colleagues at the University of Utah have a coarse-grained model of DNA solvation with explicit water and ions (R. C. DeMille et al., J. Phys. Chem. B 115, 132; 2011 – paper here). It reproduces base-pair specificity and is computationally faster by two orders of magnitude than atomistic simulations.
There is a curious paper in Nature Structural and Molecular Biology by Nathaniel Nucci and colleagues at the University of Pennsylvania (NSMB 18, 245; 2011 – paper here) on an NMR technique to identify residence times of specific clusters of water molecules around proteins. I say curious, because these useful results are presented, particularly in a News & Views article in Nature (V. J. Hilser, Nature 469, 166; 2011 – paper here), as “challenging current dogma about protein hydration”. It seems this challenge comes from the fact that the results show that not all ‘bound’ water exchanges slowly with the surrounding solvent. But a wide range of exchange times is surely already well established, especially from simulations – the old crystallographic picture in which ‘hydration water’ is all securely bound and long-lived seemed long dead. Still, it is interesting that Nucci et al., whose method relies on confining the proteins (here ubiquitin) within reverse micelles to slow the hydration dynamics, found that water molecules with similar residence times seem to cluster on the protein surface, so that the molecules in each cluster form independent networks which exhibit intra-cluster cooperativity.
In another preprint, Giancarlo Franzese and colleagues at the University of Barcelona offer something of a mini-review of hydration structure and dynamics at protein surfaces, along with some Monte Carlo simulations that investigate cooperativity and dynamical transitions of a water monolayer hydrating a protein surface at low temperatures (arxiv preprint 1010.4984; paper here).
On the still-evolving picture of pure liquid water: Alessandro Cunsolo at Brookhaven and his colleagues study it using QENS to look at single-particle diffusion rates at 200 MPa as a function of temperature, and find that their results point to the proposed existence of a second critical point at about 220 K, and of the Widom line which ends at this point (J. Phys. Chem. B 114, 16713; 2010 – paper here).
Meanwhile, Richard Henchman and Sheeba Jem Irudayam of Manchester University in the UK propose a ‘topological’ definition of hydrogen bonding in water that offers a new description of water structure and dynamics (investigated in simulations using TIP4P/2005 water) based on the character of the H-bond network (J. Phys. Chem. B 10.1021/jp105381s – paper here). They say that in this description almost all the water molecules are H-bonded and that there are an appreciable number of ‘defects’ in which molecules are acceptors for one (trigonal) and three (trigonal bipyramidal) hydrogens rather than two.
Monday, February 14, 2011
Less is more
In the spirit of maintaining continuity (do some folks really look at this site every week, as I’m told?), I will aim to post more regularly rather than exhaustively. That’s to say, this is not a complete list for what I’ve seen out there, but more will follow soon.
Sheh-Yi Sheu at National Yang-Ming University in Taiwan and Dah-Yen Yang at the Institute for Molecular Science in Okazaki, Japan, present a method for deducing the free energy of the hydration shell for a biomolecule from simulations (J. Phys. Chem. B 10.1021/jp105164t – paper here). They say that water in a protein (here myoglobin) hydration shell follows fractional Brownian motion.
Flavoproteins are electron-transfer proteins involved in a range of biological processes, including cell apoptosis and DNA repair. The nature of solvation at the active sites is of central importance for their function. Dongping Zhong and colleagues at Ohio State have used ultrafast spectroscopy to characterize the dynamics of the water network at the functional site in three redox stats of a representative flavoprotein, flavodoxin (C.-W. Chang et al., JACS 192, 12741 (2010) – paper here). Rather neatly, they are able to use the intrinsic cofactor of this protein as the fluorescent probe for the experiments. They can monitor changes in the relaxation and rigidity of the local water network between the different states, for example a retardation of the relaxation from around 2.6 to 40 ps between the oxidized to semiquinone state. They propose an intimate and biologically relevant coupling between the flexibility of the solvation network and the protein.
Gating of ion channels due to cooperative drying has been suggested as the underlying mechanism for such functions. Fangqiang Zhu and Gerhard Hummer at NIH explore this notion for the ligand-gated ion channel GLIC of the bacterium G. violaceus, for which the crystal structure of the open state is solved (PNAS 107, 19814; 2010 – paper here). They find that the pore is typically water-filled in the open state, but that a very small decrease in the channel radius can induce cooperative drying. It seems that the emptying of the pore is a response to, rather than the driving force for, changes in the pore width.
Alla Oleinikova, Ivan Brovchenko and their colleague G. Singh at Dortmund have calculated the heat capacity of hydration water of hydrophobic and hydrophilic peptides from simulations (A. Oleinikova et al., Europhys. Lett. 90, 36001; 2010 – paper here). They say that around 330 K there is a sharp change in structure from a percolating to a fragmented H-bonded network, and that this coincides with a point at which the heat capacity changes from being dominated by water interactions within the hydration shell to a situation where the hydration-shell-to bulk interactions are more important. At this stage, the ‘detachment’ of the hydration network from the peptide in effect makes the biomolecule more hydrophobic.
Anrew White and Shaoyi Jiang at the University of Washington have studied the hydration of glycine and two (zwitterionic) analogues di- and trimethylglycine using MD (J. Phys. Chem. B 115, 660; 2011 – paper here). They say that all three molecules affect the water structure out to the second hydration shell, but trimethylglycine has the greatest (retarding) effect on water dynamics and, perhaps surprisingly, does not aggregate but remains well solvated even at high concentrations. This might help to account for trimethylglycine’s antifouling properties and its suppression of protein aggregation.
There is sill a tussle going on about whether bulk water at ambient temperatures is best considered in a homogeneous or two-phase framework. Lars Pettersson and Anders Nilsson have recently teamed up with theorists including Jens Norskov at Stanford to perform ab initio MD calculations which point to a mixture of low- and high-density regions at ambient conditions (A Møgelhøj et al., arxiv preprint 1101.5666; paper here). But Niall English and John Tse dispute this, saying that such inhomogeneities are of very short range and transient, being just the ordinary density fluctuations one would expect to see in an equilibrium system (Phys. Rev. Lett. 106, 037801; 2011 – paper here).
Raymond Dagastine and colleagues at the University of Melbourne report a very striking claim: that air bubbles interact with (probably virtually all) solid surfaces via a repulsive van der Waals interaction (R. F. Tabor et al., Phys. Rev. Lett. 106, 064501; 2011 – paper here). As a bubble approaches a surface under hydrodynamic flow, they say, it will therefore start to deform and flatten at the point where the repulsive force equals the Laplace pressure. Repulsive vdW forces are well known in theory, but it seemed previously that rather special combinations of materials were needed to realise them.
Sheh-Yi Sheu at National Yang-Ming University in Taiwan and Dah-Yen Yang at the Institute for Molecular Science in Okazaki, Japan, present a method for deducing the free energy of the hydration shell for a biomolecule from simulations (J. Phys. Chem. B 10.1021/jp105164t – paper here). They say that water in a protein (here myoglobin) hydration shell follows fractional Brownian motion.
