The role of bridging bubbles in the so-called ‘long-range hydrophobic force’ seems now fairly well established. In a study of this effect, Viveca Wallqvist and colleagues argue that in cases where this is the identified mechanism of attraction, it would be preferable to call it a ‘capillary force’ rather than a ‘hydrophobic interaction’. Their study looks at the effect of surface roughness on such forces between hydrophobic surfaces (V. Wallqvist et al., Langmuir 25, 9197 (2009) – paper here). They find that the range and magnitude of the force can vary significantly at different points on nanostructured surfaces due to local variations in contact angle. A high density of nanoscale crevices leads to accumulation of air bubbles that coalesce and weaken the capillary attraction.
William Ducker offers an explanation of the low contact angle and the unusual stability of these nanobubbles, in terms of a thin film of surface-active contaminant at the air-water interface (Langmuir 25, 8907 (2009) – paper here). This, he says, will both decrease the surface tension (and thus the contact angle) and hinder gas diffusion out of the bubble. It’s an alternative to Michael Brenner and Detlef Lohse’s suggestion of a dynamic stabilization of the nanobubbles (Phys. Rev. Lett. 101, 214505 (2008)).
Yi Zhang and colleagues at the Shanghai Institute of Applied Sciences suggest that a precursor to these nanobubbles may be a multilayer (bilayer or trilayer) of adsorbed gas at the hydrophobic interface (L. Zhang et al., Langmuir 25, 8860 (2009) – paper here). They have imaged such bi- and trilayer islands of gas, of up to micron-sized lateral dimensions, at the surface of HOPG, and have watched them evolve into nanobubbles, sometimes under the influence of the AFM tip used for imaging.
And in the same vein, Bharat Bhushan and coworkers look at how the mobility of nanobubbles at hydrophobic surfaces is affected by surface heterogeneity (Y. Wang et al., Langmuir 25, 9328 (2009) – paper here). They find that surfaces partly and totally covered with polystyrene films, which form small islands or can become indented at the nanoscale by the presence of bubbles, tend to have relatively immobile nanobubbles compared with bare, smooth hydrophobic surfaces. Bubble immobility reduces the frictional drag force between such surfaces in motion, and so is sometimes desired in mechanical contexts.
How do you measure hydrophobicity? Macroscopically, that is of course done using contact angles. But what are the microscopic signatures? This question is examined by Shekhar Garde and colleagues at RPI using an extensive range of simulation studies of water at various surfaces ranging from very hydrophobic to very hydrophilic (R. Godawat et al., PNAS advance online publication - paper here). They say that water density is a poor measure of hydrophobicity, but that both the probability of cavity formation and the free energy of binding of hydrophobic solutes to the surface correlates much better with the macroscopic wetting properties. This paper adds weight to the notion that it is in the dynamic rather than the structural characteristics of water that the true nature of hydrophobicity is located.
Gerhard Hummer and colleagues have developed a rather comprehensive model of gated proton pumping in cytochrome c oxidase (Y. C. Kim et al., PNAS advance online publication - paper here). This reveals show the electrostatic interaction between the proton loading site and the electron source for reduction of oxygen at the heme site is central to the pumping efficiency, and also how gating is accomplished.
Water in protein cavities is hard to detect with diffraction methods if it is disordered. Robert Goldbeck at UC Santa Cruz, Raymond Esquerra at San Franscisco State University and their colleagues have shown that non-specific hydration of the cavities of myoglobin mutants can be detected optically via its perturbing effect on the optical spectrum of the pentcoordinate heme group (R. Goldbeck et al., JACS ASAP ja903409j - paper here).
How do membrane proteins compensate, within the hydrocarbon core of a membrane, for loss of hydrophobic interactions? One possibility is that they enhance packing efficiency and thus van der Waals interactions between the hydrophobic residues. Or they might have stronger hydrogen-bonding interactions between hydrophilic regions. But James Bowie and colleagues at UCLA report structural and thermodynamic arguments for why neither plays a strong role (JACS 131, 10846 (2009) – paper here). Rather, they suspect that the reduced entropy cost of folding in membrane proteins might be responsible for their stability.
There is a small clutch of papers on the structure of the air-water interface and other species located there. Yi Qin Gao and colleagues at Texas A&M use vibrational sum frequency spectroscopy and MD simulations to investigate orientational ordering of water molecules, and suggest that this occurs to any significant degree only in the first two layers at the surface (Y. Fan et al., J. Phys. Chem. B ASAP jp900117t - paper here). Joyce Noah-Vanhoucke and Phillip Geissler argue that the preferential segregation of some ions at the air-water interface is due primarily to the way the ions induce deformations of the interfacial geometry, causing electrostatic fluctuations that are not accounted for in the conventional picture (PNAS advance online publication - paper here).
In water confined to nanoscale dimensions (as in the crowded environment of a cell), hydration effects can be quite different from those of the bulk. Margaret Cheung and colleagues at Houston provide an illustration of this by using MD to look at the conformations of hexane in nanoscale water droplets (D. Homouz et al., J. Phys. Chem. B ASAP jp907318d - paper here). They find that the hexane molecules are situated at the droplet surface, where disruption of the H-bonding favours the all-trans conformation.
Meanwhile, Michael Fayer and colleagues at Stanford use ultrafast IR spectroscopy to look at water dynamics close to the neutral and ionic surfaces of reverse micelles (E. E. Fenn et al., PNAS advance online publication - paper here). They find that the orientational relaxations times are rather similar in both cases, both being significantly slower than in the bulk, and conclude that it is the mere presence of an interface, rather than its chemical nature, which exerts the dominant effect.
Nanoscopic water films on metals and other simple surfaces are known often to adopt ordered structures in the first one or two monolayers that may or may not be like bulk ice. On Pt(111), for example, it seems to form a monolayer that is flat rather than having the puckering expected of a ‘slice of ice’. Now Greg Kimmel, Bruce Kay and colleagues find that water on graphene (supported on Pt(111) also forms a flat film, here two monolayers thick (G. A. Kimmel et al., JACS ASAP ja904708f - paper here). This structure has been predicted previously for confined bilayers between hydrophobic walls, but it seems that confinement is not needed to induce it. The bilayer has no dangling bonds or lone pairs on either face, and so one might anticipate that it will itself be somewhat hydrophobic, as indeed Greg Kimmel and others found previously for the flat monolayer on Pt(111) (G. A. Kimmel et al., Phys. Rev. Lett. 95, 166102 (2005).).
Jürgen Köfinger and Christoph Dellago have used MD calculations to probe the dynamics and dielectric response of single-file water chains in narrow pores (Phys. Rev. Lett. 103, 080601; paper here). This supplies a baseline for using dielectric spectroscopy to investigate the properties of such highly confined water, for example enabling the diffusion of defects in the H-bonded chain to be studied.
Kafui Tay and Anne Boutin at the Université Paris-Sud XI have studied the dynamics of hydrated electrons using MD, and say that their diffusion is dictated by fluctuations in the H-bonded network: in the temperature region where the diffusion is Arrhenius-like, the activation energy is determined by H-bond breaking (J. Phys. Chem. B ASAP jp810538f - paper here).
Lars Pettersson, Anders Nilsson and their colleagues at Stanford, Stockholm and in Japan have published a controversial paper claiming to see inhomogeneities in water structure on length scales of around 1 nm (C. Huang et al., PNAS advance online publication - paper here). They say that they see these using SAXS, and argue that the density contrast is due to the coexistence of two water structures: one tetrahedral, the other with distorted H-bonds, related respectively to low- and high-density liquid water. This is, needless to say, a revival of the very old two-state picture of water structure, which in various forms goes right back to Roentgen. It will be disputed, no doubt, but demonstrates again how remarkably tenacious this two-state notion is.
Tuesday, August 25, 2009
Monday, July 27, 2009
How proteins loosen up
What happens during protein denaturation? One emerging view is that at least some forms of denaturation (such as pressure-induced) involve penetration of water into the hydrophobic interior. But that picture is challenged in a paper by Santosh Kumar Jha and Jayant Udgaonkar at the Tara Institute of Fundamental Research in Bangalore, at least for the case of denaturant-induced (GdnHCl) unfolding (PNAS 10.1073/pnas.0905744106; paper here). They have used UV circular dichroism measurements on the small plant protein monellin to show that here unfolding seems to involve a dry molten-globule intermediate, reached from the native state in a rather sharp configurational transition.
Also on this topic, Paul Cremer and colleagues at Texas A&M have used FTIR and thermodynamic measurements to probe the notion that urea denatures via direct hydrogen-bonding to the protein surface (L. B. Sagle et al., JACS 131, 9304 (2009); paper here). They challenge that idea, saying that hydrogen-bonding of urea seems to actually promote hydrophobic collapse of a polyamide (PNIPAM, here used as a protein analogue).
Ahmed Zewail and his colleagues have looked at how solvent motion couples to the unfolding of a model protein (melittin) in the presence of a denaturant (trifluoroethanol) (C. M. Othon et al., PNAS 10.1073/pnas.0905967106; paper here). Using time-resolved fluorescence spectroscopy, they see an abrupt change in solvent dynamics at a critical TFE concentration associated with a change in protein structure, in which the tetramers dissociate into loosely bound monomers owing to penetration of TFE into the hydrophobic core. The dissociation of the monomers happens in a distinct second step.
Sapna Sarupria and Shekhar Garde at RPI have studied the compressibility and fluctuations of hydration shells of hydrophobic solutes and proteins using MD simulations (Phys. Rev. Lett. 103, 037803; 2009 – paper here). They say that the compressibility is non-monotonic as a function of solute size, and that it is greater near hydrophobic solutes, relative to the bulk. The latter implies that hydrophobic interactions get weaker as pressure is increased, which may be important for pressure-induced denaturation. This pressure sensitivity is also dependent on the curvature of the solute, being greater for low-curvature surfaces. That might have a role in the pressure dissociation of multi-subunit proteins.
Incidentally, I am preparing a feature article on denaturation for Chemistry World, and would welcome any papers that might be relevant to this.
Padmanabhan Balaram and colleagues at the Indian Institute of Science in Bangalore report a very nice crystal structure of a model peptide containing a hydrophobic channel containing a linear water wire of nine molecules (U. S. Raghavender et al., JACS 10.1021/ja9038906; paper here). Looks like a good model system for studying such structures.
There is a clutch of papers on hydration dynamics of proteins. A painstaking study of femtosecond dynamics in the hydration network of apomyoglobin by Dongping Zhong and colleagues at Ohio State has revealed two distinct classes of water-network relaxation (L. Zhang et al., JACS 10.1021/ja902918p; paper here). One comes from collective hydrogen-bond rearrangements in the water shell, while the other is considerably slower and results from coupled water-protein motions. They are also able to follow changes in these motions in the transition from the native to the molten-globule state. This looks like the kind of careful study that is needed to really figure out what the intimate coupling of protein and water motions entails.
M. Vogel at the Technical University of Darmstadt has used MD simulations to look at how the dynamics of the hydration shells of peptide analogues of structural proteins (elastic and collagen) change with temperature (J. Phys. Chem. B 113, 9386 (2009); paper here). He finds that there is a change from diffusive motion at higher temperatures to jump-like motion on cooling, corresponding to a weak fragile-to-strong crossover of the water dynamics.
