Can the displacement of water from binding sites be used as a tool for drug design? John Ladbury has written a fair amount on this question in the past (e.g. Chem. Biol. 3, 973; 1996), but it remains hard to deduce any general principles. In principle both the enthalpy and the entropy of ligand binding can be enhanced by displacing water molecules, but the balance is subtle and not obviously generic. Julien Michel, Julian Tirado-Rives and William Jorgensen at Yale have now looked at what can be learnt from some specific cases, namely ligands designed to bind to three proteins: scytalone dehydratase, p38-aMAP kinase and EGFR kinase (JACS ja906058w – paper here). They find for a series of ligands that in general the binding affinity correlates with ease of water displacement, but also that it can be important to ensure that it can be important to compensate for the free-energy increase of water displacement by building in additional favourable interactions between the binding site and the displacing group – that is, it’s not necessarily enough to expel the water; one has to put something amenable in its place. My reading of this paper is that there are no wholly reliable short-cuts or rules of thumb – the details matter.
Nicolas Giovambattista, Pablo Debenedetti and Peter Rossky continue their investigations of how surface topography affects hydrophobicity (PNAS 106, 15181; 2009 – paper here). They have used simulations to look at the hydration of a silica surface on which they vary the surface polarity and topography (atomic- to micrometre-scale roughness), and find that the two can couple in such a way as make a somewhat polar surface more hydrophobic than an apolar one. This suggests that surface patterning could be a powerful tool for altering hydrophobicity.
Feng Guo and Joel Friedman at the Albert Einstein College of Medicine have probed Hofmeister effects by looking at the effect of adding anions and cations to a solution of gadolinium (III) ions, both free and coordinated to organic and biological molecules (JACS 131, 11010; 2009 – paper here). The idea is that changes in the OH stretching mode of waters in the Gd hydration shell offer a sign of what is happening elsewhere in the solution. It’s not entirely clear how the former changes relate to the latter, but Guo and Friedman suggest two possibilities. For example, the tight hydration clusters of high-charge-density cations might both alter water structure quite generally, and might sequester water molecules in a way that frees up anions to interact with the Gd hydration shell. In the first of these cases, the interpretation is predicated on a notion of inhomogeneous bulk water structure composed of a mixture of high- and low-density water clusters, based on Wilse Robinson’s model. Frankly, I’m not persuaded that this is a persuasive way to interpret the findings – the two-state water model is of course controversial. But the overall conclusion – that Hofmeister ordering of salts can be best explained by disruption of hydrogen bonding in hydration-shell water rather than bulk water – has a ring of truth to it.
But the Hofmeister plot thickens further. Yanjie Zhang and Paul Cremer at Texas A&M have also been investigating these effects, and they find that for lysozyme, aggregation in salt solution (followed by looking at cloudiness of the solution and eventual phase separation) seems to follow two different Hofmeister series depending on salt concentration (PNAS 106, 15249; 2009 – paper here). At low concentration, the usual series for anions (which dominate aggregation effects in this case) is reversed, and is correlated with size and hydration thermodynamics of the ions. At high concentrations, there is a normal Hofmeister series correlated with the ionic polarizability.
Daisuke Matsuoka and Masayoshi Nakasako at Keio University in Japan have conducted a massive study of the probability distributions of water molecules hydrating proteins, using nearly 18,000 crystal structures from the Protein Data Bank (J. Phys. Chem. B 113, 11274; 2009 – paper here). They find that the angular distributions are narrowest in the direction of N-H and O-H bonds, and that pairs of polar atoms are often arranged to satisfy the tetrahedral H-bonding geometry, suggesting that – if one may put it like this – the protein’s secondary structure is arranged to ‘suit’ the solvent rather than vice versa.
Is the hydrophobic core of a protein rigid or fluid? In reality neither extreme seems terribly likely, but Liliya Vugmeyster at the University of Alaska-Anchorage and colleagues have probed its dynamics using deuteron solid-state NMR (JACS ja902977u – paper here). Specifically, they look at the chicken villin headpiece subdomain protein HP36 labelled with deuterons at either of the two methyl groups of a leucine residue. They find that there is restricted diffusion along an arc, and larger jumps between rotameric conformers.
Eduard Schreiner and colleagues at Bochum have used ab initio MD simulations to look at the reaction kinetics and mechanisms of peptide bond formation and hydrolysis among activated amino acids (alpha-amino acid N-carboxyanhydrides, NCAs). These are used in the synthesis of large polypeptides, and may also have prebiotic relevance. The team compares the processes in water under ambient conditions and in hot pressurized water, such as might be found at hydrothermal vents (JACS ja9032742 – paper here). The hydrolysis mechanisms are different in the two cases, but in both the barrier to hydrolysis is greater than that to peptide bond formation, showing that peptide production is feasible in either case.
Ali Eftekhari-Bafrooei and Eric Borguet at Temple University use IR pump-probe spectroscopy to look at how the vibrational dynamics of O-H stretching of interfacial water groups is altered by surface charge at the interface with silica (JACS 131, 12035; 2009 – paper here). They say that, while the vibrational dynamics are retarded at the neutral surface (at low pH), surface charging at higher pH causes polarization of the water molecules that leads to more bulk-like behaviour.
