Monday, September 1, 2014

Life after Gordon

From time to time I wonder to myself if the number of folks reading this blog can be counted on the fingers of one hand – but judging from the kind comments I received at the wonderful Water Gordon Conference in July, I would need at least my toes too. More importantly, it seems to be appreciated; Shekhar Garde was even kind enough to advertise it in the New York Times, which makes me smile somewhat at the bemusement it might have elicited in some NYT readers who perhaps tried it out. In any event, you have persuaded me to keep it up; indeed, to begin the next post on the flight home [but not to finish it then, I fear…]

I spoke at the meeting about some of the myths of “water structure” and their origins. Jacob Israelachvili has previously referred to this “structure” as a deus ex machina that can be enlisted to explain anything. However, not all such explanations need be a leap of faith. For example, the notion that water inside the cavity of the chaperonin GroEL might be non-bulk-like, because of confinement and interactions with the hydrophobic cavity walls and the GroES lid, is not obviously unlikely. Song-I Han at UCSB and colleagues explore this idea in a very nice experimental paper in which they use magnetic-resonance methods to probe the water inside the GroEL-GroES complex of E. coli (J. M. Franck et al., JACS 136, 9396; 2014 – paper here). They conclude that the density and translational dynamics of the cavity water is in fact not significantly different from the bulk. There’s a caveat that they can’t fully probe the water at the bottom of the cavity, but all the same these findings support the idea that GroEL is a “passive” cavity in which folding is much the same as it is in bulk solution.

Had I the presence of mind to have looked at Nuno Galamba’s (University of Lisbon) paper on water around hydrophobic solutes (J. Phys. Chem. B 118, 4169; 2014 – paper here) before my talk, I’d certainly have referred to it, since it supports my contention that dynamics might be more fruitful than alleged “structural” effects to understand how water is modified in such circumstances. His MD simulations suggest that the slowdown in orientational dynamics in the hydration spheres of small hydrocarbons is due primarily to the decline in hydrogen-bond acceptor switches, due to excluded-volume effects, rather than to any changes in “water structuring”, such as greater tetrahedrality.

Ariel Fernandez has advanced a very provocative claim in his continuing investigation of dehydrons, structural “defects” at protein surfaces where amide-carbonyl hydrogen bonds are imperfectly hydrated due to nanoscale confinement. These sites have a net polarization arising because the water molecules are too constrained to fully align with the electrostatic field at the protein surface. This charge is negative, says Fernandez, and may behave as a proton acceptor, i.e. it has chemical functionality. He now suggests that this basicity of dehydrons may become manifest as catalytic activity, citing the high concentration of dehydrons specifically at the active site of HIV protease (J. Chem. Phys. 140, 221102; 2014 – paper here). In other words, these structural defects turn the hydration water itself into a kind of catalytic assistant of protein function. It’s a fascinating idea, though I daresay many will want to see experimental or at least computational proof that the plausibility argument that Ariel advances actually stacks up.

Sandeep Patel, Phillip Geissler, Pavel Jungwirth and several others (forgive me for the incomplete list) have been considering how ions near the air-water interface may have specific effects on the interfacial fluctuations – a new wrinkle, perhaps, on how ions induce Hofmeister-type ion-specific effects, since such modification of fluctuations might also be expected at hydrophobic aqueous interfaces. Patel now looks more closely at this idea for the case of halide ions interacting with hydrophobin II (D. Cui et al., J. Phys. Chem. B 118, 4490; 2014 – paper here). Their simulations imply that iodide is more surface-stable than chloride – consistent with what one might expect from its greater “hydrophobicity” – and that it induces more pronounced interfacial fluctuations. In contrast, there are no significant differences in behaviour of the two ions at hydrophilic interfaces – suggesting that ion-specific effects are sensitive to the nature of the surfaces with which the ions are interacting.

More on this topic comes from Tahei Tahara and colleagues at RIKEN’s Molecular Spectroscopy Lab in Saitama (S. Nihonyanagi et al., JACS 136, 6155; 2014 – paper here). They use vibrational SFG spectroscopy to look at how counterions affect interfacial water vibrations (specifically the OH band) at charged interfaces. Here the effects seem to depend on the charge of the surfaces: at positively charged surfaces (of surfactant monolayers), the OH intensity decreases in the order of the halide Hofmeister series, whereas at negative surfaces there seems to be no such effect of the counter-cations. This seems to reflect the tendency of halides to be absorbed at the interface, whereas cation effects seem to operate via changes in the hydrogen-bond strength of the interfacial water. In other words, Hofmeister effects seem to have a different mechanism for anions and cations.