And Giorgio Schirò and colleagues at the University of Rome III use dielectric spectroscopy to study the dynamics of myoglobin confined in porous silica at low hydration levels, with only one or two layers of water around the protein (G. Schirò et al., J. Phys. Chem. B 113, 9606 (2009); paper here). They find that confinement has a big effect relative to hydrated myoglobin powder, suppressing the cooperativity of the water motions and the strong coupling to the protein dynamics. All the same, there still seems to be some slaving of protein relaxation in the porous medium to one mode of solvent relaxation.
Dor Ben-Amotz and colleagues at Purdue have seen the spectroscopic signature of dangling OH bonds in the hydration shells of small dissolved nonpolar molecules, similar to those seen at macroscopic water-oil interfaces (P. N. Perera et al., PNAS 10.1073/pnas.0903675106; paper here). And Pier Luigi Silvestrelli at the University of Padova offers further evidence, from first-principles calculations, that hydrophobic groups (here the methyl of methanol) don’t immobilize water molecules, iceberg-like, in the immediate hydration shell, but rather, merely slow down many surrounding molecules (J. Phys. Chem. B 10.1021/jp9044447; paper here).
It’s occasionally and justifiably said that too little attention has been given to polysaccharide hydration, in contrast to proteins. As a result, we know relatively little about glycoprotein hydration. Claudio Margulis and colleagues at Iowa State attempt to redress that imbalance somewhat with a paper looking at the hydration shells of a diverse range of carbohydrates (S. K. Ramadugu et al., J. Phys. Chem. B 10.1021/jp904981v; paper here). I’m not sure I can easily summarize the results, but there looks to be a lot of valuable information here, for example in terms of how water structure and dynamics are affected by branching, size and type of linkage in the polysaccharides.
The behaviour of water in carbon nanotubes continues to intrigue as a model for hydrophobic protein pores. MD simulations by Biswaroop Mukherjee of the Indian Institute of Science and coworkers suggest that jump reorientation of water molecules inside narrow nanotubes involves a switch of which of the two hydrogens are H-bonded to a neighbour, in contrast to such jumps in the bulk which involve H-bonding to a different neighbour (B. Mukherjee et al., J. Phys. Chem. B 10.1021/jp904099f; paper here).
Francesco Mallamace, Gene Stanley and their collaborators have a paper in Nature Physics that describes the appearance of a fractional Stokes-Einstein relation (which provides information about viscosity, connecting the self-diffusion coefficient to temperature and relaxation time) below 290 K in water confined within silica nanopores (2 nm diameter) (Nature Physics 10.1038/nphys1328; paper here). They suggest that this switch marks a crossover to a water structure that is locally more similar to LDA ice – a point at which the proportions of HDA-like and LDA-like configurations starts to change rapidly. It’s an intriguing idea, and there is apparently some indication (I can say no more yet) that the dynamical crossover might be a more general phenomenon for liquids. Some, though, will reasonably wonder whether water within 2-nm silica pores can really be considered representative of the bulk.
Perhaps relevant in this respect, Patrick Huber at Saarland University in Germany and colleagues have studied the dynamics of capillary rise in silica pores 3-5-5 nm across (S. Gruener et al., Phys. Rev. E 79, 067301 (2009); paper here). They find that they can account for the timescales of pore filling according to macroscopic hydrodynamics, so long as they assume the presence of a ‘sticky preadsorbed boundary layer of about two monolayers of water molecules’. In other words, there is dynamical partitioning of the water ‘filling’ into two components.
Masakazu Matsumoto at Nagoya University offers a new picture of the density maximum of water cooled towards freezing (Phys. Rev. Lett. 103, 017801 (2009); paper here). He challenges the common, somewhat arm-waving idea that the decrease in density below 4 C is due to a dominance of LDA-like local configurations. Rather, he says, a proper description of the associated structural changes needs to be broken down in more detail: the anomaly seems to stem from a combination of the change in average hydrogen bond length as a function of temperature (which is monotonic) and the contraction of the HB network due to bond-angle distortion. I’m imagining (it is not made explicit) that this differs from a decline in H-bond-breaking caused by a switch from HDA-like to LDA-like.
Yizhak Marcus at the Hebrew University of Jerusalem uses standard partial molar volumes to calculate the hydration numbers of a range of univalent and divalent ions under ambient conditions (J. Phys. Chem. B 10.1021/jp9027244; paper here). And László Pusztai at the Hungarian Academy of Sciences and colleagues use simulations and neutron/X-ray diffraction to find the hydration numbers of CsCl over a range of concentrations (V. Mile et al., J. Phys. Chem. B 10.1021/jp900092g; paper here). But the numbers don’t agree: Marcus calculates hydration numbers of 1.5-2.5 (depending on the definition) for Cs and 1.4-2.0 for Cl (at 25 C), whereas Pusztai et al. find respective figures of 8-6.5 (for increasing salt concentration) and 5-7. I’m not clear why the numbers are so different. Thanks to Jan Engberts for pointing me to these two papers.
How do specific ions bind to protein surfaces? The answer to this question promises to shed light on the much debated Hofmeister effects on protein aggregation, but there is still no consensus. One common rule of thumb talks of the law of ‘matching water affinities’, whereby cations and anions form ion pairs if they are more or less matched in size. Berk Hess and Nico van der Vegt present simulations which suggest that this simple relationship breaks down for alkali metal cations binding to carboxylate groups on protein surfaces (PNAS 10.1073/pnas.0902904106 – paper here). They argue that the picture is more complicated than such as simple physico-chemical law can express, involving the nature of the hydrated ion complex and the possibility of water-bridged interactions.
The mechanism of fast proton transport in water has been long debated, with the traditional view of Grotthus-like proton hopping along water chains now refined to a picture that tends to invoke intermediates of either the Eigen or Zundel ions (H3O+.3H2O or H5O2+). Rather similar considerations have been applied to the transport on hydroxide ions – are they just a mirror image of proton transport, or do they involve other ionic species such as H3O2-? Andrei Tokmakoff at MIT and his coworkers now present femtosecond pump-probe IR spectroscopic results that they say points to the significant involvement of a Zundel-like transition state in proton transfer in hydroxide solutions, in which a proton is delocalized between a hydroxide ion and a water molecule (S. T. Roberts et al., PNAS 10.1073/pnas.0901571106 – paper here).
Shuxun Cui at Southwest Jiaotong University in Chengdu has published a paper in which he speculates about the prebiotic implications of his recent single-molecule force spectroscopy work (some with Herman Gaub) on the structures of DNA in water and non-aqueous media (see for example JACS 128, 6636 (2006) and JACS 129, 14710 (2007)). He argues that double-stranded DNA can be seen as an adaptation to an aqueous environment (S. Cui, IUBMB Life 61, 860 (2009) – paper here). I have the strong sense that this, rather than Lawrence Henderson’s ‘fitness of the environment’, is the right way round to be examining this question.
Also on this topic, Paul Cremer and colleagues at Texas A&M have used FTIR and thermodynamic measurements to probe the notion that urea denatures via direct hydrogen-bonding to the protein surface (L. B. Sagle et al., JACS 131, 9304 (2009); paper here). They challenge that idea, saying that hydrogen-bonding of urea seems to actually promote hydrophobic collapse of a polyamide (PNIPAM, here used as a protein analogue).
Ahmed Zewail and his colleagues have looked at how solvent motion couples to the unfolding of a model protein (melittin) in the presence of a denaturant (trifluoroethanol) (C. M. Othon et al., PNAS 10.1073/pnas.0905967106; paper here). Using time-resolved fluorescence spectroscopy, they see an abrupt change in solvent dynamics at a critical TFE concentration associated with a change in protein structure, in which the tetramers dissociate into loosely bound monomers owing to penetration of TFE into the hydrophobic core. The dissociation of the monomers happens in a distinct second step.
Sapna Sarupria and Shekhar Garde at RPI have studied the compressibility and fluctuations of hydration shells of hydrophobic solutes and proteins using MD simulations (Phys. Rev. Lett. 103, 037803; 2009 – paper here). They say that the compressibility is non-monotonic as a function of solute size, and that it is greater near hydrophobic solutes, relative to the bulk. The latter implies that hydrophobic interactions get weaker as pressure is increased, which may be important for pressure-induced denaturation. This pressure sensitivity is also dependent on the curvature of the solute, being greater for low-curvature surfaces. That might have a role in the pressure dissociation of multi-subunit proteins.
Incidentally, I am preparing a feature article on denaturation for Chemistry World, and would welcome any papers that might be relevant to this.
Padmanabhan Balaram and colleagues at the Indian Institute of Science in Bangalore report a very nice crystal structure of a model peptide containing a hydrophobic channel containing a linear water wire of nine molecules (U. S. Raghavender et al., JACS 10.1021/ja9038906; paper here). Looks like a good model system for studying such structures.
There is a clutch of papers on hydration dynamics of proteins. A painstaking study of femtosecond dynamics in the hydration network of apomyoglobin by Dongping Zhong and colleagues at Ohio State has revealed two distinct classes of water-network relaxation (L. Zhang et al., JACS 10.1021/ja902918p; paper here). One comes from collective hydrogen-bond rearrangements in the water shell, while the other is considerably slower and results from coupled water-protein motions. They are also able to follow changes in these motions in the transition from the native to the molten-globule state. This looks like the kind of careful study that is needed to really figure out what the intimate coupling of protein and water motions entails.
M. Vogel at the Technical University of Darmstadt has used MD simulations to look at how the dynamics of the hydration shells of peptide analogues of structural proteins (elastic and collagen) change with temperature (J. Phys. Chem. B 113, 9386 (2009); paper here). He finds that there is a change from diffusive motion at higher temperatures to jump-like motion on cooling, corresponding to a weak fragile-to-strong crossover of the water dynamics.
And Giorgio Schirò and colleagues at the University of Rome III use dielectric spectroscopy to study the dynamics of myoglobin confined in porous silica at low hydration levels, with only one or two layers of water around the protein (G. Schirò et al., J. Phys. Chem. B 113, 9606 (2009); paper here). They find that confinement has a big effect relative to hydrated myoglobin powder, suppressing the cooperativity of the water motions and the strong coupling to the protein dynamics. All the same, there still seems to be some slaving of protein relaxation in the porous medium to one mode of solvent relaxation.
Dor Ben-Amotz and colleagues at Purdue have seen the spectroscopic signature of dangling OH bonds in the hydration shells of small dissolved nonpolar molecules, similar to those seen at macroscopic water-oil interfaces (P. N. Perera et al., PNAS 10.1073/pnas.0903675106; paper here). And Pier Luigi Silvestrelli at the University of Padova offers further evidence, from first-principles calculations, that hydrophobic groups (here the methyl of methanol) don’t immobilize water molecules, iceberg-like, in the immediate hydration shell, but rather, merely slow down many surrounding molecules (J. Phys. Chem. B 10.1021/jp9044447; paper here).
It’s occasionally and justifiably said that too little attention has been given to polysaccharide hydration, in contrast to proteins. As a result, we know relatively little about glycoprotein hydration. Claudio Margulis and colleagues at Iowa State attempt to redress that imbalance somewhat with a paper looking at the hydration shells of a diverse range of carbohydrates (S. K. Ramadugu et al., J. Phys. Chem. B 10.1021/jp904981v; paper here). I’m not sure I can easily summarize the results, but there looks to be a lot of valuable information here, for example in terms of how water structure and dynamics are affected by branching, size and type of linkage in the polysaccharides.
