Thursday, April 28, 2011

Water as glue

There is a very nice crop of papers to draw on for this post, many of which speak to very central questions in this field. First up is a paper in Nature Communications from Volkhard Helms and colleagues at Saarbrücken, which looks at the detailed role of interfacial water in the association of hydrophilic protein surfaces (M. Ahmad et al., Nat. Commun. 2, 261; 2011 – paper here). Whereas hydrophobic association has been the focus of a lot of recent attention, especially with a view to the possibility of a dewetting-induced process, hydrophilic surfaces have received less attention. That’s an important lacuna, since as the authors point out, around 70% of interfacial residues are hydrophilic. The common approach is to assume direct electrostatic interaction mediated by a continuum solvent. But the water network has a more complex role. As shown in these MD simulations of the barnase-barstar complex, water molecules mediate and stabilize the interactions between native contacts. Moreover, for electrostatic interactions to be important, the interfacial water’s dielectric constant needs to be reduced to reduce screening. This happens as a consequence of changes in the structure of the interfacial layers (the dielectric permittivity is less than 50% of the bulk value for interfacial separations of less than 1.2 nm), and it preferentially promotes electrostatic interactions normal to the surfaces. In other words, you could say that (once again, though arguably to put the cart before the horse) water does exactly what is required of it.

Jeremy England, now at Princeton, has a paper in press with Structure which shows that it is possible to estimate low-energy conformational changes in a protein, such as those involved in allosteric effects, on the basis simply of residue-by-residue hydrophobic effects. Specifically, he develops a method for determining the most energetically favourable way of burying hydrophobic residues, given a particular amino-acid sequence. This amounts to identifying the particular ‘burial modes’ of any given sequence. Thus, although the stabilities of conformations are doubtless multifactorial, hydrophobicity seems to be the major governing factor.

Calculating the surface free energies of heterogeneous surfaces exposed to water (such as protein surfaces) is tough. The approach of the Cassie equation is additive, but as Alenka Luzar and colleagues point out, that doesn’t always work (J. Wang et al., PNAS 108, 6374-6379; 2011 – paper here). They show that deviations from linear additivity result when parts of a surface are unevenly exposed to solvent. In particular, it seems that polar patches exert an inordinately strong influence, being able to ‘pin’ a droplet so that it might remain closely attached to adjacent hydrophobic patches. They examine these effects with reference to water droplets first on a functionalized graphene surface and then on the surface of melittin.

Daryl Eggers at San José State University presents an interesting approach to the energetics of reactions in aqueous solution, geared especially to biochemical equilibria, that treats the water as a reactant and product, thereby subsuming the local changes in water structure that inevitably accompany the reaction (Biochemistry 50, 2004-2012; 2011 – paper here). Here the free energy of bulk water is treated as a variable, allowing for the effects of all solutes including those that may not participate directly in the reaction (such as dissolved salts). As I understand it, this offers a means of accommodating the effects of such solutes (for example, in salting in/out) that does not make any assumptions about global changes in ‘water structure’, but represents only the global average of localized changes. Also jettisoned in that process is any insistence on putative structure-makers and structure-breakers; rather, solvation effects need be discussed only in what seems like relatively uncontentious terms of subpopulations of water with differing free energies. I haven’t yet quite figured out how one gets at these free energies in experimental terms, but I like the principle, not least because it explicitly acknowledges the role of water as a participant.

Yingkai Zhang at New York University and coworkers have used ab initio MD simulations to study the mechanism of action of histone deacetylase (HDAC) enzymes, which remove acetyl groups from histone residues and have been identified as a target for anti-cancer drugs (R. Wu et al., JACS 133, 6110-6113; 2011 – paper here). They suggest that some HDACs function via a mechanism involving a modulation of water access (a hydrogen-bonded chain of waters) to the binding pocket, in which a zinc ion in the metalloenzyme binds to its substrate. The presence or absence of water alters the dielectric constant in the binding pocket and thereby affects the strength of zinc binding.

Transitions of DNA between A, B and Z forms are thought to be associated with and perhaps driven by transitions in the nature of hydration. Karim Fahmy and colleagues at the Institute of Radiochemistry in Dresden now suggest that the same applies to the more subtle sub-transitions between the BI and BII states of the B-form (H. Khesbak et al., JACS 133, 5834-5842; 2011 – paper here). Specifically, there are two sub-populations of water molecules – one bound to phosphates, the other not – that contribute to stabilizing the two conformations via entropic effects. These water rearrangements can also be involved in interactions with DNA-binding ligands, such as the antimicrobial peptide indolicidin, by a water-mediated induced fit.