Flavoproteins are electron-transfer proteins involved in a range of biological processes, including cell apoptosis and DNA repair. The nature of solvation at the active sites is of central importance for their function. Dongping Zhong and colleagues at Ohio State have used ultrafast spectroscopy to characterize the dynamics of the water network at the functional site in three redox stats of a representative flavoprotein, flavodoxin (C.-W. Chang et al., JACS 192, 12741 (2010) – paper here). Rather neatly, they are able to use the intrinsic cofactor of this protein as the fluorescent probe for the experiments. They can monitor changes in the relaxation and rigidity of the local water network between the different states, for example a retardation of the relaxation from around 2.6 to 40 ps between the oxidized to semiquinone state. They propose an intimate and biologically relevant coupling between the flexibility of the solvation network and the protein.
Gating of ion channels due to cooperative drying has been suggested as the underlying mechanism for such functions. Fangqiang Zhu and Gerhard Hummer at NIH explore this notion for the ligand-gated ion channel GLIC of the bacterium G. violaceus, for which the crystal structure of the open state is solved (PNAS 107, 19814; 2010 – paper here). They find that the pore is typically water-filled in the open state, but that a very small decrease in the channel radius can induce cooperative drying. It seems that the emptying of the pore is a response to, rather than the driving force for, changes in the pore width.
Alla Oleinikova, Ivan Brovchenko and their colleague G. Singh at Dortmund have calculated the heat capacity of hydration water of hydrophobic and hydrophilic peptides from simulations (A. Oleinikova et al., Europhys. Lett. 90, 36001; 2010 – paper here). They say that around 330 K there is a sharp change in structure from a percolating to a fragmented H-bonded network, and that this coincides with a point at which the heat capacity changes from being dominated by water interactions within the hydration shell to a situation where the hydration-shell-to bulk interactions are more important. At this stage, the ‘detachment’ of the hydration network from the peptide in effect makes the biomolecule more hydrophobic.
Anrew White and Shaoyi Jiang at the University of Washington have studied the hydration of glycine and two (zwitterionic) analogues di- and trimethylglycine using MD (J. Phys. Chem. B 115, 660; 2011 – paper here). They say that all three molecules affect the water structure out to the second hydration shell, but trimethylglycine has the greatest (retarding) effect on water dynamics and, perhaps surprisingly, does not aggregate but remains well solvated even at high concentrations. This might help to account for trimethylglycine’s antifouling properties and its suppression of protein aggregation.
There is sill a tussle going on about whether bulk water at ambient temperatures is best considered in a homogeneous or two-phase framework. Lars Pettersson and Anders Nilsson have recently teamed up with theorists including Jens Norskov at Stanford to perform ab initio MD calculations which point to a mixture of low- and high-density regions at ambient conditions (A Møgelhøj et al., arxiv preprint 1101.5666; paper here). But Niall English and John Tse dispute this, saying that such inhomogeneities are of very short range and transient, being just the ordinary density fluctuations one would expect to see in an equilibrium system (Phys. Rev. Lett. 106, 037801; 2011 – paper here).
Raymond Dagastine and colleagues at the University of Melbourne report a very striking claim: that air bubbles interact with (probably virtually all) solid surfaces via a repulsive van der Waals interaction (R. F. Tabor et al., Phys. Rev. Lett. 106, 064501; 2011 – paper here). As a bubble approaches a surface under hydrodynamic flow, they say, it will therefore start to deform and flatten at the point where the repulsive force equals the Laplace pressure. Repulsive vdW forces are well known in theory, but it seemed previously that rather special combinations of materials were needed to realise them.
Thursday, February 3, 2011
Yes, I'm still here
Apologies for the long silence. This blog is still active, but Christmas (among other things) got in the way and then I face the Sysiphean task of catching up. That task is not by any means completed here, but I want to flag up that Water in Biology hasn’t expired. Much more as soon as I can manage it.
Bruce Berne, Richard Friesner and Lingle Wang at Columbia have recently introduced the notion that ligand binding in protein receptor pockets is largely driven by the displacement of water molecules that sit in an unfavourable position in the pocket, which are replaced with groups on the ligand that are complementary to the protein surface (Young et al., PNAS 104, 808; 2007; Abel et al., JACS 130, 2817; 2008). In a new paper (Wang et al., PNAS 108, 1326; 2011 – paper here) they consider what their model, called WaterMap, has to say about regions of the binding pocket that are initially dry, being highly unfavourable environments for water. Including an interaction term in the model that represents the formation of a (hydrophobic) protein-ligand interface in dry regions, they can compute binding affinities in good agreement with experiment.
Dave Thirumalai at Maryland and his coworkers offer a striking view of how amyloid fibrils self-assemble from interdigitated beta-sheets (G. Reddy et al., PNAS 10.1073/pnas.108616107 – paper not yet online). They present a MD study of the association of beta-sheets in two amyloidogenic proteins of very different sequence, one polar and the other hydrophobic. They say that in the former case the association of the sheets is mediated by one-dimensional water wires at the interface between them, which are gradually expelled. But for the hydrophobic peptides the sheets come together in something like an abrupt drying transition, as postulated previously for some protein-folding and aggregation processes. This happens much faster (nearly 1,000-fold) than the previous case, since the trapped water wires for the polar peptide create a barrier to rapid assembly. Thus, although the final structures are very similar, the mechanisms and dynamics are quite different. It would seem that this paper ties in with a new one by Ken Dill and colleagues on the mechanisms of amyloid assembly into fibrils, of which I’ve only seen the abstract (which suggests that there’s not a big emphasis on the role of the solvent here beyond the involvement of hydrophobicity) (J. D. Schmit et al., Biophys. J. 100, 450-458; 2011 – paper here).
Cytochrome c oxidase (CcO) acts as a proton pump in which the transmembrane proton motion is thought to be facilitated by a proton wire involving strategically placed water molecules. The roles of these waters are investigated by Shelagh Ferguson-Miller and colleagues at Michigan State based on high-resolution crystals structures of two mutant forms of bacterial CcO (Liu et al., PNAS 108, 1284; 2011 – paper here). In both mutants, where proton transfer is inhibited to different degrees, the overall structural changes are very small but one or more of the bound waters is eliminated. The story is not, however, quite as simple as a mere break in the water wires, but involves subtle conformational changes between oxidized and reduced forms of the metal centres: an indication that, while bound water undoubtedly plays an active role in the catalytic function, in this case that role resists reduction to a simplistic picture.
Human telomeres contain G-rich sequences that form quadruplex structures in Hoogsteen hydrogen-bonded patterns. It’s not clear what influences the stability of this unusual motif, but John Trent and colleagues at the University of Louisville in Kentucky say that hydration plays a major part (M. C. Miller et al., JACS 132, 17105-17107; 2010 – paper here). They say that previous studies of the crystal structure of these sequences have been misleading because the dehydrating agents used to cause precipitation (PEGs) may give crystal structures that are not closely related to those in solution. Instead they use acetonitrile (which is water-soluble but does not engage in hydrogen-bonding) as the cosolvent for CD and NMR solution studies, and find that stabilization of the quadruplex seems to be caused more by dehydration than by steric crowding effects.