The behaviour of water in carbon nanotubes continues to intrigue as a model for hydrophobic protein pores. MD simulations by Biswaroop Mukherjee of the Indian Institute of Science and coworkers suggest that jump reorientation of water molecules inside narrow nanotubes involves a switch of which of the two hydrogens are H-bonded to a neighbour, in contrast to such jumps in the bulk which involve H-bonding to a different neighbour (B. Mukherjee et al., J. Phys. Chem. B 10.1021/jp904099f; paper here).
Francesco Mallamace, Gene Stanley and their collaborators have a paper in Nature Physics that describes the appearance of a fractional Stokes-Einstein relation (which provides information about viscosity, connecting the self-diffusion coefficient to temperature and relaxation time) below 290 K in water confined within silica nanopores (2 nm diameter) (Nature Physics 10.1038/nphys1328; paper here). They suggest that this switch marks a crossover to a water structure that is locally more similar to LDA ice – a point at which the proportions of HDA-like and LDA-like configurations starts to change rapidly. It’s an intriguing idea, and there is apparently some indication (I can say no more yet) that the dynamical crossover might be a more general phenomenon for liquids. Some, though, will reasonably wonder whether water within 2-nm silica pores can really be considered representative of the bulk.
Perhaps relevant in this respect, Patrick Huber at Saarland University in Germany and colleagues have studied the dynamics of capillary rise in silica pores 3-5-5 nm across (S. Gruener et al., Phys. Rev. E 79, 067301 (2009); paper here). They find that they can account for the timescales of pore filling according to macroscopic hydrodynamics, so long as they assume the presence of a ‘sticky preadsorbed boundary layer of about two monolayers of water molecules’. In other words, there is dynamical partitioning of the water ‘filling’ into two components.
Masakazu Matsumoto at Nagoya University offers a new picture of the density maximum of water cooled towards freezing (Phys. Rev. Lett. 103, 017801 (2009); paper here). He challenges the common, somewhat arm-waving idea that the decrease in density below 4 C is due to a dominance of LDA-like local configurations. Rather, he says, a proper description of the associated structural changes needs to be broken down in more detail: the anomaly seems to stem from a combination of the change in average hydrogen bond length as a function of temperature (which is monotonic) and the contraction of the HB network due to bond-angle distortion. I’m imagining (it is not made explicit) that this differs from a decline in H-bond-breaking caused by a switch from HDA-like to LDA-like.
Yizhak Marcus at the Hebrew University of Jerusalem uses standard partial molar volumes to calculate the hydration numbers of a range of univalent and divalent ions under ambient conditions (J. Phys. Chem. B 10.1021/jp9027244; paper here). And László Pusztai at the Hungarian Academy of Sciences and colleagues use simulations and neutron/X-ray diffraction to find the hydration numbers of CsCl over a range of concentrations (V. Mile et al., J. Phys. Chem. B 10.1021/jp900092g; paper here). But the numbers don’t agree: Marcus calculates hydration numbers of 1.5-2.5 (depending on the definition) for Cs and 1.4-2.0 for Cl (at 25 C), whereas Pusztai et al. find respective figures of 8-6.5 (for increasing salt concentration) and 5-7. I’m not clear why the numbers are so different. Thanks to Jan Engberts for pointing me to these two papers.
How do specific ions bind to protein surfaces? The answer to this question promises to shed light on the much debated Hofmeister effects on protein aggregation, but there is still no consensus. One common rule of thumb talks of the law of ‘matching water affinities’, whereby cations and anions form ion pairs if they are more or less matched in size. Berk Hess and Nico van der Vegt present simulations which suggest that this simple relationship breaks down for alkali metal cations binding to carboxylate groups on protein surfaces (PNAS 10.1073/pnas.0902904106 – paper here). They argue that the picture is more complicated than such as simple physico-chemical law can express, involving the nature of the hydrated ion complex and the possibility of water-bridged interactions.
The mechanism of fast proton transport in water has been long debated, with the traditional view of Grotthus-like proton hopping along water chains now refined to a picture that tends to invoke intermediates of either the Eigen or Zundel ions (H3O+.3H2O or H5O2+). Rather similar considerations have been applied to the transport on hydroxide ions – are they just a mirror image of proton transport, or do they involve other ionic species such as H3O2-? Andrei Tokmakoff at MIT and his coworkers now present femtosecond pump-probe IR spectroscopic results that they say points to the significant involvement of a Zundel-like transition state in proton transfer in hydroxide solutions, in which a proton is delocalized between a hydroxide ion and a water molecule (S. T. Roberts et al., PNAS 10.1073/pnas.0901571106 – paper here).
Shuxun Cui at Southwest Jiaotong University in Chengdu has published a paper in which he speculates about the prebiotic implications of his recent single-molecule force spectroscopy work (some with Herman Gaub) on the structures of DNA in water and non-aqueous media (see for example JACS 128, 6636 (2006) and JACS 129, 14710 (2007)). He argues that double-stranded DNA can be seen as an adaptation to an aqueous environment (S. Cui, IUBMB Life 61, 860 (2009) – paper here). I have the strong sense that this, rather than Lawrence Henderson’s ‘fitness of the environment’, is the right way round to be examining this question.
Monday, June 22, 2009
Small molecules and protein folding
The role of small molecules – denaturants and osmolytes – in protein folding is much in need of a good review article (or have I missed one?). Julio Fernández and colleagues have used single-molecule force spectroscopy to look at how the osmolyte glycerol interacts with ubiquitin as the protein is mechanically unfolded (S. Garcia-Manyes et al., PNAS 10.1073/pnas.09020106 – not yet online). Glycerol stabilizes the protein against unfolding, and apparently also promotes hydrophobic collapse of the unfolded conformation. They think that while glycerol stabilizes the folded state via direct interaction with the protein, ethanol seems to exert a weaker stabilizing effect via an indirect interaction involving the disruption of ‘water structure’. The promotion of hydrophobic collapse in the presence of glycerol (which is not seen for ethanol) seems to be a separate effect, perhaps due to the enhanced destabilization of exposed hydrophobic surface due to the polar surface area of glycerol.
The electronic state of water molecules confined in a close-packed rodlike micelle lattice is significantly different from that in the gas and bulk liquid phases, according to Jan-Erik Rubensson and colleagues at Uppsala University (J. Gråsjö et al., J. Phys. Chem. B 113, 8201; 2009 – paper here). They have probed this question using soft X-ray absorption and emission, and say that the water molecules among micelles are stabilized relative to the bulk, perhaps because of interaction with the chloride counterions in solution.
Pablo Debenedetti and coworkers have also studied nanoconfined water, here in a slit-like space between two hydrophilic silica surfaces using MD simulations (S. R.-V. Castrillón et al., J. Phys. Chem. B 10.1021/jp9025392 – paper here). They find rotational slowing within 0.5 nm of the surfaces, and translational slowing within 1 nm.
The difference in hydrophobic interactions in acidic solutions relative to salt solutions is investigated by Greg Voth and colleagues (H. Chen et al., J. Phys. Chem. B 113, 7291; 2009 – paper here). They say that in acid (HCl) solution they see interactions between the hydrophobe surface and the hydrated protons, owing to the amphiphilic character of the latter. This could explain why hydrated protons are anomalous in the Hofmeister series, promoting solubilization of nonpolar solutes despite having a similar radius to salting-out cations such as potassium and ammonium.
And on matters Hofmeister, Bernd Rode and colleagues at the University of Innsbruck have carried out quantum simulations of the hydration of beryllium ions, and find that the tetrahedral first hydration shell has very slow exchange dynamics (S. S. Azam et al., J. Phys. Chem. B 10.1021/jp903536k – paper here). They refer to this as a strong ‘structure-forming’ behaviour – I can see what they mean, but does it invite confusion with the already confused issue of ‘structure-making’?
The dynamic Stokes shift – the slower decay of a frequency-shifted fluorescent probe molecule – close to protein surfaces relative to the bulk solution has been attributed in the past to much slower water motions in the hydration shell. But Bertil Halle and Lennart Nilsson question this interpretation in a new paper (J. Phys. Chem. B 113, 8210; 2009 – paper here). They say that the slower decay can be understood by a solvent polarization effect, and does not probe hydration dynamics at all.
Zoran Arsov at the Josef Stefan Institute in Ljubljana and colleagues report the weakening of hydrogen bonds in water confined between lipid bilayers, using a form of FTIR (Z. Arsov et al., ChemPhysChem 10.1002/cphc.200900185 – paper here). The water films separating bilayers in the lamellar phases (phospholipids DMPC and POPE) studied here are very thin – 2 and 0.6 nm respectively. So a disruption of bulk structure is presumably to be expected. They suggest that this perturbation may contribute to the attractive hydration force between the bilayers.
There has been a long debate, going back to Faraday and Tyndall, on whether ice has a liquid-like layer on its surface and if so, what this looks like. Xiao-Yang Zhu and colleagues at Minnesota have investigated this with interfacial force microscopy (M. P. Goertz et al., Langmuir 10.1021/la9001994 – paper here). They see a liquid-like layer tens of nanometres thick, but suggest that it is in fact viscoelastic.
The electronic state of water molecules confined in a close-packed rodlike micelle lattice is significantly different from that in the gas and bulk liquid phases, according to Jan-Erik Rubensson and colleagues at Uppsala University (J. Gråsjö et al., J. Phys. Chem. B 113, 8201; 2009 – paper here). They have probed this question using soft X-ray absorption and emission, and say that the water molecules among micelles are stabilized relative to the bulk, perhaps because of interaction with the chloride counterions in solution.
Pablo Debenedetti and coworkers have also studied nanoconfined water, here in a slit-like space between two hydrophilic silica surfaces using MD simulations (S. R.-V. Castrillón et al., J. Phys. Chem. B 10.1021/jp9025392 – paper here). They find rotational slowing within 0.5 nm of the surfaces, and translational slowing within 1 nm.
The difference in hydrophobic interactions in acidic solutions relative to salt solutions is investigated by Greg Voth and colleagues (H. Chen et al., J. Phys. Chem. B 113, 7291; 2009 – paper here). They say that in acid (HCl) solution they see interactions between the hydrophobe surface and the hydrated protons, owing to the amphiphilic character of the latter. This could explain why hydrated protons are anomalous in the Hofmeister series, promoting solubilization of nonpolar solutes despite having a similar radius to salting-out cations such as potassium and ammonium.
And on matters Hofmeister, Bernd Rode and colleagues at the University of Innsbruck have carried out quantum simulations of the hydration of beryllium ions, and find that the tetrahedral first hydration shell has very slow exchange dynamics (S. S. Azam et al., J. Phys. Chem. B 10.1021/jp903536k – paper here). They refer to this as a strong ‘structure-forming’ behaviour – I can see what they mean, but does it invite confusion with the already confused issue of ‘structure-making’?
The dynamic Stokes shift – the slower decay of a frequency-shifted fluorescent probe molecule – close to protein surfaces relative to the bulk solution has been attributed in the past to much slower water motions in the hydration shell. But Bertil Halle and Lennart Nilsson question this interpretation in a new paper (J. Phys. Chem. B 113, 8210; 2009 – paper here). They say that the slower decay can be understood by a solvent polarization effect, and does not probe hydration dynamics at all.
