Thursday, February 24, 2011

Coarse-grained models

More on the mechanisms of urea-induced protein denaturation, this time from Ruhong Zhou at IBM and his colleagues in Beijing (M. Gao et al., J. Phys. Chem. B 114, 15687; 2010 – paper here). In simulations, they look at the populations of water and urea molecules around each residue in hen egg-white lysozyme, and find that some of the hydrophobic core residues stay virtually dry as unfolding proceeds in 8M urea. Moreover, the urea molecules are bound preferentially to uncharged rather than to charged residues. So the picture is that the protein swells to a molten globule state while keeping largely dry inside, because it is the urea rather than water that penetrates. this may not be a wholly general order of events, however – depending on the detailed shape and structure of the protein, water might sometimes penetrate first, as found for example by Bennion and Daggett (PNAS 100, 5142; 2003).

John Klassen and colleagues at the University of Alberta present an interesting comparison of protein-ligand dissociation constants in the hydrated and dehydrated states (L. Liu et al., JACS 132, 17658; 2010 – paper here). The latter are obtained from gas-phase measurements at 25-66 C. The kinetic stability of the associated state is significantly reduced in the hydrated phase: water stabilizes the dissociative transition state and might thereby be considered a kind of lubricant that facilitates the departure of the ligand.

David Beauchamp and Mazdak Khajehpour predicate their study of water-water interactions on enzyme activity with the supposition that the hydrogen-bond distribution in pure water is bimodal, with bonds that are high- and low-angle (J. Phys. Chem. B 10/1021/jp107556s – paper here). They say this is supported by some simulations, and that it is consistent with the (contentious) two-state model of the liquid. They also say that salts have the ability to perturb this distribution. OK… so given these assumptions, they see what added salts do to the activity of ribonuclease t1, and say that their spectroscopic and kinetic results are consistent with the notion that salts that promote the high-angle bonds stabilize the more compact and less active forms of the enzyme. Interesting ideas, but it seems a big leap from the data to the microscopic interpretation.

I recently described work by Martin Gruebele, Martina Havenith and colleagues on the mechanism of antifreeze glycoproteins, in which they argued that the biomolecules can effect long-range changes in water dynamics to inhibit freezing (S. Ebbinghaus et al., JACS 132, 12210; 2010). The authors now report similar findings for a 37-residue alpha-helical antifreeze protein from winter flounder (S. Ebbinghaus et al., Biophys. J. Biophys. Lett. in press). The find using CD and FRET on native and mutant versions that the antifreeze activity seems to be connected to a kinking of the helix, and that this is coupled to a suppression of bulk-like dynamics in the solvation water over a range of at least 3 nm, as indicated by THz spectroscopy.

Years ago, Royer et al. showed that a group of water molecules at the interface between the subunits of the dimeric haemoglobin of Scapharca clams seem implicated in the molecule’s allosteric cooperativity (Royer et al., PNAS 93, 14526; 1996). David Leitner and colleagues at the University of Nevada at Reno now look in detail at the dynamics of this cluster of waters using MD simulations based on the crystal structures (R. Gnanasekaran et al., J. Phys. Chem. B 114, 16989; 2010 – paper here). They find that those in the oxy form (11 molecules) exhibit slower relaxation than those (17) in the deoxy form, and that the water cluster, although rather static on ps timescales, can enhance energy transport across the interface of the subunits via vibrations.

The close and reciprocal interactions of water and protein dynamics, especially at low temperatures, seems to be echoed in the case of hydrated lipid bilayers, according to Peter Berntsen and colleagues at Chalmers University in Göteborg (J. Phys. Chem. B 10.1021/jp110899j – paper here). They have used dielectric rexlaxation measurements below 250 K to show that at low temperatures the water dynamics becomes increasingly dominated by the movements of the lipids, and is super-Arrhenius-like at low hydration levels.

Fast proton transport along peptide backbones can be assisted by water bridges, according to ab initio calculations by Po-Tuan Chen of the National Taiwan University of Science and Technology and colleagues (J. Phys. Chem. B 10.1021/jp107219r – paper here). They say that a two-molecule water bridge can make the transport between two adjacent carbonyl oxygens almost barrierless.