How hydration affects energy relaxation of cytochrome c after photoexcitation has been studied using ultrafast spectroscopy by Shuji Ye of the University of Science and Technology of China in Hefei and and Andrea Markelz of SUNY at Buffalo (J. Phys. Chem. B 114, 15151-15157; 2010 – paper here). One of the main conclusions is that hydration doesn’t in fact have a great deal of influence on the initial energy dynamics: there is an initial fast (around 300 fs) conversion from the electronically excited state to a vibrationally excited ground state, which is essentially hydration-independent. But the vibrational cooling then does involve interaction with the solvent, more or less in line with the existing notion that hydration water acts as a kind of plasticizer in this molecule.
Finally for now, and not really at all relevant to the real themes of this blog but too much of a curiosity for me to ignore, there are two papers on the arxiv investigating the notorious Mpemba effect, whereby hot water is said to sometimes freeze faster than cold: see here and here.
Bruce Berne, Richard Friesner and Lingle Wang at Columbia have recently introduced the notion that ligand binding in protein receptor pockets is largely driven by the displacement of water molecules that sit in an unfavourable position in the pocket, which are replaced with groups on the ligand that are complementary to the protein surface (Young et al., PNAS 104, 808; 2007; Abel et al., JACS 130, 2817; 2008). In a new paper (Wang et al., PNAS 108, 1326; 2011 – paper here) they consider what their model, called WaterMap, has to say about regions of the binding pocket that are initially dry, being highly unfavourable environments for water. Including an interaction term in the model that represents the formation of a (hydrophobic) protein-ligand interface in dry regions, they can compute binding affinities in good agreement with experiment.
Dave Thirumalai at Maryland and his coworkers offer a striking view of how amyloid fibrils self-assemble from interdigitated beta-sheets (G. Reddy et al., PNAS 10.1073/pnas.108616107 – paper not yet online). They present a MD study of the association of beta-sheets in two amyloidogenic proteins of very different sequence, one polar and the other hydrophobic. They say that in the former case the association of the sheets is mediated by one-dimensional water wires at the interface between them, which are gradually expelled. But for the hydrophobic peptides the sheets come together in something like an abrupt drying transition, as postulated previously for some protein-folding and aggregation processes. This happens much faster (nearly 1,000-fold) than the previous case, since the trapped water wires for the polar peptide create a barrier to rapid assembly. Thus, although the final structures are very similar, the mechanisms and dynamics are quite different. It would seem that this paper ties in with a new one by Ken Dill and colleagues on the mechanisms of amyloid assembly into fibrils, of which I’ve only seen the abstract (which suggests that there’s not a big emphasis on the role of the solvent here beyond the involvement of hydrophobicity) (J. D. Schmit et al., Biophys. J. 100, 450-458; 2011 – paper here).
Cytochrome c oxidase (CcO) acts as a proton pump in which the transmembrane proton motion is thought to be facilitated by a proton wire involving strategically placed water molecules. The roles of these waters are investigated by Shelagh Ferguson-Miller and colleagues at Michigan State based on high-resolution crystals structures of two mutant forms of bacterial CcO (Liu et al., PNAS 108, 1284; 2011 – paper here). In both mutants, where proton transfer is inhibited to different degrees, the overall structural changes are very small but one or more of the bound waters is eliminated. The story is not, however, quite as simple as a mere break in the water wires, but involves subtle conformational changes between oxidized and reduced forms of the metal centres: an indication that, while bound water undoubtedly plays an active role in the catalytic function, in this case that role resists reduction to a simplistic picture.
Human telomeres contain G-rich sequences that form quadruplex structures in Hoogsteen hydrogen-bonded patterns. It’s not clear what influences the stability of this unusual motif, but John Trent and colleagues at the University of Louisville in Kentucky say that hydration plays a major part (M. C. Miller et al., JACS 132, 17105-17107; 2010 – paper here). They say that previous studies of the crystal structure of these sequences have been misleading because the dehydrating agents used to cause precipitation (PEGs) may give crystal structures that are not closely related to those in solution. Instead they use acetonitrile (which is water-soluble but does not engage in hydrogen-bonding) as the cosolvent for CD and NMR solution studies, and find that stabilization of the quadruplex seems to be caused more by dehydration than by steric crowding effects.
How hydration affects energy relaxation of cytochrome c after photoexcitation has been studied using ultrafast spectroscopy by Shuji Ye of the University of Science and Technology of China in Hefei and and Andrea Markelz of SUNY at Buffalo (J. Phys. Chem. B 114, 15151-15157; 2010 – paper here). One of the main conclusions is that hydration doesn’t in fact have a great deal of influence on the initial energy dynamics: there is an initial fast (around 300 fs) conversion from the electronically excited state to a vibrationally excited ground state, which is essentially hydration-independent. But the vibrational cooling then does involve interaction with the solvent, more or less in line with the existing notion that hydration water acts as a kind of plasticizer in this molecule.
Finally for now, and not really at all relevant to the real themes of this blog but too much of a curiosity for me to ignore, there are two papers on the arxiv investigating the notorious Mpemba effect, whereby hot water is said to sometimes freeze faster than cold: see here and here.
Friday, October 22, 2010
Pores for thought
Two papers in Science look at the mechanics of proton conduction in the M2 pore of influenza viruses (F. Hu et al., Science 330, 505-508; M. Sharma et al., Science 330, 509-512; 2010 – papers here and here). Hu et al. say that the key is whether a complex of histidine groups (His37) in the tetrameric pore is or is not in contact with a water chain threading the pore, which changes in a pH-dependent manner. Previously it has been controversial whether the His37 group participates in an active fashion by protonation/deprotonation or merely alters the channel diameter electrostatically. Hu et al. say that the latter does happen, but is accompanied by increased rotational freedom of the His imidazole group to make contact with the ‘water wire’ and relay a hopping proton. Sharma et al. could be said to refine this picture by considering the interactions between all the His37s in the tetramer and their relation to the adjacent Trp41 residues. They say that the proton-conducting state is activated at low pH by ‘unlocking’ of the imidazole group in a way that is gated by Trp41 via pi-cation interactions.
More pores. Not all aquaporins are selective for water only – some will admit glycerol and other alcohols. David Savage at UCSF and colleagues have determined their X-ray crystal structures to figure out what determines the selectivity (D. Savage et al., PNAS 10.1073/pnas.1009864107 – paper here). The details are complex, but the basic features arguably those one might expect: in the region of the pore’s selectivity filter, the energetics of water transport are controlled by channel hydrophilicity, while selectivity for larger molecules such as glycerol is steric, governed by channel width.