Zoran Arsov at the Josef Stefan Institute in Ljubljana and colleagues report the weakening of hydrogen bonds in water confined between lipid bilayers, using a form of FTIR (Z. Arsov et al., ChemPhysChem 10.1002/cphc.200900185 – paper here). The water films separating bilayers in the lamellar phases (phospholipids DMPC and POPE) studied here are very thin – 2 and 0.6 nm respectively. So a disruption of bulk structure is presumably to be expected. They suggest that this perturbation may contribute to the attractive hydration force between the bilayers.
There has been a long debate, going back to Faraday and Tyndall, on whether ice has a liquid-like layer on its surface and if so, what this looks like. Xiao-Yang Zhu and colleagues at Minnesota have investigated this with interfacial force microscopy (M. P. Goertz et al., Langmuir 10.1021/la9001994 – paper here). They see a liquid-like layer tens of nanometres thick, but suggest that it is in fact viscoelastic.
Tuesday, June 16, 2009
More catching up
Changes in my circumstances have delayed this one, and of course the longer I delay, the worse it gets. I bring things somewhat up to date here, but there’s still more to come.
First, an ad: there is an RSC Faraday Discussion on ‘Wetting Dynamics of Hydrophobic and Structured Surfaces’ in Richmond, Virginia on 12-14 April 2010. Given the list of organizers and invited speakers, it is sure to be very good. Details are here.
More on water flow inside carbon nanotubes, which is attracting increasing interest because of the possibilities for water purification and desalination. John Thomas and Alan McGaughey at Carnegie Mellon find in MD simulations that the water structure changes significantly for tubes of 0.83 to 1.39 nm – from single chains to stacked pentagons and hexagons and finally to bulk-like (Phys. Rev. Lett. 102, 184502; 2009 – paper here). This seems to significantly affect the (pressure-driven) flow velocity in a non-monotonic way, particularly when the liquid has a layer-like profile.
Thomas Angel and his coworkers have looked at the roles of water molecules in photosensitive rhodopsin-like G protein-coupled receptors (T. E. Angel et al., PNAS 10.1073/pnas.0903545106 – paper here). They find that waters associated with highly conserved residues seem to be crucial to function, in particular providing the plasticity needed to transmit a signal from the retinal binding pocket to the intracellular surface.
Sow-Hsin Chen and coworkers find, using QENS, that lysozyme remains flexible (‘soft’) at low temperatures (210-240 K) when moderate pressure (around 1 kbar) is applied (X.-q. Chu et al., J. Phys. Chem. B 10.1021/jp900557w – paper here). Surprisingly, the dynamics under these conditions are actually faster than those under ambient conditions, and reflect those of the hydration water.
And speaking of low-temperature environments, David Wharton and Craig Marshall have outlined some of the survival strategies of Antarctic organisms in a nice brief review in J. Biol. 8, 39; 2009 – paper here. And Todd Sformo at the University of Alaska at Fairbanks has told me about a very interesting paper reporting an Arctic gnat that simultaneously uses freeze tolerance and freeze avoidance in different parts of its body – these strategies are usually mutually exclusive (T. Sformo et al., J. Compar. Physiol. B: Biochem. System. Envir. Physiol. 10.1007/s00360-009-0369-x; 2009 - paper here. (You see, this is the kind of nice stuff I fear I’m missing all the time…)
Huib Bakker’s group has used THz and femtosecond IR spectroscopy to study proton hydration (K. J. Tielrooij et al., Phys. Rev. Lett. 102, 198303; 2009 – paper here). They find that protons induce a drop in dielectric constant corresponding to an effect on 19 water molecules per proton. Four of these are involved in direct solvation, being irrotationally bound to the proton, but the others are perturbed by becoming implicated in proton motion.
Staying with proton transport, Greg Voth and colleagues have used the MS-EVB method to look at proton transfer in human carbonic anhydrase II (C. M. Maupin et al., JACS 10.1021/ja8091938 – paper here). The proton transfer here, between a zinc-bound OH group and the His64 residue, is the rate-limiting step, and involves a water cluster in the active site. There are some insights here into the ways proteins may use hydrophobic interfaces to control and facilitate proton transport. And Ana-Nicoleta Bondar at the University of California at Irvine and colleagues have studied how protons achieve long-distance transport in bacteriorhodopsin from the acceptor residue Asp85 to the extracellular proton release group (P. Phatak et al., JACS 10.1021/ja809767v – paper here). Bound water molecules in the active site are again implicated.
Prashanth Athri and W. David Wilson at Georgia State University show how interfacial water can help the DNA-binding agent DB921 to bind in the minor groove despite an imperfect geometric match (JACS 10.1021/ja809249h – paper here). These results might offer clues to exploiting water mediation in designing DNA-binding molecules.
More on urea and denaturation: Frank Gabel at the Institut de Biologie Structurale in Grenoble and colleagues have used SANS and SAXS to study the binding of urea to denatured ubiquitin (JACS 10.1021/ja9013248 – paper here). They find that acid-induced denaturation recruits about 20 urea molecules from solution to bind to the protein, supporting the view that these direct interactions between protein and denaturant are the cause of denaturation.
Some studies of water at lipid membranes. M. D. Fayer and colleagues at Stanford look at the hydration of AOT reverse micelles, compared to the lamellar phase, using ultrafast IR spectroscopy, and conclude that short-range, direct interactions with the head groups, rather than more general nanoconfinement effects, seen to be responsible for the orientiation retardation of water molecules (D. E. Moilanen et al., JACS 131, 8318; 2009 – paper here). And Zhancheng Zhang and Max Berkowitz at UNC have looked at the slowing of water orientational relaxation in the hydration layer of phospholipids bilayers using MD (J. Phys. Chem. B 113, 7676; 2009 – paper here). Berkowitz and Changsun Eun have also looked (via MD) at the hydration of lipid headgroups attached to two parallel graphene plates, as a model for interactions between bilayers (J. Phys. Chem. B 10.1021/jp901747s – paper here). They find a repulsive interaction between the plates that has three regimes, dependent on the plate separation. At small distances (0.75-1 nm) the repulsion is steric. At intermediate distances (1-1.6 nm) it results from dehydration of the head groups, and at large separations (1.7-2.4 nm) – well, I must be missing something in my rapid reading here, but all I can glean is that this is water-mediated too.
Alenka Luzar and colleagues have compared MD simulations of the hydration of monosodium glutamate with the recent neutron data from Sylvia McLain et al. (J. Phys. Chem. B 110, 21251; 2006). They find that the simulations could not reproduce the reduction in water-water correlations seen experimentally, pointing to some of the shortcomings of the classical potentials used (C. D. Daub et al., J. Phys. Chem. B. 113, 7687; 2009 – paper here). And Janusz Stangret and colleagues have characterized the hydration of carboxylate ions using FTIR spectroscopy (E. Gojlo et al., J. Phys. Chem. B 10.1021/jp811346x – paper here). They find that two water molecules induce symmetry-breaking of the carboxylate group, providing non-equivalent proton donors to the oxygen atoms.
Jacob Petrich and colleagues at Iowa State describe a new method for probing the dynamics of proteins – specifically, measuring the solvation correlation function – by monitoring the fluorescence from two coumarins with different lifetimes (S. Bose et al., J. Phys. Chem. B 10.1021/jp9004345 – paper here).
Benoît Roux at Chicago and coworkers consider the ‘topological control hypothesis’ for selective ion binding to proteins, which postulates that selectivity is controlled primarily by the number of ligands coordinating the ion – which can in turn be predicted from the average coordination structure in bulk water – and not from their chemical nature (H. Yu et al., J. Phys. Chem. B 10.1021/jp901233v – paper here). They find, perhaps not surprisingly, that this hypothesis has some serious limitations in predicting binding free energies.
Kelly Gaffney and coworkers at Stanford use ultrafast IR spectroscopy to look at hydrogen-bond dynamics in sodium perchlorate solution (S. Park et al., J. Phys. Chem. B 10.1021/jp9016739 – paper here). They find that the dynamics support an orientational jump model in which the making and breaking of H-bonds is the predominant control on reorientation times. MD simulations also indicate that the anion hydration shells have two distinct shells, and that the molecules in the inner shell donate one H-bond each to the perchlorate ion.
Nicolas Giovambattista, Peter rossky and Pablo Debenedetti have been trying to map out the phase behaviour of water confined between hydropholic, hydrophobic and heterogeneous plates at various temperatures and pressures (Phys. Rev. E 73, 041604; 2006 and J. Phys. Chem. C 11, 1323; 2007). They have now extended this work by looking at the effects of varying the T and P simultaneously between 220-300 K and –0.2 to 0.2 GPa (J. Phys. Chem. B 10.1021/jp9018266 – paper here). It’s hard to summarize all the information in this rich paper, but one general conclusion is that the plates become effectively less hydrophobic (the vapour phase is suppressed) as the temperature drops. An underlying motive for this work is to understand the pressure- and cold-denaturation of proteins and how this is tied up with invasion of hydrophobic cavities by water.
First, an ad: there is an RSC Faraday Discussion on ‘Wetting Dynamics of Hydrophobic and Structured Surfaces’ in Richmond, Virginia on 12-14 April 2010. Given the list of organizers and invited speakers, it is sure to be very good. Details are here.
More on water flow inside carbon nanotubes, which is attracting increasing interest because of the possibilities for water purification and desalination. John Thomas and Alan McGaughey at Carnegie Mellon find in MD simulations that the water structure changes significantly for tubes of 0.83 to 1.39 nm – from single chains to stacked pentagons and hexagons and finally to bulk-like (Phys. Rev. Lett. 102, 184502; 2009 – paper here). This seems to significantly affect the (pressure-driven) flow velocity in a non-monotonic way, particularly when the liquid has a layer-like profile.
Thomas Angel and his coworkers have looked at the roles of water molecules in photosensitive rhodopsin-like G protein-coupled receptors (T. E. Angel et al., PNAS 10.1073/pnas.0903545106 – paper here). They find that waters associated with highly conserved residues seem to be crucial to function, in particular providing the plasticity needed to transmit a signal from the retinal binding pocket to the intracellular surface.
Sow-Hsin Chen and coworkers find, using QENS, that lysozyme remains flexible (‘soft’) at low temperatures (210-240 K) when moderate pressure (around 1 kbar) is applied (X.-q. Chu et al., J. Phys. Chem. B 10.1021/jp900557w – paper here). Surprisingly, the dynamics under these conditions are actually faster than those under ambient conditions, and reflect those of the hydration water.
And speaking of low-temperature environments, David Wharton and Craig Marshall have outlined some of the survival strategies of Antarctic organisms in a nice brief review in J. Biol. 8, 39; 2009 – paper here. And Todd Sformo at the University of Alaska at Fairbanks has told me about a very interesting paper reporting an Arctic gnat that simultaneously uses freeze tolerance and freeze avoidance in different parts of its body – these strategies are usually mutually exclusive (T. Sformo et al., J. Compar. Physiol. B: Biochem. System. Envir. Physiol. 10.1007/s00360-009-0369-x; 2009 - paper here. (You see, this is the kind of nice stuff I fear I’m missing all the time…)
Huib Bakker’s group has used THz and femtosecond IR spectroscopy to study proton hydration (K. J. Tielrooij et al., Phys. Rev. Lett. 102, 198303; 2009 – paper here). They find that protons induce a drop in dielectric constant corresponding to an effect on 19 water molecules per proton. Four of these are involved in direct solvation, being irrotationally bound to the proton, but the others are perturbed by becoming implicated in proton motion.