In a preprint (not sure where it is destined, but it looks like JCP format), David Chandler and his coworkers present a coarse-grained lattice model to implement the Lum-Chandler-Weeks dewetting theory of hydrophobic interactions (P. Varilly et al., arxiv: 1010.5750 – paper here). The model captures the essential features of the model at far less computational cost than full MD simulations, in particular modelling the solvent fluctuations that are essential for the dewetting mechanism.

With much the same objective of computational cheapness, Ken Dill at UCSF and colleagues present a new solvation model that they call semi-explicit self-assembly (C. J. Fennell et al., PNAS 108, 3234; 2011 – paper here). They basically construct a solute’s solvation shell as some combination of pre-computed solvation shells for simple spheres in explicit TIP3P water. They have so far only tested it here on simple small molecules such as sugars.

And Valeria Molinero and colleagues at the University of Utah have a coarse-grained model of DNA solvation with explicit water and ions (R. C. DeMille et al., J. Phys. Chem. B 115, 132; 2011 – paper here). It reproduces base-pair specificity and is computationally faster by two orders of magnitude than atomistic simulations.

There is a curious paper in Nature Structural and Molecular Biology by Nathaniel Nucci and colleagues at the University of Pennsylvania (NSMB 18, 245; 2011 – paper here) on an NMR technique to identify residence times of specific clusters of water molecules around proteins. I say curious, because these useful results are presented, particularly in a News & Views article in Nature (V. J. Hilser, Nature 469, 166; 2011 – paper here), as “challenging current dogma about protein hydration”. It seems this challenge comes from the fact that the results show that not all ‘bound’ water exchanges slowly with the surrounding solvent. But a wide range of exchange times is surely already well established, especially from simulations – the old crystallographic picture in which ‘hydration water’ is all securely bound and long-lived seemed long dead. Still, it is interesting that Nucci et al., whose method relies on confining the proteins (here ubiquitin) within reverse micelles to slow the hydration dynamics, found that water molecules with similar residence times seem to cluster on the protein surface, so that the molecules in each cluster form independent networks which exhibit intra-cluster cooperativity.

In another preprint, Giancarlo Franzese and colleagues at the University of Barcelona offer something of a mini-review of hydration structure and dynamics at protein surfaces, along with some Monte Carlo simulations that investigate cooperativity and dynamical transitions of a water monolayer hydrating a protein surface at low temperatures (arxiv preprint 1010.4984; paper here).

On the still-evolving picture of pure liquid water: Alessandro Cunsolo at Brookhaven and his colleagues study it using QENS to look at single-particle diffusion rates at 200 MPa as a function of temperature, and find that their results point to the proposed existence of a second critical point at about 220 K, and of the Widom line which ends at this point (J. Phys. Chem. B 114, 16713; 2010 – paper here).

Meanwhile, Richard Henchman and Sheeba Jem Irudayam of Manchester University in the UK propose a ‘topological’ definition of hydrogen bonding in water that offers a new description of water structure and dynamics (investigated in simulations using TIP4P/2005 water) based on the character of the H-bond network (J. Phys. Chem. B 10.1021/jp105381s – paper here). They say that in this description almost all the water molecules are H-bonded and that there are an appreciable number of ‘defects’ in which molecules are acceptors for one (trigonal) and three (trigonal bipyramidal) hydrogens rather than two.

Monday, February 14, 2011

Less is more

In the spirit of maintaining continuity (do some folks really look at this site every week, as I’m told?), I will aim to post more regularly rather than exhaustively. That’s to say, this is not a complete list for what I’ve seen out there, but more will follow soon.

Sheh-Yi Sheu at National Yang-Ming University in Taiwan and Dah-Yen Yang at the Institute for Molecular Science in Okazaki, Japan, present a method for deducing the free energy of the hydration shell for a biomolecule from simulations (J. Phys. Chem. B 10.1021/jp105164t – paper here). They say that water in a protein (here myoglobin) hydration shell follows fractional Brownian motion.