Some other protein pores will also allow water and other small molecules to pass, such as the sodium-glucose cotransporter, which permits water flow in the presence of Na+ or glucose. This class of proteins allows passive water flow in the presence of an osmotic Na+ or glucose gradient, but also flow against such a gradient if Na+ or glucose is present. To what extent, then, is such flow passive, and to what extent actively pumped in the presence of these solutes? Michael Grabe at the University of Pittsburgh and colleagues investigate that question using MD simulations (S. Choe et al., Biophys. J. 99, L56-L58; 2010 – paper here). They find that water will pass through the sodium-dependent galactose cotransporter vSGLT both in the absence and the presence of galactose. In the former case the flow is passive (and occurs through the galactose-binding region), but that in the latter case the release of galactose ‘pushes’ water molecules through the pore in the same direction as its exit – as the authors put it, galactose acts as a Brownian piston that rectifies the passive water motion through the pore.
Comparable rectification of proton motion through a proton pumps such as bacteriorhodopin, resulting in a ‘proton diode’, is described by Klaus Gerwert and colleagues at Bochum (S. Wolf et al., Angew. Chem. Int. Ed. 49, 6889-6893; 2010 – paper here). This team draw on their detailed investigations of bR over recent years, and new studies of point mutations, to explain how conformational changes in a few residues can control access between internally bound and external water molecules in such a way as to bias the direction of proton flow in a general mechanism that they suspect might be more general to other proton pumps.
Biological processes involving proton motion are prime candidates for manifesting quantum-mechanical effects. A rather striking instance of this is claimed by George Reiter of the University of Houston and colleagues, who say that the zero-point motions of protons in are entirely responsible for the binding of water to A-DNA (G. Reiter et al., Phys. Rev. Lett. 105, 148101; 2010 – paper here). Changes in hydration seem to be what drive the A-to-B transition in DNA (the A phase forms in dehydrated conditions), and Reiter et al. say that this is accompanied by a change in the zero-point kinetic energy of the protons in the hydrated B-DNA that is sufficient in itself to motivate the transition. Whether the protons concerned are those of water molecules in the hydration shell or those in the DNA’s H-bonds (or, presumably, a bit of both) is not yet clear.
It’s many years ago now that David Tirrell, now at Caltech, developed ways to incorporate fluorinated amino acids into proteins using recombinant DNA technology – a feat popularized with reference to non-stick fried eggs. David has now teamed up with Ahmed Zewail and colleagues to investigate what fluorinated residues do to the hydration of such proteins, using ultrafast time-dependent fluorescent Stokes shift spectroscopy on fluorinated coiled-coil peptides (O.-H. Kwon et al., PNAS 10.1073/pnas.1011569107 – paper here). They find that the hydration dynamics are retarded around fluorinated residues, in marked contrast to an acceleration of the dynamics for the corresponding cases of hydrogenated residues, which are of comparable size.
Some mini-proteins, such as the villin headpiece domains HP35 and HP36, with just 35 and 36 residues, have an unusual ability to fold quickly into a conformation with a securely buried hydrophobic core despite their small size. Takao Yoda of the Nagahama Institute of Bio-science and Technology and colleagues have used simulations to investigate how this happens (T. Yoda et al., Biophys. J. 99, 1637-1644; 2010 – paper here). The cores in the folded state are fully dehydrated, but some water molecules remain therein until the final stages of folding. This is an unusually large system for which the folding process has been followed in detail from a fully extended state in explicit solvent. Meanwhile, David Cerutti at Rutgers and coworkers have simulated the crystal structures of a scorpion toxin protein to probe the performance of different protein and water force-field models in predicting the observed structure (D. S. Cerutti et al., J. Phys. Chem. B 114, 12811-12824; 2010 – paper here). They find that the results are not very sensitive to the water model, and far more dependent on the protein model (FF99SB does best) in terms of correctly predicting the right contacts in the peptide chain.
Whether we can understand the various forces involved in protein folding sufficiently to design peptides and other heteropolymers to adopt specific conformations is of course one of the big challenges not only for protein design but for polymer chemistry more generally. Shekhar Garde and colleagues at RPI have studied how water-mediated interactions might be exploited in this endeavour (S. N. Jamadagni et al., J. Phys. Chem. B jp104924g – paper here). In particular, they explore the sequence space of model polymers containing one or two pairs of charged monomers, in cases where the other monomers are more or less hydrophobic, and at the effect of adding salt to such systems. The results reveal subtle factors at play: for example, ion pairs among hydrophobic monomers can stabilize hairpin conformations over collapsed globules via water-mediated Coulombic interactions, but this depends on where the charged monomers appear along the chain. And adding salt can open up these hairpins, whereas salt stabilizes the globular forms of hydrophobic homopolymers.
Some membrane-binding proteins induce curvature of the membrane (see H. T. McMahon & J. L. Gallop, Nature 438, 590; 2005) – for example, the so-called BAR domain of amphiphysin will remodel lipid vesicles into tubules. Greg Voth and colleagues have performed MD simulations to try to figure out how this works, and they find that, surprisingly, there is a layer of water intervening between BAR and the membrane even when the protein domain is strongly bound (E. Lyman et al., Biophys. J. 99, 1783-1790; 2010 – paper here). This implies that the charged region of BAR is screened from the lipid headgroups, so that the bending mechanism is not electrostatic.
How homogeneous are solutions of denaturing guanidinium salts? Recently, Mason and coworkers have reported evidence that the cations form nanoscale aggregates (e.g. P. E. Mason et al., PNAS 100, 4557; 2003). Using dielectric relaxation spectroscopy, Richard Buchner of the University of Regensburg question this conclusion (J. Hunger et al., J. Phys. Chem. B jp101520h – paper here). In other words, perhaps after all Gdm+ ions can ‘fit’ comfortably into the structure of bulk water without altering it – which would seem to support the ‘direct’ mechanism of denaturation whereby Gdm+ interacts with the protein backbone rather than loosening up the folded state by influencing hydration.
More evidence for the direct intermediation of water in enzyme action: Sason Shaik at the Hebrew University of Jerusalem and colleagues say that a water cluster in the binding site of heme oxygenase participates in its ring-opening degradation of heme groups (W. Lai et al., JACS 132, 12960-12970; 2010 – paper here). The water cluster organizes the substrate into the proper geometry, serves as a proton shuttle, and stabilizes the hydroxyl nucleophile that attacks the ring. And Dongping Zhong at Ohio State University and colleagues say that flavoproteins, which act as redox coenzymes, contain water networks in the active site with fast relaxation dynamics that probably controls the protein flexibility in a functionally relevant manner (C.-W. Chang et al., JACS 132,12741-12747; 2010 – paper here). Meanwhile, Peter Brzezinski at Stockholm University and colleagues offer evidence that water molecules are involved in proton transport through cytochrome c oxidase, which actively pumps protons across a membrane to sustain a proton-motive force for ATP synthesis (H. J. Lee et al., JACS ja107244g – paper here).