Staying with proton transport, Greg Voth and colleagues have used the MS-EVB method to look at proton transfer in human carbonic anhydrase II (C. M. Maupin et al., JACS 10.1021/ja8091938 – paper here). The proton transfer here, between a zinc-bound OH group and the His64 residue, is the rate-limiting step, and involves a water cluster in the active site. There are some insights here into the ways proteins may use hydrophobic interfaces to control and facilitate proton transport. And Ana-Nicoleta Bondar at the University of California at Irvine and colleagues have studied how protons achieve long-distance transport in bacteriorhodopsin from the acceptor residue Asp85 to the extracellular proton release group (P. Phatak et al., JACS 10.1021/ja809767v – paper here). Bound water molecules in the active site are again implicated.
Prashanth Athri and W. David Wilson at Georgia State University show how interfacial water can help the DNA-binding agent DB921 to bind in the minor groove despite an imperfect geometric match (JACS 10.1021/ja809249h – paper here). These results might offer clues to exploiting water mediation in designing DNA-binding molecules.
More on urea and denaturation: Frank Gabel at the Institut de Biologie Structurale in Grenoble and colleagues have used SANS and SAXS to study the binding of urea to denatured ubiquitin (JACS 10.1021/ja9013248 – paper here). They find that acid-induced denaturation recruits about 20 urea molecules from solution to bind to the protein, supporting the view that these direct interactions between protein and denaturant are the cause of denaturation.
Some studies of water at lipid membranes. M. D. Fayer and colleagues at Stanford look at the hydration of AOT reverse micelles, compared to the lamellar phase, using ultrafast IR spectroscopy, and conclude that short-range, direct interactions with the head groups, rather than more general nanoconfinement effects, seen to be responsible for the orientiation retardation of water molecules (D. E. Moilanen et al., JACS 131, 8318; 2009 – paper here). And Zhancheng Zhang and Max Berkowitz at UNC have looked at the slowing of water orientational relaxation in the hydration layer of phospholipids bilayers using MD (J. Phys. Chem. B 113, 7676; 2009 – paper here). Berkowitz and Changsun Eun have also looked (via MD) at the hydration of lipid headgroups attached to two parallel graphene plates, as a model for interactions between bilayers (J. Phys. Chem. B 10.1021/jp901747s – paper here). They find a repulsive interaction between the plates that has three regimes, dependent on the plate separation. At small distances (0.75-1 nm) the repulsion is steric. At intermediate distances (1-1.6 nm) it results from dehydration of the head groups, and at large separations (1.7-2.4 nm) – well, I must be missing something in my rapid reading here, but all I can glean is that this is water-mediated too.
Alenka Luzar and colleagues have compared MD simulations of the hydration of monosodium glutamate with the recent neutron data from Sylvia McLain et al. (J. Phys. Chem. B 110, 21251; 2006). They find that the simulations could not reproduce the reduction in water-water correlations seen experimentally, pointing to some of the shortcomings of the classical potentials used (C. D. Daub et al., J. Phys. Chem. B. 113, 7687; 2009 – paper here). And Janusz Stangret and colleagues have characterized the hydration of carboxylate ions using FTIR spectroscopy (E. Gojlo et al., J. Phys. Chem. B 10.1021/jp811346x – paper here). They find that two water molecules induce symmetry-breaking of the carboxylate group, providing non-equivalent proton donors to the oxygen atoms.
Jacob Petrich and colleagues at Iowa State describe a new method for probing the dynamics of proteins – specifically, measuring the solvation correlation function – by monitoring the fluorescence from two coumarins with different lifetimes (S. Bose et al., J. Phys. Chem. B 10.1021/jp9004345 – paper here).
Benoît Roux at Chicago and coworkers consider the ‘topological control hypothesis’ for selective ion binding to proteins, which postulates that selectivity is controlled primarily by the number of ligands coordinating the ion – which can in turn be predicted from the average coordination structure in bulk water – and not from their chemical nature (H. Yu et al., J. Phys. Chem. B 10.1021/jp901233v – paper here). They find, perhaps not surprisingly, that this hypothesis has some serious limitations in predicting binding free energies.
Kelly Gaffney and coworkers at Stanford use ultrafast IR spectroscopy to look at hydrogen-bond dynamics in sodium perchlorate solution (S. Park et al., J. Phys. Chem. B 10.1021/jp9016739 – paper here). They find that the dynamics support an orientational jump model in which the making and breaking of H-bonds is the predominant control on reorientation times. MD simulations also indicate that the anion hydration shells have two distinct shells, and that the molecules in the inner shell donate one H-bond each to the perchlorate ion.
Nicolas Giovambattista, Peter rossky and Pablo Debenedetti have been trying to map out the phase behaviour of water confined between hydropholic, hydrophobic and heterogeneous plates at various temperatures and pressures (Phys. Rev. E 73, 041604; 2006 and J. Phys. Chem. C 11, 1323; 2007). They have now extended this work by looking at the effects of varying the T and P simultaneously between 220-300 K and –0.2 to 0.2 GPa (J. Phys. Chem. B 10.1021/jp9018266 – paper here). It’s hard to summarize all the information in this rich paper, but one general conclusion is that the plates become effectively less hydrophobic (the vapour phase is suppressed) as the temperature drops. An underlying motive for this work is to understand the pressure- and cold-denaturation of proteins and how this is tied up with invasion of hydrophobic cavities by water.
Wednesday, May 6, 2009
Catching up
I have been on travel and caught up with numerous other things for several weeks, which not only means I have been unable to post but also that I’ve doubtless missed some interesting things over the recent period. If so, apologies for that – and feel free to let me know! But note also that my email address at Nature won’t be active for much longer, as I am very shortly leaving my role there as a writer – I’m no longer able to keep that going alongside the other demands on my time. I will no doubt keep writing occasionally for Nature nonetheless, but will be henceforth reachable at p.ball@btinternet.com.
To business, and in no particular order from the stack of papers in my pile…
Martina Havenith and her coworkers at Bochum have continued their highly revealing work on hydration structures using terahertz spectroscopy. In a new paper (B. Born et al., JACS 131, 3752 (2009) – paper here) they look at the hydration networks around various small peptides at low hydration levels, and find that the collective motions of peptide + solvent that seem to characterize protein hydration shells disappear below a minimum number of hydration waters, which appears to be well below that required for monolayer coverage.
This issue of solvent-protein dynamical correlations is also studied by Nigel Scrutton and colleagues at the University of Manchester (D.J. Heyes et al., Angew. Chem. Int. Ed. 48, 3850; 2009 – paper here). They find that proton tunnelling in protochlorophyllide oxireductase, a light-driven enzyme involved in chlorophyll biosynthesis, requires protein motions that appear to be slaved to the solvent, whereas hydride transfer in this species does not. It seems significant that proton, but not hydride, transfer occurs only close to the protein’s glass transition temperature, when the protein-solvent coupling is likely to be most acute.
In my recent ChemPhysChem paper (here), I referred to some recent work on denaturants by Jeremy England and coworkers, inadvertently describing it as though it came out of Vijay Pande’s lab (J. L. England, V. S. Pande & G. Haran, JACS 130, 11854; 2008). Actually I gather it was done mostly at the lab of Gilad Haran at the Weizmann Institute in Israel. Apologies for that oversight. Gilad has told me of his recent work on protein collapse using single-molecule FRET (G. Ziv & G. Haran, JACS 131, 2942; 2009 – paper here; and G. Ziv et al., Phys. Chem. Chem. Phys. 11, 83; 2009 – paper here). The former paper argues that the action of denaturants operates primarily by modulating the collapse of the denatured state, rather than acting on the transition from molten globule to folded state.
A recent special issue of J. Phys. Chem. B on aqueous solutions and interfaces (113(13)) has given me a lot to catch up with. Sotiris Xantheas and Greg Voth give a nice overview here. Among the interesting papers therein, Greg profiles the case for the amphiphilic nature of the hydrated proton at the interface with hydrophobic media (S. Iuchi et al., J. Phys. Chem. B 113, 4017; 2009 – paper here); Janamejaya Chowdhary and Branka Ladanyi use MD to investigate the dynamics of hydrogen-bond making and breaking (113, 4045; 2009 – paper here), and Yves Rezus and Huib Bakker use femtosecond IR spectroscopy to look at how various amphiliphilic small molecules alter water structure in the bulk (113, 4038; 2009 – paper here). Rezus and Bakker find that trimethylamine-N-oxide seems to be special in the latter regard, increasing the rate of reorientation of mobile water, which might be interpreted as a sign that it increases the number of defects in the H-bonded network.
On much the same topic, Greg Voth and colleagues have used MD to look at the interactions of hydrophobic, nonpolar solvents in aqueous salt (NaCl) and acid (HCl) solution (H. Chen et al., J. Phys. Chem. B ASAP; paper here). They find unusual solvated-proton structures in the acid which are bound to the hydrophobes, again supporting the idea that the hydrated protons act as amphiphiles. This might explain why protons seem anomalous in the Hofmeister series. And Michael Brindza and Robert Walker at the University of Maryland use SHG to look at solvation mechanisms of small molecules (p-nitroanisole, indoline) at the interface of polar solids and various liquids, offering a broader context for understanding what water in particular does in such cases (JACS 131, 6207; 2009 – paper here). Alenka Luzar and her coworkers have used MD to look at the solvation of monosodium glutamate, making a comparison to experimental data on this system (C. D. Daub et al., J. Phys. Chem. B ASAP; paper here). On the whole the agreement is good with the neutron-diffraction data, but there are some important differences – for example, the simulations couldn’t reproduce the experimentally observed reduction in water-water correlations – that presumably point to inadequacies of using classical potentials. (Incidentally, my spellchecker tirelessly insists that ‘solvation’ should be ‘salvation’ – forgive me if I don’t fail to catch them all…)
Alenka’s comparison with experiment here relies heavily on Alan Soper’s neutron data and its analysis using empirical potential structure refinement, which was conducted for those data by Alan with Sylvia McLain and Anthony Watts. Sylvia has sent me a paper in which she, with Soper and Watts alongside Jeremy Smith and Isabella Daidone, use this same technique to deduce the nature of hydration and interaction between various amino acid dimmers (S. E. McLain et al., Angew. Chem. Int. Ed. 47, 9059; 2008 – paper here). This is extremely interesting, as it challenges the conventional view that the main driving force for association is the interaction of hydrophobic regions. In contrast, this study finds that it is the charged sites on the peptides that dominate the association, and that interaction decreases as hydrophobicity increases. Could the same apply in protein folding itself?
Sason Shaik and his collaborators have now published the full analysis of the role on internal waters in the action of cytochrome P450 StaP (Y. Wang et al., JACS ASAP; 2009 – paper here), the preliminary account of which I discussed in my CPC paper.