Flavoproteins are electron-transfer proteins involved in a range of biological processes, including cell apoptosis and DNA repair. The nature of solvation at the active sites is of central importance for their function. Dongping Zhong and colleagues at Ohio State have used ultrafast spectroscopy to characterize the dynamics of the water network at the functional site in three redox stats of a representative flavoprotein, flavodoxin (C.-W. Chang et al., JACS 192, 12741 (2010) – paper here). Rather neatly, they are able to use the intrinsic cofactor of this protein as the fluorescent probe for the experiments. They can monitor changes in the relaxation and rigidity of the local water network between the different states, for example a retardation of the relaxation from around 2.6 to 40 ps between the oxidized to semiquinone state. They propose an intimate and biologically relevant coupling between the flexibility of the solvation network and the protein.

Gating of ion channels due to cooperative drying has been suggested as the underlying mechanism for such functions. Fangqiang Zhu and Gerhard Hummer at NIH explore this notion for the ligand-gated ion channel GLIC of the bacterium G. violaceus, for which the crystal structure of the open state is solved (PNAS 107, 19814; 2010 – paper here). They find that the pore is typically water-filled in the open state, but that a very small decrease in the channel radius can induce cooperative drying. It seems that the emptying of the pore is a response to, rather than the driving force for, changes in the pore width.

Alla Oleinikova, Ivan Brovchenko and their colleague G. Singh at Dortmund have calculated the heat capacity of hydration water of hydrophobic and hydrophilic peptides from simulations (A. Oleinikova et al., Europhys. Lett. 90, 36001; 2010 – paper here). They say that around 330 K there is a sharp change in structure from a percolating to a fragmented H-bonded network, and that this coincides with a point at which the heat capacity changes from being dominated by water interactions within the hydration shell to a situation where the hydration-shell-to bulk interactions are more important. At this stage, the ‘detachment’ of the hydration network from the peptide in effect makes the biomolecule more hydrophobic.

Anrew White and Shaoyi Jiang at the University of Washington have studied the hydration of glycine and two (zwitterionic) analogues di- and trimethylglycine using MD (J. Phys. Chem. B 115, 660; 2011 – paper here). They say that all three molecules affect the water structure out to the second hydration shell, but trimethylglycine has the greatest (retarding) effect on water dynamics and, perhaps surprisingly, does not aggregate but remains well solvated even at high concentrations. This might help to account for trimethylglycine’s antifouling properties and its suppression of protein aggregation.

There is sill a tussle going on about whether bulk water at ambient temperatures is best considered in a homogeneous or two-phase framework. Lars Pettersson and Anders Nilsson have recently teamed up with theorists including Jens Norskov at Stanford to perform ab initio MD calculations which point to a mixture of low- and high-density regions at ambient conditions (A Møgelhøj et al., arxiv preprint 1101.5666; paper here). But Niall English and John Tse dispute this, saying that such inhomogeneities are of very short range and transient, being just the ordinary density fluctuations one would expect to see in an equilibrium system (Phys. Rev. Lett. 106, 037801; 2011 – paper here).

Raymond Dagastine and colleagues at the University of Melbourne report a very striking claim: that air bubbles interact with (probably virtually all) solid surfaces via a repulsive van der Waals interaction (R. F. Tabor et al., Phys. Rev. Lett. 106, 064501; 2011 – paper here). As a bubble approaches a surface under hydrodynamic flow, they say, it will therefore start to deform and flatten at the point where the repulsive force equals the Laplace pressure. Repulsive vdW forces are well known in theory, but it seemed previously that rather special combinations of materials were needed to realise them.

Thursday, February 3, 2011

Yes, I'm still here

Apologies for the long silence. This blog is still active, but Christmas (among other things) got in the way and then I face the Sysiphean task of catching up. That task is not by any means completed here, but I want to flag up that Water in Biology hasn’t expired. Much more as soon as I can manage it.