The structures of amyloid fibrillar assemblies are still far from well understood. The hydration state of the peptides is a particularly important issue in determining their stability and perhaps their mode of formation. Beat Meier at ETH and colleagues report some tricks that enable this question to be probed by NMR (Van Melckebeke et al., J. Mol. Biol. 405, 765; 2011 – paper here). For a particular prion domain called HET-s(218-289) they show that, although these protofibrils have a hydrophobic core and a semi-hydrophobic pocket, they do not engage in ‘dry’ interfibril contacts but are each surrounded by water.

The behaviour of water close to and between lipid bilayers has been much studied, but there doesn’t seem to have been much consideration of how that behaviour might feature in biological membrane processes such as fusion. This issue is investigated by Vijay Pande at Stanford and colleagues using simulations (P. M. Kasson, E. Lindahl & V. S. Pande, JACS 133, 3812-3815; 2011 – paper here). They look at the water trapped between the faces of two approaching membranes – that is, in hydrophilic confinement – and find that the dynamics are altered significantly. Specifically, the trapped water has reduced rotational entropy, and it helps the two membranes to adhere. However, the slower dynamics also retards the process of fusion itself – the formation of the ‘stalk’ that bridges the lipid membranes.

Mafumi Hishida and Koichiro Tanaka at Kyoto have also looked at the hydration of phospholipid bilayers, here experimentally using terahertz spectroscopy and SAXS (Phys. Rev. Lett. 106, 158102; 2011 – paper here). They conclude that water structure is perturbed up to 4-5 layers from the surface, over a distance of at least 1 nm, and that the average density in this hydration layer is slightly greater than that in the bulk.

Meanwhile, Joshua Layfield and Diego Troya at Virginia Tech have considered a water droplet confined between hydrophobic surfaces of self-assembled monolayers (J. Phys. Chem. B 115, 4662-4670; 2011 – paper here). Here the water motions (lateral translational diffusion) are accelerated by confinement, and this effect seems to operate over distances of more than 1 nm from the surfaces. Structural effects (preferential orientation of the water molecules) aren’t evident beyond 1 nm, however – but while the authors consider this to be a relatively short-ranged effect, I’d have been surprised to see anything structural with a longer reach.

Daniela Russo at the ILL and colleagues have used inelastic neutron scattering to probe the low-frequency densities of states of water hydrating small ‘model peptides’ (N-acetyl-leucine-methylamide, NALMA, and N-acetyl-glycine-methylamide, NAGMA) at low temperatures (Russo et al., JACS 133, 4882-4888; 2011 – paper here). At 200K they find that the hydration water for the hydrophilic NAGMA is similar to high-density amorphous ice, while that of the hydrophobic NALMA is more like low-density amorphous ice. Something similar has been reported at 100 K by Paciaroni et al. (Phys. Rev. Lett. 101, 148104; 2008), but was in that case attributed to curvature of the biomolecular surface – which is evidently not the case for these small molecules.

Aquaporins seem to play a crucial role in water regulation in arid periods during the life cycle of the major malaria vector mosquito Anopheles gambiae, according to Kun Liu of the Johns Hopkins Malaria Research Institute in Baltimore and colleagues (K. Liu et al., PNAS 108, 6062-6066; 2011 – paper here). The authors don’t say whether this makes these AQPs a potential target for controlling the spread of malaria, though I suppose that is a possible implication.

There’s still more to be understood about what hydrogen bonds are, as evidenced by a recent IUPAC working group set up to redefine them (see here). Angelos Michaelides at UCL (who I have to thank for my water-crested football shirt) and colleagues have now refined the quantum picture of the H-bond, showing how quantum nuclear effects due to the anharmonicity of the bond and the small proton mass can alter the bond strength, weakening weak H-bonds (like those in water) and strengthening strong ones (X.-Z. Li et al., PNAS 108, 6369-6373; 2011 – paper here).

There are one or two other papers I’ve still to get to, including some that folks have kindly sent to me. Apologies for that – more soon, I hope.

1 comment:

Daryl Eggers said...

thanks for including my work - I value Philip's comments and insights.