Anders Nilsson, Lars Pettersson and their coworkers have now published the work that I referred to in a Nature article last year, in which they challenge the view that X-ray and neutron diffraction data uniquely support the conventional tetrahedral-coordinate picture of water structure (K. T. Wikfeldt et al., J. Phys. Chem. B 113, 6246; 2009 – paper here). Needless to say, this remains highly controversial stuff.
Pedro de Pablo and colleagues at Madrid have reported some very striking results on the desiccation of viruses. They say that drying of two different viruses causes the ejection of DNA and, in one case, collapse of the remaining capsid owing to capillary forces of the water menisci inside (C. Carrasco et al., PNAS 106, 5475; 2009 – paper here).
A couple more papers on nanoconfined water, in hydrophobic but less explicitly biological environments. Sow-Hsin Chen and colleagues say that supercooled water, which shows a density minimum under confinement in hydrophilic mesoporous materials, has none such in a hydrophobic material (Y. Zhang et al., J. Phys. Chem. B ASAP: paper here). And Gene Stanley and colleagues look at the H-bond dynamics of TIP5P water in a hydrophobic nanopore slit (S. Han et al., Phys. Rev. E 79, 041202; 2009 – paper here). They say that the H-bonds are shorter-lived in this case than in the bulk, and the relaxation time is smaller, but the general qualitative behaviour is much the same (e.g. the temperature-dependence of the average H-bond lifetime, and non-exponential lifetime distributions).
Ahmed Zewail and Ding-Shyue Yang recently reported ultrafast electron crystallography of water at low temperatures (c. 150 K) at the surface of graphite (PNAS 106, 4122; 2009 – paper here). It’s not strictly relevant to water in biology, perhaps, but an issue that I’ve started to follow increasingly and which touches on water’s general ability to order at interfaces. The results imply that, perhaps contrary to expectation (especially when compared with hydrophobic H-terminated silicon), this hydrophobic surface doesn’t disrupt a highly ordered interfacial structure. It seems this may be because the graphite surface is stepped, which apparently allows it to template a cubic-ice structure.
I recently wrote a column for Nature Materials (8, 250; 2009 – see here) on hydrophobicity at larger scales than the molecular, and in particular on the discussions of wetting by water of nano- and microstructured surfaces via Wenzel or Cassie states. This is relevant to biology insofar as it bears on the question of wettability of, e.g. insect legs and lotus leaves. There is a nice recent simulation paper on the topic by Takahiro Koishi at the University of Fukui and colleagues (PNAS doi:10.1073/pnas.0902027106 – not yet online), which describes the different conditions (of surface topology and so forth) under which Wenzel and Cassie wetting exist, and the possibility of their coexistence. And Abraham Marmur has flagged up his paper from last year (Langmuir 24, 7573; 2008 – paper here) in which he too looks at general geometric considerations that might promote such high-contact-angle states.
Here’s an intriguing thing that had escaped my notice until now: it seems that voltages may be generated in carbon nanotubes along the tube axis when water flows through them (see S. Ghosh et al., Science 299, 1042; 2003 – paper here). That’s suggestive from the perspective that views nanotubes as simple analogues of hydrophobic protein channels. Already it seems that this idea has been explored for power conversion (Y. C. Zhao et al., Adv. Mater. 20, 1772; 2008). Now Quanzi Yuan and Ya-Pu Zhao of the Institute of Mechanics in Beijing offer an explanation for the phenomenon in terms of the alignment of water molecules in the hydrogen-bonded chain within the nanotube (JACS ASAP; paper here).
More on this general topic from Bo Liu at the Graduate University of the Chinese Academy of Sciences in Beijing and coworkers, who describe simulations of a model system in which end-functionalized short carbon nanotubes are embedded in a phospholipid bilayer as mimics of aquaporin (B. Liu et al., Nano Lett. 9, 1386; 2009 – paper here). Two charges are placed near the tube midpoints, to simulate the NPA region of aquaporin where water selectivity and proton gating is thought to happen. But proton conduction couldn’t be studied explicitly in these classical MD simulations. That aside, the device seems to work more or less as planned, in theory. But can we make it?
Well, that’s not the end of it, but my desk looks a whole lot better.
To business, and in no particular order from the stack of papers in my pile…
Martina Havenith and her coworkers at Bochum have continued their highly revealing work on hydration structures using terahertz spectroscopy. In a new paper (B. Born et al., JACS 131, 3752 (2009) – paper here) they look at the hydration networks around various small peptides at low hydration levels, and find that the collective motions of peptide + solvent that seem to characterize protein hydration shells disappear below a minimum number of hydration waters, which appears to be well below that required for monolayer coverage.
This issue of solvent-protein dynamical correlations is also studied by Nigel Scrutton and colleagues at the University of Manchester (D.J. Heyes et al., Angew. Chem. Int. Ed. 48, 3850; 2009 – paper here). They find that proton tunnelling in protochlorophyllide oxireductase, a light-driven enzyme involved in chlorophyll biosynthesis, requires protein motions that appear to be slaved to the solvent, whereas hydride transfer in this species does not. It seems significant that proton, but not hydride, transfer occurs only close to the protein’s glass transition temperature, when the protein-solvent coupling is likely to be most acute.
In my recent ChemPhysChem paper (here), I referred to some recent work on denaturants by Jeremy England and coworkers, inadvertently describing it as though it came out of Vijay Pande’s lab (J. L. England, V. S. Pande & G. Haran, JACS 130, 11854; 2008). Actually I gather it was done mostly at the lab of Gilad Haran at the Weizmann Institute in Israel. Apologies for that oversight. Gilad has told me of his recent work on protein collapse using single-molecule FRET (G. Ziv & G. Haran, JACS 131, 2942; 2009 – paper here; and G. Ziv et al., Phys. Chem. Chem. Phys. 11, 83; 2009 – paper here). The former paper argues that the action of denaturants operates primarily by modulating the collapse of the denatured state, rather than acting on the transition from molten globule to folded state.
A recent special issue of J. Phys. Chem. B on aqueous solutions and interfaces (113(13)) has given me a lot to catch up with. Sotiris Xantheas and Greg Voth give a nice overview here. Among the interesting papers therein, Greg profiles the case for the amphiphilic nature of the hydrated proton at the interface with hydrophobic media (S. Iuchi et al., J. Phys. Chem. B 113, 4017; 2009 – paper here); Janamejaya Chowdhary and Branka Ladanyi use MD to investigate the dynamics of hydrogen-bond making and breaking (113, 4045; 2009 – paper here), and Yves Rezus and Huib Bakker use femtosecond IR spectroscopy to look at how various amphiliphilic small molecules alter water structure in the bulk (113, 4038; 2009 – paper here). Rezus and Bakker find that trimethylamine-N-oxide seems to be special in the latter regard, increasing the rate of reorientation of mobile water, which might be interpreted as a sign that it increases the number of defects in the H-bonded network.
On much the same topic, Greg Voth and colleagues have used MD to look at the interactions of hydrophobic, nonpolar solvents in aqueous salt (NaCl) and acid (HCl) solution (H. Chen et al., J. Phys. Chem. B ASAP; paper here). They find unusual solvated-proton structures in the acid which are bound to the hydrophobes, again supporting the idea that the hydrated protons act as amphiphiles. This might explain why protons seem anomalous in the Hofmeister series. And Michael Brindza and Robert Walker at the University of Maryland use SHG to look at solvation mechanisms of small molecules (p-nitroanisole, indoline) at the interface of polar solids and various liquids, offering a broader context for understanding what water in particular does in such cases (JACS 131, 6207; 2009 – paper here). Alenka Luzar and her coworkers have used MD to look at the solvation of monosodium glutamate, making a comparison to experimental data on this system (C. D. Daub et al., J. Phys. Chem. B ASAP; paper here). On the whole the agreement is good with the neutron-diffraction data, but there are some important differences – for example, the simulations couldn’t reproduce the experimentally observed reduction in water-water correlations – that presumably point to inadequacies of using classical potentials. (Incidentally, my spellchecker tirelessly insists that ‘solvation’ should be ‘salvation’ – forgive me if I don’t fail to catch them all…)
Alenka’s comparison with experiment here relies heavily on Alan Soper’s neutron data and its analysis using empirical potential structure refinement, which was conducted for those data by Alan with Sylvia McLain and Anthony Watts. Sylvia has sent me a paper in which she, with Soper and Watts alongside Jeremy Smith and Isabella Daidone, use this same technique to deduce the nature of hydration and interaction between various amino acid dimmers (S. E. McLain et al., Angew. Chem. Int. Ed. 47, 9059; 2008 – paper here). This is extremely interesting, as it challenges the conventional view that the main driving force for association is the interaction of hydrophobic regions. In contrast, this study finds that it is the charged sites on the peptides that dominate the association, and that interaction decreases as hydrophobicity increases. Could the same apply in protein folding itself?
Sason Shaik and his collaborators have now published the full analysis of the role on internal waters in the action of cytochrome P450 StaP (Y. Wang et al., JACS ASAP; 2009 – paper here), the preliminary account of which I discussed in my CPC paper.
Anders Nilsson, Lars Pettersson and their coworkers have now published the work that I referred to in a Nature article last year, in which they challenge the view that X-ray and neutron diffraction data uniquely support the conventional tetrahedral-coordinate picture of water structure (K. T. Wikfeldt et al., J. Phys. Chem. B 113, 6246; 2009 – paper here). Needless to say, this remains highly controversial stuff.
Pedro de Pablo and colleagues at Madrid have reported some very striking results on the desiccation of viruses. They say that drying of two different viruses causes the ejection of DNA and, in one case, collapse of the remaining capsid owing to capillary forces of the water menisci inside (C. Carrasco et al., PNAS 106, 5475; 2009 – paper here).
A couple more papers on nanoconfined water, in hydrophobic but less explicitly biological environments. Sow-Hsin Chen and colleagues say that supercooled water, which shows a density minimum under confinement in hydrophilic mesoporous materials, has none such in a hydrophobic material (Y. Zhang et al., J. Phys. Chem. B ASAP: paper here). And Gene Stanley and colleagues look at the H-bond dynamics of TIP5P water in a hydrophobic nanopore slit (S. Han et al., Phys. Rev. E 79, 041202; 2009 – paper here). They say that the H-bonds are shorter-lived in this case than in the bulk, and the relaxation time is smaller, but the general qualitative behaviour is much the same (e.g. the temperature-dependence of the average H-bond lifetime, and non-exponential lifetime distributions).
Ahmed Zewail and Ding-Shyue Yang recently reported ultrafast electron crystallography of water at low temperatures (c. 150 K) at the surface of graphite (PNAS 106, 4122; 2009 – paper here). It’s not strictly relevant to water in biology, perhaps, but an issue that I’ve started to follow increasingly and which touches on water’s general ability to order at interfaces. The results imply that, perhaps contrary to expectation (especially when compared with hydrophobic H-terminated silicon), this hydrophobic surface doesn’t disrupt a highly ordered interfacial structure. It seems this may be because the graphite surface is stepped, which apparently allows it to template a cubic-ice structure.