Bruce Berne, Richard Friesner and Lingle Wang at Columbia have recently introduced the notion that ligand binding in protein receptor pockets is largely driven by the displacement of water molecules that sit in an unfavourable position in the pocket, which are replaced with groups on the ligand that are complementary to the protein surface (Young et al., PNAS 104, 808; 2007; Abel et al., JACS 130, 2817; 2008). In a new paper (Wang et al., PNAS 108, 1326; 2011 – paper here) they consider what their model, called WaterMap, has to say about regions of the binding pocket that are initially dry, being highly unfavourable environments for water. Including an interaction term in the model that represents the formation of a (hydrophobic) protein-ligand interface in dry regions, they can compute binding affinities in good agreement with experiment.

Dave Thirumalai at Maryland and his coworkers offer a striking view of how amyloid fibrils self-assemble from interdigitated beta-sheets (G. Reddy et al., PNAS 10.1073/pnas.108616107 – paper not yet online). They present a MD study of the association of beta-sheets in two amyloidogenic proteins of very different sequence, one polar and the other hydrophobic. They say that in the former case the association of the sheets is mediated by one-dimensional water wires at the interface between them, which are gradually expelled. But for the hydrophobic peptides the sheets come together in something like an abrupt drying transition, as postulated previously for some protein-folding and aggregation processes. This happens much faster (nearly 1,000-fold) than the previous case, since the trapped water wires for the polar peptide create a barrier to rapid assembly. Thus, although the final structures are very similar, the mechanisms and dynamics are quite different. It would seem that this paper ties in with a new one by Ken Dill and colleagues on the mechanisms of amyloid assembly into fibrils, of which I’ve only seen the abstract (which suggests that there’s not a big emphasis on the role of the solvent here beyond the involvement of hydrophobicity) (J. D. Schmit et al., Biophys. J. 100, 450-458; 2011 – paper here).

Cytochrome c oxidase (CcO) acts as a proton pump in which the transmembrane proton motion is thought to be facilitated by a proton wire involving strategically placed water molecules. The roles of these waters are investigated by Shelagh Ferguson-Miller and colleagues at Michigan State based on high-resolution crystals structures of two mutant forms of bacterial CcO (Liu et al., PNAS 108, 1284; 2011 – paper here). In both mutants, where proton transfer is inhibited to different degrees, the overall structural changes are very small but one or more of the bound waters is eliminated. The story is not, however, quite as simple as a mere break in the water wires, but involves subtle conformational changes between oxidized and reduced forms of the metal centres: an indication that, while bound water undoubtedly plays an active role in the catalytic function, in this case that role resists reduction to a simplistic picture.

Human telomeres contain G-rich sequences that form quadruplex structures in Hoogsteen hydrogen-bonded patterns. It’s not clear what influences the stability of this unusual motif, but John Trent and colleagues at the University of Louisville in Kentucky say that hydration plays a major part (M. C. Miller et al., JACS 132, 17105-17107; 2010 – paper here). They say that previous studies of the crystal structure of these sequences have been misleading because the dehydrating agents used to cause precipitation (PEGs) may give crystal structures that are not closely related to those in solution. Instead they use acetonitrile (which is water-soluble but does not engage in hydrogen-bonding) as the cosolvent for CD and NMR solution studies, and find that stabilization of the quadruplex seems to be caused more by dehydration than by steric crowding effects.

How hydration affects energy relaxation of cytochrome c after photoexcitation has been studied using ultrafast spectroscopy by Shuji Ye of the University of Science and Technology of China in Hefei and and Andrea Markelz of SUNY at Buffalo (J. Phys. Chem. B 114, 15151-15157; 2010 – paper here). One of the main conclusions is that hydration doesn’t in fact have a great deal of influence on the initial energy dynamics: there is an initial fast (around 300 fs) conversion from the electronically excited state to a vibrationally excited ground state, which is essentially hydration-independent. But the vibrational cooling then does involve interaction with the solvent, more or less in line with the existing notion that hydration water acts as a kind of plasticizer in this molecule.

Finally for now, and not really at all relevant to the real themes of this blog but too much of a curiosity for me to ignore, there are two papers on the arxiv investigating the notorious Mpemba effect, whereby hot water is said to sometimes freeze faster than cold: see here and here.