A rather exquisite water-mediated mechanism of enzymatic activity is reported by Qiang Cui at Wisconsin-Madison and colleagues (P. Goyal et al., PNAS 110, 18886 – paper here). They describe a computational study of cytochrome c oxidase, which uses oxygen reduction to pump protons across a membrane. During this process a glutamate residue is believed to act as a temporary proton donor. Cui and colleagues show that the proton affinity of this Glu is controlled by the degree of hydration in an internal hydrophobic cavity, which is itself governed by protonation of a substituent on the heme group 10Å away, triggering movement of a loop gating the cavity’s entrance.
Enthalpy/entropy compensation in protein-ligand binding is the topic of a nice study by George Whitesides’ group in a special issue of the European Physical Journal (doi:10.1140/epjst/e2013-01818-y – paper here). The group examines this issue further in a paper in JACS (B. Breiten et al., JACS 135, 15579; 2013 – paper here), where they look at the human carbonic anhydrase system that they have also studied earlier (see P. W. Snyder et al., PNAS 108, 17889; 2011). This new paper expands on that earlier work, in which a series of ligands modified with various thiazole-based sulfonamides was used to probe the effects of solvent rearrangements within the binding cavity. They find that the changes in the free energy of binding, and the contributions from enthalpy and entropy, are largely determined by the rearrangements or displacements of water, and voice a telling conclusion: “This water- centric view of ligand binding – and H/S-compensation – cannot be rationalized by the lock-and-key principle and suggests that the molecules of water surrounding the ligand and filling the active site of a protein are as important as the structure of the ligand and the surface of the active site.”
Myoglobin binds various ligands, such as O2, CO and NO, in an internal cavity. It also binds water in internal sites, but crystallographic studies have given conflicting views on where these cavities are and how occupied they are. Shuji Kaieda and Bertil Halle at Lund have used deuteron and 17O magnetic relaxation dispersion spectroscopy to probe these hydration sites and the dynamics of the water molecules occupying them (J. Phys. Chem. B 117, 14676; 2013 – paper here). They find that the waters come and go on a microsecond timescale in all four sites, despite their significant separation, and conclude that these dynamics share a global mechanism involving transient penetration of the protein by hydrogen-bonded chains that may intermittently ‘flush’ the cavity network.
More on small-molecule solute perturbations to protein structure: Warren Beck and colleagues at Michigan State University report fluorescence spectroscopic measurements on zinc-substituted cytochrome c in the presence of guanidinium ions, in an effort to discover why Gdm+ perturbs the protein dynamics by making it apparently more flexible (J. Tripathy et al., J. Phys. Chem. B 117, 14589; 2013 – paper here). They conclude that part of this response comes from a change in structure of the protein’s hydration shell because of direct binding of Gdm+ to the protein surface.
How do magnesium ion channels attain their high specificity in the presence of high concentrations of calcium? Todor Dudev at the Academia Sinica and Carmay Lim at National Tsing Hua University in Taiwan say that the differences in the metals’ hydration shells are the key (JACS 135, 17200; 2013 – paper here). Their calculations suggest that the hexacoordinated magnesium ions polarize the bound water more strongly, resulting in stronger ion-water-protein interactions.
How water diffuses at the surface of a lipid membrane has been studied before, but it can be hard to ensure that just the water molecules immediately at the interface are probed. Robert Bryant at the University of Virginia Charlottesville and colleagues claim to be able to do that using magnetic relaxation dispersion spectroscopy for phospholipid vesicles in deuterated water (K. G. Victor et al., J. Phys. Chem. B 117, 12475; 2013 – paper here). They report that the water molecules explore the interface via essentially two-dimensional diffusion over the vesicle surface, with a translational correlation time that seems relatively long: about 70 ps. This modified dimensionality of water motions, they say, stems from an excluded-volume effect.