Changes in water dynamics are also the subject of a paper by Matías Pomata in the National Commission for Atomic Energy of Argentina and colleagues, who consider this issue for carbohydrate (fructose) solutions (J. Phys. Chem. B jp904019c – paper here). They say that for sugar concentrations above about 45%, the sugar molecules form a percolating H-bonded network encompassing patches of solvent, resulting in a slowing of translational, rotational and H-bonding dynamics (especially for water-solute) that is comparable to what is seen for the hydration layers of proteins (e.g. Pizzitutti et al., J. Phys. Chem. B 111, 7584; 2007).
Most of the work on the pseudo-glass transition of proteins around 200 K has been based on globular proteins. How do extended structural proteins such as elastin and collagen compare? That question is probed by Catalin Gainaru and colleagues at TU Dortmund (J. Phys. Chem. B jp9065899 – paper here). Elastin exhibits something like a glass transition at temperatures only slightly below physiological, but not collagen. Yet the dielectric relaxation appears to be the same for both molecules between about 140 and 220 K, showing that relaxation is Arrhenius-like (thermally activated) over the entire temperature range: there seems in this case nothing ‘anomalous’ about the dynamics in this regime.
Some time ago Haiping Fang at the Shanghai Institute of Applied Physics sent me a preprint describing MD simulations of the wetting properties of water films on polar, neutral surfaces. This has now been published (C. Wang et al., Phys. Rev. Lett. 103, 137801 (2009) – paper here). The paper looks at the behaviour of a water monolayer on a surface designed to resemble a semiconductor such as InSb(110). On some such surfaces (including metals), a monolayer at low temperatures is found to adopt a 2D ice-like structure with no dangling bonds, making it somewhat hydrophobic. But one would expect thermal fluctuations to create some dangling OH bonds at room temperature, increasing the hydrophilicity. That does happen here, but surprisingly the monolayer nevertheless remains significantly hydrophobic even at room temperature, so that a water droplet does not wet it.
On the same theme of interfacial water at solid surfaces, Andrei Sommer at Ulm and colleagues have continued their investigations of thin water films on diamond (Crystal Growth and Design 9, 3852; 2009 – paper here). They have studied the nature of water fimls on hydrogenated and non-hydrogenated nanocrystalline diamond at room temperature with atomic force acoustic microscopy. For the hydrogenated (hydrophobic) surfaces, water monolayers seem to be securely anchored and crystalline, promoting lubrication. The authors suggest that similar water layers might exist at the surfaces of biological fibrous tissues such as elastin, promoting easy sliding – an idea proposed in 1971 by Albert Szent-Györgyi (Perspect. Biol. Med. 14, 239; 1971).
Andrei and colleagues also found that red laser light can influence the structure of the water films, from which they think they may be able to develop new skin treatments. This is what Andrei has just sent to me:
“From what we learned about the interaction of red light with interfacial water layers on hydrophobic and hydrophilic surfaces, we designed a model of physiological aging and applied it in a real skin rejuvenation study. The good news is that the paper dealing with the model and its results (Facial Rejuvenation in the Triangle of ROS, Crystal Growth & Design, October 7 issue) produced an extraordinary impact in Google (Key words: green tea, light, wrinkles.)
“The bad news is that the journalists who wrote about the work overlooked the point in the study, whose implications are more interesting: we put forward the first physicochemical explanation of the shortening of the telomeres, and thereby of cellular aging. In a nutshell: we postulated that the shortening of telomeres is due to the coincidence of mechanical pulling during cell division and the build-up of a glue-like interfacial water in the space between the nuclear matrix and telomeres. The latter is modulated by an increase in interfacial pH, triggered by the emergence of reactive oxygen species (ROS) in the cell. The increase of intracellular ROS is induced by oxidative stress, which can have two different causes: external (e.g., UV radiation, air pollution), or internal (e.g., replicative stress). In both scenarios the principal actors involved in the production of ROS are mitochondria in the cell. This part of the process is known and comprehensively described in the literature.
“The exciting thing in all this is that, according to our research, it is possible to liquidify the glue-like interfacial water layers (to reduce the viscosity) by shining moderately intense red light on them. (Albert Szent Györgyi would like to read this, because it relates interfacial water with the the biological clock underlying the limited division potential of somatic cells, which is the length of the telomeres.)
“In our study we used to rejuvenate the skin a combination of topically applied green tea and red light (670 nm). We just discovered a recent paper (R. Chan et al., Brit. J. Nutr., August 12, 2009) in which the authors report that green tea is instrumental in preventing the shortening of the telomeres, and they extrapolate that drinking green tea might extend our life by 5 years.
“Interestingly the cells of turtles - the methuselahs in our world - present no or only very limited shortening of their telomeres. Their shells provide them a perfect protection from destructive environmental impacts, including UV, and air pollution (i.e. volcanic ashes on a primitive Earth). In addition, their oxygen turnover rate is very low.”
This is fascinating stuff, and I must explore it some more. In the meantime, I think I will put the kettle on.