Mischa Bonn of the FOM Institute AMOLF in Amsterdam and colleagues say that the hydration region of lipid headgroups in monolayers contains two populations of water molecules, one with bulk-like relaxation and the other that relaxes faster (M. Bonn et al., JACS ja106194u – paper here). Their VSF spectroscopic measurements thus imply the presence of a group of water molecules that are strongly hydrogen-bonded to the headgroups, decoupled from the bulk, and potentially involved in rapid, in-plane proton transfer, as previous studies have suggested for lipid membranes.
How does the hydration of antifreeze proteins differ from that of regular proteins? Ann McDermott and colleagues at Columbia use NMR methods to study this question by investigating the hydration shells of ubiquitin and an ice-binding (type III) antifreeze protein at cryogenic temperatures (-35 C) (A. B. Siemer et al., PNAS 10.1073/pnas.1009369107 – paper here). They find that the ubiquitin hydration shell remains unfrozen and uncoupled to the ice lattice, whereas this is true of only parts of the AFP III shell: as one might expect, the ice-binding interface establishes direct contact with ice.
The ability of sufficiently narrow carbon nanotubes to admit water but exclude ions has been proposed as a basis for desalination technologies. But Daejoong Kim and coworkers at Sogang University in South Korea show that admission or exclusion of ions can be a subtle business. They say that at certain nanotube diameters, strong sodium hydration can lead to a preferential admission of potassium ions over sodium in mixed ionic solutions, while at other diameters sodium can be preferred, or that both ions can be increasingly excluded even as the tube diameter increases (J. J. Cannon et al., J. Phys. Chem. B jp104609d – paper here). So it is conceivable that selective filtration and separation might be achieved. It seems quite conceivable that Ilan Benjamin’s new analysis of the hydration of alkali-metal halides in hydrophobic environments, and the formation of ion pairs (J. Phys. Chem. B jp1050673 – paper here), might be relevant here to the state inside the nanotubes.
Finally, bulk water, and a suggestion that the structural picture here is still not fully resolved. Peter Hamm at the University of Freiburg and colleagues use the theoretical tools developed for the study of complex networks (such as those in social science) to reveal hidden topological aspects of the H-bonded network in MD simulations of liquid water (F. Rao et al., J. Phys. Chem. B jp1060792 – paper here). They say this approach reveals structural inhomogeneities, extending at least to the second hydration shell, that are not evident from methods that focus on a single scalar order parameter such as tetrahedrality. Needless to say, the same technique might be used to look at solute hydration shells.
More pores. Not all aquaporins are selective for water only – some will admit glycerol and other alcohols. David Savage at UCSF and colleagues have determined their X-ray crystal structures to figure out what determines the selectivity (D. Savage et al., PNAS 10.1073/pnas.1009864107 – paper here). The details are complex, but the basic features arguably those one might expect: in the region of the pore’s selectivity filter, the energetics of water transport are controlled by channel hydrophilicity, while selectivity for larger molecules such as glycerol is steric, governed by channel width.
Some other protein pores will also allow water and other small molecules to pass, such as the sodium-glucose cotransporter, which permits water flow in the presence of Na+ or glucose. This class of proteins allows passive water flow in the presence of an osmotic Na+ or glucose gradient, but also flow against such a gradient if Na+ or glucose is present. To what extent, then, is such flow passive, and to what extent actively pumped in the presence of these solutes? Michael Grabe at the University of Pittsburgh and colleagues investigate that question using MD simulations (S. Choe et al., Biophys. J. 99, L56-L58; 2010 – paper here). They find that water will pass through the sodium-dependent galactose cotransporter vSGLT both in the absence and the presence of galactose. In the former case the flow is passive (and occurs through the galactose-binding region), but that in the latter case the release of galactose ‘pushes’ water molecules through the pore in the same direction as its exit – as the authors put it, galactose acts as a Brownian piston that rectifies the passive water motion through the pore.
Comparable rectification of proton motion through a proton pumps such as bacteriorhodopin, resulting in a ‘proton diode’, is described by Klaus Gerwert and colleagues at Bochum (S. Wolf et al., Angew. Chem. Int. Ed. 49, 6889-6893; 2010 – paper here). This team draw on their detailed investigations of bR over recent years, and new studies of point mutations, to explain how conformational changes in a few residues can control access between internally bound and external water molecules in such a way as to bias the direction of proton flow in a general mechanism that they suspect might be more general to other proton pumps.
Biological processes involving proton motion are prime candidates for manifesting quantum-mechanical effects. A rather striking instance of this is claimed by George Reiter of the University of Houston and colleagues, who say that the zero-point motions of protons in are entirely responsible for the binding of water to A-DNA (G. Reiter et al., Phys. Rev. Lett. 105, 148101; 2010 – paper here). Changes in hydration seem to be what drive the A-to-B transition in DNA (the A phase forms in dehydrated conditions), and Reiter et al. say that this is accompanied by a change in the zero-point kinetic energy of the protons in the hydrated B-DNA that is sufficient in itself to motivate the transition. Whether the protons concerned are those of water molecules in the hydration shell or those in the DNA’s H-bonds (or, presumably, a bit of both) is not yet clear.
It’s many years ago now that David Tirrell, now at Caltech, developed ways to incorporate fluorinated amino acids into proteins using recombinant DNA technology – a feat popularized with reference to non-stick fried eggs. David has now teamed up with Ahmed Zewail and colleagues to investigate what fluorinated residues do to the hydration of such proteins, using ultrafast time-dependent fluorescent Stokes shift spectroscopy on fluorinated coiled-coil peptides (O.-H. Kwon et al., PNAS 10.1073/pnas.1011569107 – paper here). They find that the hydration dynamics are retarded around fluorinated residues, in marked contrast to an acceleration of the dynamics for the corresponding cases of hydrogenated residues, which are of comparable size.
Some mini-proteins, such as the villin headpiece domains HP35 and HP36, with just 35 and 36 residues, have an unusual ability to fold quickly into a conformation with a securely buried hydrophobic core despite their small size. Takao Yoda of the Nagahama Institute of Bio-science and Technology and colleagues have used simulations to investigate how this happens (T. Yoda et al., Biophys. J. 99, 1637-1644; 2010 – paper here). The cores in the folded state are fully dehydrated, but some water molecules remain therein until the final stages of folding. This is an unusually large system for which the folding process has been followed in detail from a fully extended state in explicit solvent. Meanwhile, David Cerutti at Rutgers and coworkers have simulated the crystal structures of a scorpion toxin protein to probe the performance of different protein and water force-field models in predicting the observed structure (D. S. Cerutti et al., J. Phys. Chem. B 114, 12811-12824; 2010 – paper here). They find that the results are not very sensitive to the water model, and far more dependent on the protein model (FF99SB does best) in terms of correctly predicting the right contacts in the peptide chain.