I recently wrote a column for Nature Materials (8, 250; 2009 – see here) on hydrophobicity at larger scales than the molecular, and in particular on the discussions of wetting by water of nano- and microstructured surfaces via Wenzel or Cassie states. This is relevant to biology insofar as it bears on the question of wettability of, e.g. insect legs and lotus leaves. There is a nice recent simulation paper on the topic by Takahiro Koishi at the University of Fukui and colleagues (PNAS doi:10.1073/pnas.0902027106 – not yet online), which describes the different conditions (of surface topology and so forth) under which Wenzel and Cassie wetting exist, and the possibility of their coexistence. And Abraham Marmur has flagged up his paper from last year (Langmuir 24, 7573; 2008 – paper here) in which he too looks at general geometric considerations that might promote such high-contact-angle states.
Here’s an intriguing thing that had escaped my notice until now: it seems that voltages may be generated in carbon nanotubes along the tube axis when water flows through them (see S. Ghosh et al., Science 299, 1042; 2003 – paper here). That’s suggestive from the perspective that views nanotubes as simple analogues of hydrophobic protein channels. Already it seems that this idea has been explored for power conversion (Y. C. Zhao et al., Adv. Mater. 20, 1772; 2008). Now Quanzi Yuan and Ya-Pu Zhao of the Institute of Mechanics in Beijing offer an explanation for the phenomenon in terms of the alignment of water molecules in the hydrogen-bonded chain within the nanotube (JACS ASAP; paper here).
More on this general topic from Bo Liu at the Graduate University of the Chinese Academy of Sciences in Beijing and coworkers, who describe simulations of a model system in which end-functionalized short carbon nanotubes are embedded in a phospholipid bilayer as mimics of aquaporin (B. Liu et al., Nano Lett. 9, 1386; 2009 – paper here). Two charges are placed near the tube midpoints, to simulate the NPA region of aquaporin where water selectivity and proton gating is thought to happen. But proton conduction couldn’t be studied explicitly in these classical MD simulations. That aside, the device seems to work more or less as planned, in theory. But can we make it?
Well, that’s not the end of it, but my desk looks a whole lot better.
Friday, March 13, 2009
There’s more to life than sequence
I have been meaning for some time to write about an interesting paper in JACS by Naoki Sugimoto’s group in Kobe. It found its way into an article that I wrote this week for Nature’s online news. So I’ve decided to simply post this article here – it’s not all strictly relevant to water in biology, but hopefully is interesting stuff anyway. This is the version before editing, which has more detail.
Shape might be one of the key factors in the function of mysterious ‘non-coding’ DNA.
Everyone knows what DNA looks like. Its double helix decorates countless articles on genetics, has been celebrated in sculpture, and was even engraved on the Golden Record, our message to the cosmos on board the Voyager spacecraft.
The entwined strands, whose form was deduced in 1953 by James Watson and Francis Crick, are admired as much for their beauty as for the light they shed on the mechanism of inheritance: the complementarity between juxtaposed chemical building blocks on the two strands, held together by weak ‘hydrogen’ bonds like a zipper, immediately suggested to Crick and Watson how information encoded in the sequence of blocks could be transmitted to a new strand assembled on the template of an existing one.
With the structure of DNA ‘solved’, genetics switched its focus to the sequence of the four constituent units (called nucleotide bases). By using biotechnological methods to deduce this sequence, they claimed to be ‘reading the book of life’, with the implication that all the information needed to build an organism was held within this abstract linear code.
But beauty has a tendency to inhibit critical thinking. There is now increasing evidence that the molecular structure of DNA is not a delightfully ordered epiphenomenon of its function as a digital data bank but a crucial – and mutable – aspect of the way genomes work. A new study in Science [1] underlines that notion by showing that the precise shape of some genomic DNA has been determined by evolution. In other words, genetics is not simply about sequence, but about structure too.
The standard view – indeed, part of biology’s ‘central dogma’ – is that in its sequence of the four fundamental building blocks (called nucleotide bases) DNA encodes corresponding sequences of amino-acid units that are strung together to make a protein enzyme, with the protein’s compact folded shape (and thus its function) being uniquely determined by that sequence.
This is basically true enough. Yet as the human genome was unpicked nucleotide base by base, it became clear that most of the DNA doesn’t ‘code for’ proteins at all. Fully 98 percent of the human genome is non-coding. So what does it do?
We don’t really know, except to say that it’s clearly not all ‘junk’, as was once suspected – the detritus of evolution, like obsolete files clogging up a computer. Much of the non-coding DNA evidently has a role in cell function, since mutations (changes in nucleotide sequence) in some of these regions have observable (phenotypic) consequences for the organism. We don’t know, however, how the former leads to the latter.
This is the question that Elliott Margulies of the National Institutes of Health in Bethesda, Maryland, Tom Tullius of Boston University, and their coworkers set out to investigate. According to the standard picture, the function of non-coding regions, whatever it is, should be determined by their sequence. Indeed, one way of identifying important non-coding regions is to look for ones that are sensitive to sequence, with the implication that the sequence has been finely tuned by evolution.
But Margulies and colleagues wondered if the shape of non-coding DNA might also be important. As they point out, DNA isn’t simply a uniform double helix: it can be bent or kinked, and may have a helical pitch of varying width, for example. These differences depend on the sequence, but not in any straightforward manner. Two near-identical sequences can adopt quite different shapes, or two very different sequences can have a similar shape.
The researchers used a chemical method to deduce the relationship between sequence and shape. They then searched for shape similarities between analogous non-coding regions in the genomes of 36 different species. Such similarity implies that the shapes have been selected and preserved by evolution – in other words, that shape, rather than sequence per se, is what is important. They found twice as many evolutionarily constrained (and thus functionally important) parts of the non-coding genome than were evident from trans-species correspondences using only sequence data.
So in these non-coding regions, at least, sequence appears to be important only insofar as it specifies a certain molecular shape and not because if its intrinsic information content – a different sequence with the same shape might do just as well.
That doesn’t answer why shape matters to DNA. But it suggests that we are wrong to imagine that the double helix is the beginning and end of the story.
There are plenty of other good reasons to suspect that is true. For example, DNA can adopt structures quite different from Watson and Crick’s helix, called the B-form. It can, under particular conditions of saltiness or temperature, switch to at least two other double-helical structures, called the A and Z forms. It may also from triple- and quadruple-stranded variants, linked by different types of hydrogen-bonding matches between nucleotides. One such is called Hoogsteen base-pairing.
Biochemist Naoki Sugimoto and colleagues at Konan University in Kobe, Japan, have recently shown that, when DNA in solution is surrounded by large polymer molecules, mimicking the crowded conditions of a real cell, Watson-Crick base pairing seems to be less stable than it is in pure, dilute solution, while Hoogsteen base-pairing, which favours the formation of triple and quadruple helices, becomes more stable [2-4].
The researchers think that this is linked to the way water molecules surround the DNA in a ‘hydration shell’. Hoogsteen pairing demands less water in this shell, and so is promoted when molecular crowding makes water scarce.
Changes to the hydration shell, for example induced by ions, may alter DNA shape in a sequence-dependent manner, perhaps being responsible for the sequence-structure relationships studied by Margulies and his colleagues. After all, says Tullius, the method they use to probe structure is a measure of “the local exposure of the surface of DNA to the solvent.”
The importance of DNA’s water sheath on its structure and function is also revealed in work that uses small synthetic molecules as drugs that bind to DNA and alter its behaviour, perhaps switching certain genes on or off. It is conventionally assumed that these molecules must fit snugly into the screw-like groove of the double helix. But some small molecules seem able to bind and show useful therapeutic activity even without such a fit, apparently because they can exploit water molecules in the hydration shell as ‘bridges’ to the DNA itself [5]. So here there is a subtle and irreducible interplay between sequence, shape and ‘environment’.
Then there are mechanical effects too. Some proteins bend and deform DNA significantly when they dock, making the molecule’s stiffness (and its dependence on sequence) a central factor in that process. And the shape and mechanics of DNA can influence gene function at larger scales. For example, the packaging of DNA and associated proteins into a compact form, called chromatin, in cells can affect whether particular genes are active or not. Special ‘chromatin-remodelling’ enzymes are needed to manipulate its structure and enable processes such as gene expression of DNA repair.
None of this is yet well understood. But it feels reminiscent of the way early work on protein structure in the 1930s and 40s grasped for dimly sensed principles before an understanding of the factors governing shape and function transformed our view of life’s molecular machinery. Are studies like these, then, a hint at some forthcoming insight that will reveal gene sequence to be just one element in the logic of life?
References
1. Parker, S. C. J. et al., Science Express doi:10.1126/science.1169050 (2009). Paper here.
2. Miyoshi, D., Karimata, H. & Sugimoto, N. J. Am. Chem. Soc. 128, 7957-7963 (2006). Paper here.
3. Nakano, S. et al., J. Am. Chem. Soc. 126, 14330-14331 (2004). Paper here.
4. Miyoshi, D. et al., J. Am. Chem. Soc. doi:10.1021/ja805972a (2009). Paper here.
5. Nguyen, B., Neidle, S. & Wilson, W. D. Acc. Chem. Res. 42, 11-21 (2009). Paper here.
Shape might be one of the key factors in the function of mysterious ‘non-coding’ DNA.
Everyone knows what DNA looks like. Its double helix decorates countless articles on genetics, has been celebrated in sculpture, and was even engraved on the Golden Record, our message to the cosmos on board the Voyager spacecraft.
The entwined strands, whose form was deduced in 1953 by James Watson and Francis Crick, are admired as much for their beauty as for the light they shed on the mechanism of inheritance: the complementarity between juxtaposed chemical building blocks on the two strands, held together by weak ‘hydrogen’ bonds like a zipper, immediately suggested to Crick and Watson how information encoded in the sequence of blocks could be transmitted to a new strand assembled on the template of an existing one.
With the structure of DNA ‘solved’, genetics switched its focus to the sequence of the four constituent units (called nucleotide bases). By using biotechnological methods to deduce this sequence, they claimed to be ‘reading the book of life’, with the implication that all the information needed to build an organism was held within this abstract linear code.
But beauty has a tendency to inhibit critical thinking. There is now increasing evidence that the molecular structure of DNA is not a delightfully ordered epiphenomenon of its function as a digital data bank but a crucial – and mutable – aspect of the way genomes work. A new study in Science [1] underlines that notion by showing that the precise shape of some genomic DNA has been determined by evolution. In other words, genetics is not simply about sequence, but about structure too.
The standard view – indeed, part of biology’s ‘central dogma’ – is that in its sequence of the four fundamental building blocks (called nucleotide bases) DNA encodes corresponding sequences of amino-acid units that are strung together to make a protein enzyme, with the protein’s compact folded shape (and thus its function) being uniquely determined by that sequence.
This is basically true enough. Yet as the human genome was unpicked nucleotide base by base, it became clear that most of the DNA doesn’t ‘code for’ proteins at all. Fully 98 percent of the human genome is non-coding. So what does it do?
We don’t really know, except to say that it’s clearly not all ‘junk’, as was once suspected – the detritus of evolution, like obsolete files clogging up a computer. Much of the non-coding DNA evidently has a role in cell function, since mutations (changes in nucleotide sequence) in some of these regions have observable (phenotypic) consequences for the organism. We don’t know, however, how the former leads to the latter.
This is the question that Elliott Margulies of the National Institutes of Health in Bethesda, Maryland, Tom Tullius of Boston University, and their coworkers set out to investigate. According to the standard picture, the function of non-coding regions, whatever it is, should be determined by their sequence. Indeed, one way of identifying important non-coding regions is to look for ones that are sensitive to sequence, with the implication that the sequence has been finely tuned by evolution.
