Friday, July 24, 2015

Goodbye to "biological water" (hello water in biology)

Surely an essential read for any reader of this blog is a commentary by Pavel Jungwirth in JPC Lett. (6, 2449; 2015 – paper here) called “Biological water or rather water in biology?” (which I only just realize now I can decide to interpret as an homage to this site – you can see which of these alternatives I prefer!). Pavel expresses the issue perfectly, saying that his piece has two main messages:
“The first one, addressed to biologists and biochemists, who tend to focus their attention primarily to the biomolecules, is that water does matter.”
“The second and arguably more important message is addressed to our community of physical chemists:… Although water… plays a key role in establishing the homeostasis, it is primarily the biomolecule itself which carries the biological function… As physical chemists who naturally tend to understand water better than biomolecules, we may sometimes have a tendency to overemphasize the role of the former at the expense of the latter.”

In particular, Pavel suggests that the term “biological water” be dropped. He is quite right that this kind of terminology risks becoming a deus ex machina, if not indeed a kind of “vital force”, and I’d be happy never to see it again. This also gives me an opportunity to say explicitly that, while this blog aims to focus on all the important, often under-valued and occasionally amazing things that water does in the cell, there should be no doubt that proteins, DNA, lipids and carbohydrates are still the main players.

I mentioned in an earlier post a study by Bob Evans at Bristol a study suggesting an explanation for the enhanced density fluctuations in water near a hydrophobic surface that David Chandler, Shekhar Garde and others have advanced as the driving force behind dewetting transitions. Bob and his coauthor Nigel Wilding at Bath have now published this paper (Phys. Rev. Lett. 115, 016103; 2015 – paper here). They argue that the fluctuations can be regarded as a divergence in the local compressibility associated with the approach to a critical (continuous) drying transition. Frankly, it seems rather splendid to have this phenomenon rooted in a general and well understood physical effect – and moreover one that is not at all specific to water or hydrogen-bonding networks.

This seems to bear directly on what Rick Remsing, Amish Patel, Shekhar and others say in their latest paper on “pathways to dewetting” (R. C. Remsing et al., PNAS 112, 8181; 2015 – paper here). Their MD simulations of water confined in the nanospace between two square hydrophobic plates confirm that it undergoes enhanced density fluctuations that can nucleate a vapour tube connecting the plates of a radius greater than the critical radius needed for spontaneous growth to a dry state, according to standard nucleation theory. This means that the free-energy barrier to dewetting is lower than standard macroscopic theory would predict. That’s very striking and illuminating, but still doesn’t obviously say in itself where those enhanced fluctuations come from – which is what Bob’s paper seems to address. You should talk to each other, chaps! – it seems as though there could even be the prospect of tying this story together once and for all.

Suzanne Zoë Fisher at Los Alamos National Laboratory and colleagues have used neutron scattering and NMR to characterize the details of the proton transfer system in human carbonic anhydrase, in which a water network linked to hydrophilic residues plays a key role (R. Michalczyk et al., PNAS 112, 5673; 2015 – paper here). It’s a nice, thorough study which shows how the environment lowers the pKa of the Tyr7 residue bound to the water molecules.

More water wires in a first-principles simulation study by Daniel Sebastiani at the University of Halle-Wittenberg and colleagues – but this time looking at their transient formation in pure water itself (G. Bekçioglu et al., JPCB 119, 4053; 2015 – paper here). In their calculations they use hydroquinoline as a fluorescent probe to study proton transfer along the wires, and find that wires of up to six or seven water molecules, reaching 1.5 nm or so, may persist for up to a few picoseconds. These might facilitate proton transfer (here between donor and acceptor sites on the probe molecule) by a stepwise mechanism.

Samir Kumar Pal at the Bose National Centre for Basic Sciences in Kolkata and colleagues report a nice model system for studying the dynamical coupling between a macromolecule and its hydration sphere (S. Choudhury et al., JPCB 10.1021/jp511899q – paper here). They have used micelles with different degrees of packing rigidity as model macromolecules, and use FRET, polarization-gated fluorescence anisotropy and quasielastic neutron scattering to look at the dynamics of the micelles and their hydration shells. There is slower water motion around the less flexible micelles, consistent with the standard “slaving” picture of dynamical coupling.