Whether we can understand the various forces involved in protein folding sufficiently to design peptides and other heteropolymers to adopt specific conformations is of course one of the big challenges not only for protein design but for polymer chemistry more generally. Shekhar Garde and colleagues at RPI have studied how water-mediated interactions might be exploited in this endeavour (S. N. Jamadagni et al., J. Phys. Chem. B jp104924g – paper here). In particular, they explore the sequence space of model polymers containing one or two pairs of charged monomers, in cases where the other monomers are more or less hydrophobic, and at the effect of adding salt to such systems. The results reveal subtle factors at play: for example, ion pairs among hydrophobic monomers can stabilize hairpin conformations over collapsed globules via water-mediated Coulombic interactions, but this depends on where the charged monomers appear along the chain. And adding salt can open up these hairpins, whereas salt stabilizes the globular forms of hydrophobic homopolymers.
Some membrane-binding proteins induce curvature of the membrane (see H. T. McMahon & J. L. Gallop, Nature 438, 590; 2005) – for example, the so-called BAR domain of amphiphysin will remodel lipid vesicles into tubules. Greg Voth and colleagues have performed MD simulations to try to figure out how this works, and they find that, surprisingly, there is a layer of water intervening between BAR and the membrane even when the protein domain is strongly bound (E. Lyman et al., Biophys. J. 99, 1783-1790; 2010 – paper here). This implies that the charged region of BAR is screened from the lipid headgroups, so that the bending mechanism is not electrostatic.
How homogeneous are solutions of denaturing guanidinium salts? Recently, Mason and coworkers have reported evidence that the cations form nanoscale aggregates (e.g. P. E. Mason et al., PNAS 100, 4557; 2003). Using dielectric relaxation spectroscopy, Richard Buchner of the University of Regensburg question this conclusion (J. Hunger et al., J. Phys. Chem. B jp101520h – paper here). In other words, perhaps after all Gdm+ ions can ‘fit’ comfortably into the structure of bulk water without altering it – which would seem to support the ‘direct’ mechanism of denaturation whereby Gdm+ interacts with the protein backbone rather than loosening up the folded state by influencing hydration.
More evidence for the direct intermediation of water in enzyme action: Sason Shaik at the Hebrew University of Jerusalem and colleagues say that a water cluster in the binding site of heme oxygenase participates in its ring-opening degradation of heme groups (W. Lai et al., JACS 132, 12960-12970; 2010 – paper here). The water cluster organizes the substrate into the proper geometry, serves as a proton shuttle, and stabilizes the hydroxyl nucleophile that attacks the ring. And Dongping Zhong at Ohio State University and colleagues say that flavoproteins, which act as redox coenzymes, contain water networks in the active site with fast relaxation dynamics that probably controls the protein flexibility in a functionally relevant manner (C.-W. Chang et al., JACS 132,12741-12747; 2010 – paper here). Meanwhile, Peter Brzezinski at Stockholm University and colleagues offer evidence that water molecules are involved in proton transport through cytochrome c oxidase, which actively pumps protons across a membrane to sustain a proton-motive force for ATP synthesis (H. J. Lee et al., JACS ja107244g – paper here).
Mischa Bonn of the FOM Institute AMOLF in Amsterdam and colleagues say that the hydration region of lipid headgroups in monolayers contains two populations of water molecules, one with bulk-like relaxation and the other that relaxes faster (M. Bonn et al., JACS ja106194u – paper here). Their VSF spectroscopic measurements thus imply the presence of a group of water molecules that are strongly hydrogen-bonded to the headgroups, decoupled from the bulk, and potentially involved in rapid, in-plane proton transfer, as previous studies have suggested for lipid membranes.
How does the hydration of antifreeze proteins differ from that of regular proteins? Ann McDermott and colleagues at Columbia use NMR methods to study this question by investigating the hydration shells of ubiquitin and an ice-binding (type III) antifreeze protein at cryogenic temperatures (-35 C) (A. B. Siemer et al., PNAS 10.1073/pnas.1009369107 – paper here). They find that the ubiquitin hydration shell remains unfrozen and uncoupled to the ice lattice, whereas this is true of only parts of the AFP III shell: as one might expect, the ice-binding interface establishes direct contact with ice.
The ability of sufficiently narrow carbon nanotubes to admit water but exclude ions has been proposed as a basis for desalination technologies. But Daejoong Kim and coworkers at Sogang University in South Korea show that admission or exclusion of ions can be a subtle business. They say that at certain nanotube diameters, strong sodium hydration can lead to a preferential admission of potassium ions over sodium in mixed ionic solutions, while at other diameters sodium can be preferred, or that both ions can be increasingly excluded even as the tube diameter increases (J. J. Cannon et al., J. Phys. Chem. B jp104609d – paper here). So it is conceivable that selective filtration and separation might be achieved. It seems quite conceivable that Ilan Benjamin’s new analysis of the hydration of alkali-metal halides in hydrophobic environments, and the formation of ion pairs (J. Phys. Chem. B jp1050673 – paper here), might be relevant here to the state inside the nanotubes.
Finally, bulk water, and a suggestion that the structural picture here is still not fully resolved. Peter Hamm at the University of Freiburg and colleagues use the theoretical tools developed for the study of complex networks (such as those in social science) to reveal hidden topological aspects of the H-bonded network in MD simulations of liquid water (F. Rao et al., J. Phys. Chem. B jp1060792 – paper here). They say this approach reveals structural inhomogeneities, extending at least to the second hydration shell, that are not evident from methods that focus on a single scalar order parameter such as tetrahedrality. Needless to say, the same technique might be used to look at solute hydration shells.
Friday, September 17, 2010
Water in cavities
How hydration affects ligand binding in protein cavities is a subtle business. Not only is it still imperfectly understood, but it seems possible that it might be hard to generalize about how the various enthalpic and entropic effects of dehydration of the cavity and the ligand balance out. Yet such issues could be central to the rational design of drugs. Andrew McCammon at UCSD and his coworkers have used MD simulations to try to bring some order to the problem (R. Baron et al., JACS 132, 12091-12097; 2010 – paper here). They point out that both positive and negative entropy changes have been reported previously for water entering protein cavities, and that the result probably depends both on the chemistry and the geometry of the cavity. The key question, they rightly say, is: does water have a passive or active role in cavity-ligand recogniton? They investigate that question using an idealized cavity-ligand combination with various permutations of surface charges on both, looking to develop ‘thermodynamic profiles’ of the binding events. And indeed, the signs and magnitudes of the enthalpy and entropy changes prove to vary widely for the different cases (their Figure 6 tells the story). One finding is that, coincidentally, the net free energy change is similar both for binding driven electrostatically and by hydrophobic interactions.
Similar issues are explored by Hongtao Yu and Steven Rick at the University of New Orleans, who calculate the entropy, enthalpy and free-energy changes on transferring a water molecule from the bulk to various types of protein cavity large enough to hold only a single water (J. Phys. Chem. B 10.1021/jp104209w – paper here). They look in particular at the effects of having different numbers of H-bond donors and acceptors in the cavity. It is again not easy to generalize, but it seems that the thermodynamic consequences of H-bond formation are greater than those exerted, via entropic effects, by the cavity size.