But Margulies and colleagues wondered if the shape of non-coding DNA might also be important. As they point out, DNA isn’t simply a uniform double helix: it can be bent or kinked, and may have a helical pitch of varying width, for example. These differences depend on the sequence, but not in any straightforward manner. Two near-identical sequences can adopt quite different shapes, or two very different sequences can have a similar shape.
The researchers used a chemical method to deduce the relationship between sequence and shape. They then searched for shape similarities between analogous non-coding regions in the genomes of 36 different species. Such similarity implies that the shapes have been selected and preserved by evolution – in other words, that shape, rather than sequence per se, is what is important. They found twice as many evolutionarily constrained (and thus functionally important) parts of the non-coding genome than were evident from trans-species correspondences using only sequence data.
So in these non-coding regions, at least, sequence appears to be important only insofar as it specifies a certain molecular shape and not because if its intrinsic information content – a different sequence with the same shape might do just as well.
That doesn’t answer why shape matters to DNA. But it suggests that we are wrong to imagine that the double helix is the beginning and end of the story.
There are plenty of other good reasons to suspect that is true. For example, DNA can adopt structures quite different from Watson and Crick’s helix, called the B-form. It can, under particular conditions of saltiness or temperature, switch to at least two other double-helical structures, called the A and Z forms. It may also from triple- and quadruple-stranded variants, linked by different types of hydrogen-bonding matches between nucleotides. One such is called Hoogsteen base-pairing.
Biochemist Naoki Sugimoto and colleagues at Konan University in Kobe, Japan, have recently shown that, when DNA in solution is surrounded by large polymer molecules, mimicking the crowded conditions of a real cell, Watson-Crick base pairing seems to be less stable than it is in pure, dilute solution, while Hoogsteen base-pairing, which favours the formation of triple and quadruple helices, becomes more stable [2-4].
The researchers think that this is linked to the way water molecules surround the DNA in a ‘hydration shell’. Hoogsteen pairing demands less water in this shell, and so is promoted when molecular crowding makes water scarce.
Changes to the hydration shell, for example induced by ions, may alter DNA shape in a sequence-dependent manner, perhaps being responsible for the sequence-structure relationships studied by Margulies and his colleagues. After all, says Tullius, the method they use to probe structure is a measure of “the local exposure of the surface of DNA to the solvent.”
The importance of DNA’s water sheath on its structure and function is also revealed in work that uses small synthetic molecules as drugs that bind to DNA and alter its behaviour, perhaps switching certain genes on or off. It is conventionally assumed that these molecules must fit snugly into the screw-like groove of the double helix. But some small molecules seem able to bind and show useful therapeutic activity even without such a fit, apparently because they can exploit water molecules in the hydration shell as ‘bridges’ to the DNA itself [5]. So here there is a subtle and irreducible interplay between sequence, shape and ‘environment’.
Then there are mechanical effects too. Some proteins bend and deform DNA significantly when they dock, making the molecule’s stiffness (and its dependence on sequence) a central factor in that process. And the shape and mechanics of DNA can influence gene function at larger scales. For example, the packaging of DNA and associated proteins into a compact form, called chromatin, in cells can affect whether particular genes are active or not. Special ‘chromatin-remodelling’ enzymes are needed to manipulate its structure and enable processes such as gene expression of DNA repair.
None of this is yet well understood. But it feels reminiscent of the way early work on protein structure in the 1930s and 40s grasped for dimly sensed principles before an understanding of the factors governing shape and function transformed our view of life’s molecular machinery. Are studies like these, then, a hint at some forthcoming insight that will reveal gene sequence to be just one element in the logic of life?
References
1. Parker, S. C. J. et al., Science Express doi:10.1126/science.1169050 (2009). Paper here.
2. Miyoshi, D., Karimata, H. & Sugimoto, N. J. Am. Chem. Soc. 128, 7957-7963 (2006). Paper here.
3. Nakano, S. et al., J. Am. Chem. Soc. 126, 14330-14331 (2004). Paper here.
4. Miyoshi, D. et al., J. Am. Chem. Soc. doi:10.1021/ja805972a (2009). Paper here.
5. Nguyen, B., Neidle, S. & Wilson, W. D. Acc. Chem. Res. 42, 11-21 (2009). Paper here.
Tuesday, March 3, 2009
Making sense of solvent slaving
In my previous post I mentioned work by Pablo Debenedetti on ‘toy models’ of water. The places to look are: Buldyrev et al., PNAS 104, 20177 (2007) (here) for the solvation thermodynamics of ‘spherical’ water; and Patel et al., Biophys. J. 93, 4116 (2007) (here) and J. Chem. Phys. 128, 175102 (2008) (here) for water-explicit lattice models of proteins.
And in discussing recent work on the mechanism of urea-induced protein denaturation, I neglected to mention Bruce Berne’s PNAS paper from late last year with Ruhong Zhou, Dave Thirumalai and Lan Hua (105, 16928; paper here). That paper on MD simulations for lysozyme anticipated the more recent work showing that denaturation seems to be caused by direct urea-protein interactions: the urea displaced water from the first hydration shell and penetrates into the hydrophobic core to give a ‘dry globule’.
The notion that protein dynamics are ‘slaved’ to those of the hydration shell has been floating around for some time now. Hans Frauenfelder and colleagues have now brought considerable focus to the idea (PNAS doi:10.1073/pnas.0900336106; paper here) with dynamical measurements using dielectric spectroscopy, Mossbauer and neutron scattering. They find that large-scale protein motions follow the fluctuations of the solvent and are dependent on solvent viscosity. There are two classes of fluctuation in the solvent, alpha and beta, with different timescales. It seems that the former are ‘structural’ in nature and control protein shape; the latter are those to which the protein’s internal motions are slaved.
Jianxing Song at the National University of Singapore, who I met in Hangzhou, has sent me three papers on the intriguing solubilisation of ‘water-insoluble’ proteins in pure water. He and his coworkers found this effect in 2006 for a range of diverse proteins (M. Li et al., Protein Science 15, 1835 (2006) – paper here; M. Li et al., Biophys. J. 91, 4201 (2006) – paper here). They attributed it to the tendency of the ‘insoluble’ proteins to form partially folded states with many exposed hydrophobic residues, such that only a very low ionic strength is sufficient to screen out repulsive interactions and cause aggregation. In pure water, however, those electrostatic interactions remain sufficiently strong to suppress aggregation and precipitation. Jianxing has now provided an overview of this work, expanding on the importance of pH for this effect, in FEBS Letters (doi:10.1016/j.febslet.2009.02.022; paper here).
Roberto Righini at the University of Florence and colleagues have used IR spectroscopy to identify and quantify the various aqueous species that solvate the polar heads of phospholipids in bilayers (V. V. Volkov et al., J. Phys. Chem. B doi:10.1021/jp806650c; paper here). And Davide Donadio and coworkers in California have shown how electronic charge fluctuations show up in the IR spectra of water close to nonpolar surfaces (here graphite) (D. Donadio et al., J. Phys. Chem. B doi:10.1021/jp807709z; paper here). Still in that neck of the woods, Chuan-Shan Tian and Ron Shen have used sum-frequency-IR spectroscopy to sort out the nature of hydrogen-bonding at the air-water interface (JACS 131, 2791 (2009) – paper here). And Heather Allen and colleagues at Ohio State University have used this and other spectroscopic techniques to study hydration structure of the air-water interface for various divalent nitrates (M. Xu et al., J. Phys. Chem. B doi:10.1021/jp806565a; paper here).
Haiping Fang in Shanghai continues his exploration of how water and solutes can be manipulated within the confinement of carbon nanotubes. He and colleagues now show, using MD simulations, how a single charge outside a nanotube can be used to move a hydrated peptide inside it, regardless of whether the peptide itself is charged (P. Xiu et al., JACS 131, 2840 (2009) – paper here). This is due to the dipole-orientational ordering of the water molecules caused by confinement and interaction with the external charge.
There’s more, but later.
And in discussing recent work on the mechanism of urea-induced protein denaturation, I neglected to mention Bruce Berne’s PNAS paper from late last year with Ruhong Zhou, Dave Thirumalai and Lan Hua (105, 16928; paper here). That paper on MD simulations for lysozyme anticipated the more recent work showing that denaturation seems to be caused by direct urea-protein interactions: the urea displaced water from the first hydration shell and penetrates into the hydrophobic core to give a ‘dry globule’.
The notion that protein dynamics are ‘slaved’ to those of the hydration shell has been floating around for some time now. Hans Frauenfelder and colleagues have now brought considerable focus to the idea (PNAS doi:10.1073/pnas.0900336106; paper here) with dynamical measurements using dielectric spectroscopy, Mossbauer and neutron scattering. They find that large-scale protein motions follow the fluctuations of the solvent and are dependent on solvent viscosity. There are two classes of fluctuation in the solvent, alpha and beta, with different timescales. It seems that the former are ‘structural’ in nature and control protein shape; the latter are those to which the protein’s internal motions are slaved.
Jianxing Song at the National University of Singapore, who I met in Hangzhou, has sent me three papers on the intriguing solubilisation of ‘water-insoluble’ proteins in pure water. He and his coworkers found this effect in 2006 for a range of diverse proteins (M. Li et al., Protein Science 15, 1835 (2006) – paper here; M. Li et al., Biophys. J. 91, 4201 (2006) – paper here). They attributed it to the tendency of the ‘insoluble’ proteins to form partially folded states with many exposed hydrophobic residues, such that only a very low ionic strength is sufficient to screen out repulsive interactions and cause aggregation. In pure water, however, those electrostatic interactions remain sufficiently strong to suppress aggregation and precipitation. Jianxing has now provided an overview of this work, expanding on the importance of pH for this effect, in FEBS Letters (doi:10.1016/j.febslet.2009.02.022; paper here).
Roberto Righini at the University of Florence and colleagues have used IR spectroscopy to identify and quantify the various aqueous species that solvate the polar heads of phospholipids in bilayers (V. V. Volkov et al., J. Phys. Chem. B doi:10.1021/jp806650c; paper here). And Davide Donadio and coworkers in California have shown how electronic charge fluctuations show up in the IR spectra of water close to nonpolar surfaces (here graphite) (D. Donadio et al., J. Phys. Chem. B doi:10.1021/jp807709z; paper here). Still in that neck of the woods, Chuan-Shan Tian and Ron Shen have used sum-frequency-IR spectroscopy to sort out the nature of hydrogen-bonding at the air-water interface (JACS 131, 2791 (2009) – paper here). And Heather Allen and colleagues at Ohio State University have used this and other spectroscopic techniques to study hydration structure of the air-water interface for various divalent nitrates (M. Xu et al., J. Phys. Chem. B doi:10.1021/jp806565a; paper here).
Haiping Fang in Shanghai continues his exploration of how water and solutes can be manipulated within the confinement of carbon nanotubes. He and colleagues now show, using MD simulations, how a single charge outside a nanotube can be used to move a hydrated peptide inside it, regardless of whether the peptide itself is charged (P. Xiu et al., JACS 131, 2840 (2009) – paper here). This is due to the dipole-orientational ordering of the water molecules caused by confinement and interaction with the external charge.
There’s more, but later.
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