Some water of course may penetrate into amphiphile assemblies of this sort. It’s known that cholesterol reduces the permeability of lipid membranes to water, but it’s not clear why. Bilkiss Issack and Gilles Peslherbe at Concordia University in Montreal have studied the question with MD simulations (JPCB 119, 9391; 2015 – paper here). The results imply that this is a thermodynamic and not a kinetic effect – water diffusion doesn’t vary much with cholesterol concentration, but the free-energy barrier to water penetration through a bilayer does increase with concentration, probably because cholesterol increases the hydrophobicity of the core region.

Pooja Rani and Parbati Biswas at the University of Delhi say that intrinsically disordered proteins have a larger binding capacity for water than do globular proteins (JPCB 10.1021/jp511961c – paper here). What’s more, their MD simulations show more tetrahedral ordering, and slower dynamics, of water around disordered protein segments. In a loose sense this seems consistent with the different water dynamics around IDPs observed by Martin Weik and colleagues using neutron scattering – which they see as a difference in degree rather than in kind.

But modelling IDPs accurately using MD requires better water models, according to Stefano Piana of D. E. Shaw Research in New York and colleagues (JPCB 119, 5113; 2015 – paper here). They say that most simulations produce IDP conformations that are too compact, but that they can do better using a new water potential called TIP4P-D, which includes a better representation of the dispersion forces between water molecules. There’s more optimization still to be done, but it’s presumably possible that such improvements aren’t unique to IDPs, even if they are particularly sensitive to them.

Not unrelated is a study by Yuichi Ogawa and colleagues at Kyoto University of the coil-to-globule transition of a “model peptide”, poly(N-isopropylacrylamide) (K. Shiraga et al., JPCB 119, 5576; 2015 – paper here). They follow changes in the hydration state of the polymer during this conformational switch using attenuated total reflection spectroscopy, which is a new one on me but apparently probes changes in the dielectric response in the terahertz region, providing information about the hydrogen-bond network. The transition to globule form corresponds with a reduction in the average hydration number of each monomer from around 10 to about 6.5, and it seems that these changes happen mostly in hydrophobic regions of the polymer. The authors interpret these changes as (I don’t entirely follow the reasoning) changes not so much in the hydration state of the polymer as in the structure of the hydrogen-bond network, and so speculate that the conformational change involves not just alterations to polymer-water interactions but also water-water interactions.

Time-dependent fluorescence Stokes shifts (TDFSS) are becoming a useful tool to look at water and protein dynamics, the usual approach being to measure the decay of tryptophan fluorescence as a probe of local dynamics. Jay Knutson at NIH and colleagues have used this method to look at relaxation processes in the protein monellin and their coupling to the solvent (J. Xu et al., JPCB 119, 4230; 2015 – paper here). They distinguish two emission processes, which they call genuine and pseudo-TDFSS, and show how to separate them; only the former tells us about the coupling of water and protein dipoles.

One aspect of water’s cell behaviour that is less often discussed is hydrodynamics, which must evidently become important at the mesoscale. Of course, that’s the scale which is very hard to model – but here fluid motions are likely to influence things like protein relaxation and crowding. Fabio Sterpone at the Université Paris Diderot and colleagues present a coarse-grained protein model called OPEP that enables this when combined with a Lattice Boltzmann approach to the fluid kinetics (F. Sterpone et al., J. Chem. Theor. Comput. 11, 1843; 2015 – paper here). They demonstrate its use to look at, e.g. protein transport properties, amyloid aggregation and crowding.

A new approach to modeling water is presented by Vlad Sokhan of the National Physical Laboratory in England and colleagues (V. P. Sokhan et al., PNAS 112, 6341; 2015 – paper here). They say that they can incorporate many-body effects into a coarse-grained parametrization of the electronic structure, which, along with fairly standard point charges and short-range pair potentials, allows accurate prediction of all the bulk behaviour, from liquid-gas coexistence to criticality, freezing and the temperature of maximum density. It’s apparently relatively easy to implement, and they hope to use it to look at effects such as hydrophobic hydration and drying and water’s role in protein association.

More to follow rather soon, I hope.