More on how denaturants work, this time from Ilja K. Voets at the University of Fribourg and colleagues (J. Phys. Chem. B 10.1021/jp103515b – paper here). They use light scattering, SANS, NMR, IR and UV-Vis spectroscopy to study how the size and flexibility of the lysozyme molecule changes in a mixed water/DMSO solvent at varying compositional ratios. They see three regimes, in which the protein is compact, wholly unfolded, and partially unfolded, and deduce that there are three major factors influencing these conformational changes: changes in water’s H-bonded structure induced by DMSO, the propensity of DMSO to act as an H-bond acceptor, and DMSO’s role as a poor solvent for polar groups and the polypeptide backbone but a good one for apolar sidechains.
Meanwhile, Yi Qin Gao at Texas A&M and colleagues look at urea denaturation (H. Wei et al., J. Phys. Chem. B 10.1021/jp103770y – paper here). Here the big debate has been whether urea acts indirectly, via its effect on water’s H-bonded network, or directly by interactions with the protein backbone. This group proposed previously that it’s a bit of both. Now they take that idea further by looking at urea denaturation of the chicken villin headpiece protein and some of its mutants. They consider in particular how urea affects the breaking of backbone hydrogen bonds and the penetration of water into the hydrophobic core. In both respects, the influence of urea seems again to be both direct and indirect. For example, the presence of urea seems to enhance water penetration of the core (just as it has been found previously to enhance the hydration of the interiors of carbon nanotubes), and that this enhancement is correlated with binding of urea to the protein surface. Moreover, as the protein unfolds, the exposed hydrophilic regions are stabilized by binding of urea. It seems, then, that the denaturing action cannot be explained by a ‘physical effect’ so much as by a ‘narrative’ of the dynamical process.
The mechanism(s) of anti-freeze glycoproteins also continue to be debated, and Martina Havenith at Bochum and her colleagues raise the intriguing idea that they owe their protective role to an ability to perturb the collective dynamics of water over long ranges, retarding them in the extended hydration shell in a way that suppresses freezing (S. Ebbinghaus et al., JACS 10.1021/ja1051632 – paper here). This proposal, based on terahertz spectroscopic data for an anti-freeze glycoprotein from an Antarctic fish, is quite different from any other that I know of, and could be quite different from the way anti-freeze proteins work – unlike AFP, AFGPs are flexible and don’t have a well-defined structure, so probably do not operate by binding to the surface of ice crystals.
One of my finer moments in my former life at Nature was getting Reza Ghadiri’s work on cyclic peptide nanotubes published in 1993 in the face of scepticism during the review process. The work was soon vindicated, and these self-assembling tubes showed evidence of being able to mediate transport of dissolved species through lipid membranes. Jianfen Fan at Soochow University in Suzhou and colleagues have now used MD to investigate the mechanism of water diffusion through such pores (J. Liu et al., J. Phys. Chem. B 10.1021/jp1039207 – paper here). Water molecules form a linear chain threading a hexapeptide channel, but the H-bonded structure is increasingly three-dimensional for wider cyclic molecules. Understanding the transport process could be valuable for, say, the potential use of self-assembling channels like this in water purification and desalination.
The dynamics and evolution of such water ‘filaments’ in pores and other biological systems, such as lipid membranes, are studied by Marek Orzechowski and Markus Meuwly at the University of Basel, using MD simulations (J. Phys. Chem. B 10.1021/jp1051003 – paper here). Their medium is, however, not explicitly a biological one: it is a monolayer of alkylsilica chains about 1 nm thick, like those used in some chromatographic columns; and the solvent is a water/acetonitrile mixture. They find that water filaments, containing typically tens of molecules, form intermittently in the alkyl layer, and can persist for around 1 ns before being dispersed by thermal fluctuations.
The transition of lipid membranes from a gel to a liquid-crystal phase may significantly alter the membrane’s interactions with water and aqueous ions, say Tomasz Róg at the Tampere University of Technology in Finland and coworkers (M. Stepniewski et al., J. Phys. Chem. B 10.1021/jp104739a – paper here). Both phases might exist in vivo, although the LC phase is the usual one. The authors’ simulations show that in the gel phase the lipid headgroups are partially dehydrated and sodium ions cannot penetrate to the interfacial region to bind to the carbonyl groups.
A new method for estimating hydration free energies of organic molecules with an implicit solvent is described by Maxim Federov of the MPI for Mathematics in the Sciences in Leipzig and coworkers (E. L. Ratkova et al., J. Phys. Chem. B 10.1021/jp103955r – paper here). It’s a modification of the RISM model of Chandler and Anderson, which provides a reasonably computationally cheap way of accounting for solvent structure along with some empirical parametrization of the solvation of specific chemical functionalities (alkyl, hydroxy, carbonyl etc.), ‘trained on’ and tested with small organics. No indication of whether it might be extended to macromolecules, although the authors intend to try it on bioactive compounds.
But the method for predicting hydration structures outlined by Karl Freed at Chicago and colleagues is explicitly geared towards proteins (J. J. Virtanen et al., Biophys. J. 99, 1611-1619; 2010 – paper here). They use simulations of the hydration of ubiquitin, lysozyme and myoglobin to calculate electron radial distribution functions for the different atom types, and then show that these can be used to generate electron densities – and from them, hydration structures – for other proteins. The electron distributions can also be used to calculate X-ray scattering intensity, and the authors intend to use this in future work to compare their predictions with experiment.
It’s the absence of water in the core of the ‘alpha-solenoid’ protein importin-beta that gives this spring-like molecule its astonishing elasticity, according to Helmut Grubmüller and colleagues at the MPI for Biophysical Chemistry in Göttingen (C. Kappel et al., Biophys. J. 99, 1596-1603; 2010 – paper here). Specifically, their simulations indicate that the hydrophobic core has a molten-globule-like conformation that governs its mechanical properties. As such, the protein occupies a middle ground between fully folded and intrinsically disordered, showing how what one might call ‘secondary unstructure’ determined by hydrophobicity allows fine-tuning of a biologically relevant physical property.
And not really ‘water in biology’ at all, but a neat experiment on water at a hydrophilic (mica) surface is reported by Jim Heath at Caltech and colleagues (K. Xu et al., Science 329, 1188-1191; 2010 – paper here). They deposit graphene sheets on mica, and observe islands on the surface with the AFM that appear to be water monolayers ‘sealed in’ by the graphene. These often have faceted edges, suggesting that they are ice-like even at room temperature, and they may be nucleated at surface defects. At 90 percent humidity a water monolayer appears to cover the entire mica surface, and a second adlayer may grow patchily on top.