The molecular basis of anaesthesia is still unclear, although it seems to involve low-affinity binding of the anaesthetic to proteins. Hai-Jing Wang of UNC and colleagues say that hydration water plays a crucial role in this process (H.-J. Wang et al., J. Phys. Chem. B 117, 12007; 2013 – paper here). They use NMR to look at the binding of volatile halogenated alkanes (known anaesthetics) to BSA, which has binding pockets for such molecules. They find that binding occurs only once the hydration level of the protein surpasses a critical threshold. The molecular details of what this hydration water does remain to be elucidated, but Wang et al. suppose that the threshold hydration level is needed to “establish a favourable free-energy landscape for the binding of anaesthetics to the pre-existing binding sites.”
Peter Rossky and Lauren Kapcha at Texas at Austin have introduced a new hydrophobicity scale for protein constituents that works at the level of individual polar and non-polar atoms rather than classifying each residue as a whole (J. Mol. Biol. 10.1016/j.jmb.2013.09.039 – paper here). They say that it gives an appropriate measure of hydrophobicity in cases where a residue-based approach fails – without being any more computationally intense – and that it shows that this atomistic level of detail is therefore sometimes indispensable.
Another computational challenge is addressed by Sergio Pantano of the Institut Pasteur de Montevideo in Uruguay and coworkers (H. C. Gonzalez et al., J. Phys. Chem. B 117, 14438; 2013 – paper here). They describe a way to combine the common SPC, TIP3P and SPC/E atomistic water models with a coarse-grained model called WatFour or WT4, demonstrating its effectiveness via (among other things) simulations of the β1 domain of streptococcal protein G.
There’s a curious and interesting paper by Akira Yamakata of the Toyota Technical Institute in Nagoya and colleagues on the observation of hydration shells of ions being destroyed by electrochemical control of the ions’ binding to an electrode surface (A. Yamakata et al., JACS 135, 15033; 2013 – paper here). The researchers use a platinum electrode rendered hydrophobic by coverage with a CO monolayer, and use time-resolved IR spectroscopy to monitor the hydration shells of tetrapropylammonium (Pr4N) and sodium ions as they are pulled onto the surface by the electric field. They can monitor the destruction of the hydration shells as this happens, and say that while that of Pr4N is rather easily destroyed at high field so that the ion interacts directly with the CO layer, the shell of sodium is more rigid and remains intact.
Lawrence Pratt and colleagues at Tulane University use simulations to demonstrate that the hydrophobic interactions between hard-sphere solutes in water are more attractive and endothermic than is predicted by the molecular-scale Pratt-Chandler theory (M. I. Chaudhari et al., PNAS 10.1073/pnas.1312458110 – paper here). This shows what an improved theory will have to shoot at.
Peter Hamm and coworkers at the University of Zurich have used 2D Raman-THz spectroscopy to probe collective intermolecular modes of pure liquid water, and conclude that there are different types of hydrogen-bonded networks – albeit only on a very short (100-fs) timescale, which is not compatible with controversial proposals for persistent heterogeneity of these networks like that of Anders Nilssen et al. (J. Savolainen et al., PNAS 10.1073/pnas.1317459110 – paper here). This seems to add to the growing view that this apparent controversy is best seen as a question of the different timescales being examined, and that at room temperature any ‘two-state’ picture is very rapidly averaged away.
Finally, a curiosity about the macroscopic mechanical roles of water in plants. Peter Fratzl of the Max Planck Institute of Colloids and Interfaces in Potsdam and colleagues look at how changes in hydration can produce stresses and movement in plants via swelling and shrinkage (L. Bertinetti et al., Phys. Rev. Lett. 111, 238001; 2013 – paper here). The free energy needed for such actuation can be considered to be provided, at least in part, by the formation of new hydrogen bonds. The authors propose a model that allows them to estimate the free energy made available by water absorption into woody plant tissue, and find that (except in the case of nearly dry tissue) it amounts to about 1.2 kT per water molecule, suggesting that the water bound to the macromolecules in the tissue acquires about one additional hydrogen bond for every eight molecules. Frankly, I don’t fully understand the arguments here: the authors say that “This would suggest that the main driving force for water absorption in non living plant tissues is a phase transition of water to a liquid state, characterized by a stronger H-bond network, occurring when H2O is confined within the macromolecular components of the wood cell wall material.” I’m going to have to get back to you on that.