I guess there is, broadly speaking, some resonance here with a study by Yoshikata Koga at UBC in Vancouver and colleagues, who look at differences in the molecular organization of cation and anion hydration spheres (T. Morita et al., J. Phys. Chem B 118, 8744; 2014 – paper here). They use a thermodynamic methodology they have developed previously which involves addition of a cosolvent 1-propanol. They make the interesting proposal that there are five different classes of solute, which one might regard as a rather more sophisticated and physically meaningful variant of the chaotrope/kosmotrope picture. Crudely speaking, cations such as Na+ and K+ simply acquire a tight hydration shell while leaving the water beyond it unperturbed, while anions have a stronger influence with some hydrophobic character. I must say that I like this idea of trying to salvage a useable qualitative classification scheme from the confusion of the chaotrope/kosmotrope view.

Several measures of hydrophobicity have been proposed for amino acid residues, but they aren’t always consistent. There seems to be an emerging view that this is because hydrophobicity and hydrophilicity are context-dependent parameters. That idea is supported by work from Sara Bonella and colleagues at Sapienza University in Rome (S. Bonella et al., J. Phys. Chem. B 118, 6604; 2014 – paper here). They assess hydrophobicity in simulations based on the orientiation of water molecules at a certain distance from the amino acid in question, and say that a single quantity is not sufficient to characterize it. Rather, they suggest a three-parameter index, the components of which emerge from the statistical analysis of water orientation in ways that seem clear enough but which I can’t easily see how to summarize. The authors say that this method seems to work for predicting which regions of membrane proteins are the transmembrane sections.

Lei Zhou and Qinglian Liu at Virginia Commonwealth University say that adding a layer of explicit water on the surface of proteins whose normal modes are being calculated to predict anisotropic B-factors in their crystallographic structures improves the agreement with experiment (J. Phys. Chem. B 118, 4069; 2014 – paper here). It’s a nice illustration of the intimate coupling of protein and solvent.

It’s possible to engineer a buried ion pair in the hydrophobic interior of a protein without significant structural reorganization of the rest of the protein. That’s the conclusion of a study by Bertrand Garcia-Moreno E. of Johns Hopkins and colleagues (A. C. Robinson et al., PNAS 111, 11685; 2014 – paper here). They have re-engineered staphylococcal nuclease (SNase) so that it incorporates an ionizable Glu-Lys pairing (2.6 Å apart) in its interior. Although the Coulomb interaction of these largely unscreened charges is appreciable, it is not enough to offset the dehydration of the buried charges. However, two water molecules are able to penetrate deeply into the core to provide some hydration, and one of these seems able to participate in a water wire to facilitate proton transport to and from the buried ion pair. As a result, the pair is accommodated well without disrupting the protein’s structure significantly. This is useful to know because such buried ion pairs participate in some important enzymatic processes, including proton transfer and electron transfer – so there is no obvious reason why this sort of catalytic capability might not be engineered artificially into proteins.

More on the mode of operation of osmolytes: Francisco Rodríguez-Ropero and Nico van der Vegt at the TU Darmstadt say, on the basis of MD simulations, that urea stabilizes the folded state of PNiPAM via direct interactions (J. Phys. Chem. B 118, 7327; 2014 – paper here). The urea molecules enter the first hydration shell thanks to vdW interactions with the hydrophobic isopropyl groups of the polymer, creating an entropic driving force for folding via the formation of this “urea cloud”.

Irisbel Guzman and Martin Gruebele at Illinois offer a nice review of methods (especially fast relaxation imaging) for probing protein folding in vivo, where interactions with other proteins, aggregation and macromolecular crowding effects can be important (J. Phys. Chem. B 118, 8459; 2014 – paper here).

And Fabio Sterpone at the Université Paris Diderot and colleagues provide a nice review of the coarse-grained OPEP protein model for investigating all manner of cell phenomena ranging from DNA complexation and amyloid formation to crowding and hydrodynamics – the latter applied, for example, to protein unfolding (F. Sterpone et al., Chem. Soc. Rev. 43, 4871; 2014 – paper here).

Sambhu Datta at the Indian Institute of Technology and coworkers propose a comprehensive quantum-chemical treatment of the solubility of CO2 in water that includes a consideration of how hydrogen-bonding changes alter phonon energies in the fluid (T. Sadhukhan et al., J. Phys. Chem. B 118, 8782; 2014 – paper here). They say may explain how it is that RuBP in chloroplasts seems able to significantly enhance the gas solubility, increasing the rate of photosynthesis.

For anyone who wants to check out the full details (and can read French), Guillaume Jeanmairet has made available ( his PhD thesis on a computationally inexpensive DFT treatment of water (see G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619; 2013).