Similar issues are explored by Hongtao Yu and Steven Rick at the University of New Orleans, who calculate the entropy, enthalpy and free-energy changes on transferring a water molecule from the bulk to various types of protein cavity large enough to hold only a single water (J. Phys. Chem. B 10.1021/jp104209w – paper here). They look in particular at the effects of having different numbers of H-bond donors and acceptors in the cavity. It is again not easy to generalize, but it seems that the thermodynamic consequences of H-bond formation are greater than those exerted, via entropic effects, by the cavity size.
More on how denaturants work, this time from Ilja K. Voets at the University of Fribourg and colleagues (J. Phys. Chem. B 10.1021/jp103515b – paper here). They use light scattering, SANS, NMR, IR and UV-Vis spectroscopy to study how the size and flexibility of the lysozyme molecule changes in a mixed water/DMSO solvent at varying compositional ratios. They see three regimes, in which the protein is compact, wholly unfolded, and partially unfolded, and deduce that there are three major factors influencing these conformational changes: changes in water’s H-bonded structure induced by DMSO, the propensity of DMSO to act as an H-bond acceptor, and DMSO’s role as a poor solvent for polar groups and the polypeptide backbone but a good one for apolar sidechains.
Meanwhile, Yi Qin Gao at Texas A&M and colleagues look at urea denaturation (H. Wei et al., J. Phys. Chem. B 10.1021/jp103770y – paper here). Here the big debate has been whether urea acts indirectly, via its effect on water’s H-bonded network, or directly by interactions with the protein backbone. This group proposed previously that it’s a bit of both. Now they take that idea further by looking at urea denaturation of the chicken villin headpiece protein and some of its mutants. They consider in particular how urea affects the breaking of backbone hydrogen bonds and the penetration of water into the hydrophobic core. In both respects, the influence of urea seems again to be both direct and indirect. For example, the presence of urea seems to enhance water penetration of the core (just as it has been found previously to enhance the hydration of the interiors of carbon nanotubes), and that this enhancement is correlated with binding of urea to the protein surface. Moreover, as the protein unfolds, the exposed hydrophilic regions are stabilized by binding of urea. It seems, then, that the denaturing action cannot be explained by a ‘physical effect’ so much as by a ‘narrative’ of the dynamical process.
The mechanism(s) of anti-freeze glycoproteins also continue to be debated, and Martina Havenith at Bochum and her colleagues raise the intriguing idea that they owe their protective role to an ability to perturb the collective dynamics of water over long ranges, retarding them in the extended hydration shell in a way that suppresses freezing (S. Ebbinghaus et al., JACS 10.1021/ja1051632 – paper here). This proposal, based on terahertz spectroscopic data for an anti-freeze glycoprotein from an Antarctic fish, is quite different from any other that I know of, and could be quite different from the way anti-freeze proteins work – unlike AFP, AFGPs are flexible and don’t have a well-defined structure, so probably do not operate by binding to the surface of ice crystals.
One of my finer moments in my former life at Nature was getting Reza Ghadiri’s work on cyclic peptide nanotubes published in 1993 in the face of scepticism during the review process. The work was soon vindicated, and these self-assembling tubes showed evidence of being able to mediate transport of dissolved species through lipid membranes. Jianfen Fan at Soochow University in Suzhou and colleagues have now used MD to investigate the mechanism of water diffusion through such pores (J. Liu et al., J. Phys. Chem. B 10.1021/jp1039207 – paper here). Water molecules form a linear chain threading a hexapeptide channel, but the H-bonded structure is increasingly three-dimensional for wider cyclic molecules. Understanding the transport process could be valuable for, say, the potential use of self-assembling channels like this in water purification and desalination.
The dynamics and evolution of such water ‘filaments’ in pores and other biological systems, such as lipid membranes, are studied by Marek Orzechowski and Markus Meuwly at the University of Basel, using MD simulations (J. Phys. Chem. B 10.1021/jp1051003 – paper here). Their medium is, however, not explicitly a biological one: it is a monolayer of alkylsilica chains about 1 nm thick, like those used in some chromatographic columns; and the solvent is a water/acetonitrile mixture. They find that water filaments, containing typically tens of molecules, form intermittently in the alkyl layer, and can persist for around 1 ns before being dispersed by thermal fluctuations.
The transition of lipid membranes from a gel to a liquid-crystal phase may significantly alter the membrane’s interactions with water and aqueous ions, say Tomasz Róg at the Tampere University of Technology in Finland and coworkers (M. Stepniewski et al., J. Phys. Chem. B 10.1021/jp104739a – paper here). Both phases might exist in vivo, although the LC phase is the usual one. The authors’ simulations show that in the gel phase the lipid headgroups are partially dehydrated and sodium ions cannot penetrate to the interfacial region to bind to the carbonyl groups.
A new method for estimating hydration free energies of organic molecules with an implicit solvent is described by Maxim Federov of the MPI for Mathematics in the Sciences in Leipzig and coworkers (E. L. Ratkova et al., J. Phys. Chem. B 10.1021/jp103955r – paper here). It’s a modification of the RISM model of Chandler and Anderson, which provides a reasonably computationally cheap way of accounting for solvent structure along with some empirical parametrization of the solvation of specific chemical functionalities (alkyl, hydroxy, carbonyl etc.), ‘trained on’ and tested with small organics. No indication of whether it might be extended to macromolecules, although the authors intend to try it on bioactive compounds.
But the method for predicting hydration structures outlined by Karl Freed at Chicago and colleagues is explicitly geared towards proteins (J. J. Virtanen et al., Biophys. J. 99, 1611-1619; 2010 – paper here). They use simulations of the hydration of ubiquitin, lysozyme and myoglobin to calculate electron radial distribution functions for the different atom types, and then show that these can be used to generate electron densities – and from them, hydration structures – for other proteins. The electron distributions can also be used to calculate X-ray scattering intensity, and the authors intend to use this in future work to compare their predictions with experiment.
It’s the absence of water in the core of the ‘alpha-solenoid’ protein importin-beta that gives this spring-like molecule its astonishing elasticity, according to Helmut Grubmüller and colleagues at the MPI for Biophysical Chemistry in Göttingen (C. Kappel et al., Biophys. J. 99, 1596-1603; 2010 – paper here). Specifically, their simulations indicate that the hydrophobic core has a molten-globule-like conformation that governs its mechanical properties. As such, the protein occupies a middle ground between fully folded and intrinsically disordered, showing how what one might call ‘secondary unstructure’ determined by hydrophobicity allows fine-tuning of a biologically relevant physical property.
And not really ‘water in biology’ at all, but a neat experiment on water at a hydrophilic (mica) surface is reported by Jim Heath at Caltech and colleagues (K. Xu et al., Science 329, 1188-1191; 2010 – paper here). They deposit graphene sheets on mica, and observe islands on the surface with the AFM that appear to be water monolayers ‘sealed in’ by the graphene. These often have faceted edges, suggesting that they are ice-like even at room temperature, and they may be nucleated at surface defects. At 90 percent humidity a water monolayer appears to cover the entire mica surface, and a second adlayer may grow patchily on top.
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