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Jumat, 28 Juni 2013

Complexity of osmolytes

More on the mechanisms of denaturation and osmolyte stabilization. Trimethylamine-N-oxide (TMAO) is known to confer protection against protein denaturation by urea. Rahul Sarma and Sandip Paul at the Indian Institute of Technology have carried out MD simulations to try to figure out why (J. Phys. Chem. B 117, 5691; 2013 – paper here). They say that TMAO interacts with a model peptide, N-methylacetamide (NMA), so as to cause some dehydration by replacing solvation water. However, this interaction with the peptide is relatively inefficient, especially because TMAO cannot donate its hydrogen to the backbone carbonyls. As a result, TMAO is not efficient at stabilizing the unfolded peptide chain. If the protein folds, then TMAO is more available for forming very strong hydrogen bonds with water, and indeed with urea. It’s a subtle argument in which the direct interactions between all four components – TMAO, urea, peptide and water – are implicated.

Much the same issues are explored in a new preprint by Bruce Berne and coworkers at Columbia (J. Mondal et al., They look at the interactions of urea and TMAO separately with a model 32-mer made of Lennard-Jones beads whose hydrophobicity can be varied. Although both small solutes interact strongly with the polymer, TMAO destabilizes extended conformations while urea stabilizes them. This seems to be because TMAO molecules are more stable (via van der Waals interactions) next to the collapsed rather than the extended polymer. The results provide further support for an interpretation of osmolyte effects that invokes direct interactions rather than indirect effects on “water structure”.

The subtlety of mixed-osmolyte solutions is revealed in simulations of a hydrophobic polymer in urea and guanidinium chloride by Payel Das at IBM Yorktown Heights and colleagues (P. Das et al., Langmuir 29, 4877; 2013 – paper here). They find that, while both of these molecules act as denaturants on their own, in combination they actually promote collapse of the polymer. It is hard to tell a simple story about why this happens, although apparently Paul Flory predicted back in 1955 that two good solvents could combine to induce polymer chain collapse. Although Gdm has the stronger interaction with the polymer, its enhanced concentration in the vicinity of the polymer attracts urea due to the favourable urea-Gdm interaction, with the result that urea is in fact preferentially adsorbed onto the polymer. This sets up a long-ranged interaction between the monomers mediated by their clouds of urea molecules, ultimately driving collapse.

The effect of progressive dehydration of a protein (lysozyme) on its structure and dynamics is studied using Raman spectroscopy by Gediminas Niaura of Vilnius University of colleagues (J. Phys. Chem. B 117, 4981; 2013 – paper here). They find that there is a structural change in the dry protein crystal that begins at about 7-10 wt% water, and that the native state is reached at about 35 wt% water (which amounts to appreciably more than monolayer coverage). In the dry state the protein is dynamically glassy, with a diminished proportion of alpha helices and an enhanced content of beta-sheet contacts.

And on the question of ‘dry’ proteins, Eric Gloaguen at the CNRS Laboratoire Francis Perrin in Gif-sur-Yvette and colleagues report that small peptides with aromatic residues will fold into hydrophobic domains even in the solvent-free gas phase, showing that this is a favourable conformation even in the earliest stages of protein folding (E. Gloaguen et al., J. Phys. Chem. B 117, 4945; 2013 – paper here).

Somedatta Pal and Sanjoy Bandyopadhyay at the Indian Institute of Technology in Kharagpur have used MD simulations to look at the complementary issue of how protein (here barstar) dynamics affect the dynamics of hydration water (J. Phys. Chem. B 117, 5848; 2013 – paper here). They compare the normal situation of the hydrated protein with that in which the protein is kept frozen, looking specifically at the effect of the change on the low-frequency vibrations of the water molecules. Freezing the protein results in stronger confinement of water bound to the protein surface, with a corresponding blue shift of the vibrational frequency for transverse water oscillations – but much less effect on longitudinal oscillations.

An intriguing paper by Nicholas Spencer and colleagues at ETH investigates hydration forces for glycoproteins using the surface force apparatus (R. M. Espinosa-Marzel et al., Biophys. J. 104, 2686; 2013 – paper here). They attach these onto hydrophobic and hydrophobic surfaces, and find that there is a rather long-ranged repulsive force (several tens of nanometres) between the surfaces. It is good to see this neglected class of biological molecules get some attention in terms of their fundamental hydration characteristics. However, I don’t buy the interpretation that the repulsion is due to some “long-ranged structuring of water”. The whole discussion around the results seems to be something of a throwback, starting with the whole notion of “vicinal water” and involving two-state water theories, kosmotropes and all the rest of the paraphernalia that tended to surround discussions of ‘water structure’ 20 years ago. “Ordering” of water over 30 nm or so just isn’t any longer consistent with what is known of other systems, and it’s been suggested to me that steric repulsion of the surfaces due to a few of the macromolecules protruding from the monolayer is a much more likely explanation of the effects observed.

But could it be that long-ranged water structuring is going to try to stage a little comeback? I ask this because it is invoked in another recent paper too, by Jan Christer Eriksson and Ulf Henriksson of the Royal Institute of Technology in Sweden (Langmuir 29, 4789; 2013 – paper here). They develop their earlier argument (Langmuir 23, 1126; 2007) that the long-ranged hydrophobic attraction might be accounted for by the formation of roughly cylindrical bridging water clusters that are “slightly more organized than the rest of the film”. Their analysis suggests that such a proposal can explain some recent measurements on water thin films with the SFA (Wang et al., J. Coll. Int. Sci. 364, 257; 2011). But I think I will stick with the bridging-nanobubbles idea.

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