Monday, June 22, 2009

Small molecules and protein folding

The role of small molecules – denaturants and osmolytes – in protein folding is much in need of a good review article (or have I missed one?). Julio Fernández and colleagues have used single-molecule force spectroscopy to look at how the osmolyte glycerol interacts with ubiquitin as the protein is mechanically unfolded (S. Garcia-Manyes et al., PNAS 10.1073/pnas.09020106 – not yet online). Glycerol stabilizes the protein against unfolding, and apparently also promotes hydrophobic collapse of the unfolded conformation. They think that while glycerol stabilizes the folded state via direct interaction with the protein, ethanol seems to exert a weaker stabilizing effect via an indirect interaction involving the disruption of ‘water structure’. The promotion of hydrophobic collapse in the presence of glycerol (which is not seen for ethanol) seems to be a separate effect, perhaps due to the enhanced destabilization of exposed hydrophobic surface due to the polar surface area of glycerol.

The electronic state of water molecules confined in a close-packed rodlike micelle lattice is significantly different from that in the gas and bulk liquid phases, according to Jan-Erik Rubensson and colleagues at Uppsala University (J. Gråsjö et al., J. Phys. Chem. B 113, 8201; 2009 – paper here). They have probed this question using soft X-ray absorption and emission, and say that the water molecules among micelles are stabilized relative to the bulk, perhaps because of interaction with the chloride counterions in solution.

Pablo Debenedetti and coworkers have also studied nanoconfined water, here in a slit-like space between two hydrophilic silica surfaces using MD simulations (S. R.-V. Castrillón et al., J. Phys. Chem. B 10.1021/jp9025392 – paper here). They find rotational slowing within 0.5 nm of the surfaces, and translational slowing within 1 nm.

The difference in hydrophobic interactions in acidic solutions relative to salt solutions is investigated by Greg Voth and colleagues (H. Chen et al., J. Phys. Chem. B 113, 7291; 2009 – paper here). They say that in acid (HCl) solution they see interactions between the hydrophobe surface and the hydrated protons, owing to the amphiphilic character of the latter. This could explain why hydrated protons are anomalous in the Hofmeister series, promoting solubilization of nonpolar solutes despite having a similar radius to salting-out cations such as potassium and ammonium.

And on matters Hofmeister, Bernd Rode and colleagues at the University of Innsbruck have carried out quantum simulations of the hydration of beryllium ions, and find that the tetrahedral first hydration shell has very slow exchange dynamics (S. S. Azam et al., J. Phys. Chem. B 10.1021/jp903536k – paper here). They refer to this as a strong ‘structure-forming’ behaviour – I can see what they mean, but does it invite confusion with the already confused issue of ‘structure-making’?

The dynamic Stokes shift – the slower decay of a frequency-shifted fluorescent probe molecule – close to protein surfaces relative to the bulk solution has been attributed in the past to much slower water motions in the hydration shell. But Bertil Halle and Lennart Nilsson question this interpretation in a new paper (J. Phys. Chem. B 113, 8210; 2009 – paper here). They say that the slower decay can be understood by a solvent polarization effect, and does not probe hydration dynamics at all.

Zoran Arsov at the Josef Stefan Institute in Ljubljana and colleagues report the weakening of hydrogen bonds in water confined between lipid bilayers, using a form of FTIR (Z. Arsov et al., ChemPhysChem 10.1002/cphc.200900185 – paper here). The water films separating bilayers in the lamellar phases (phospholipids DMPC and POPE) studied here are very thin – 2 and 0.6 nm respectively. So a disruption of bulk structure is presumably to be expected. They suggest that this perturbation may contribute to the attractive hydration force between the bilayers.

There has been a long debate, going back to Faraday and Tyndall, on whether ice has a liquid-like layer on its surface and if so, what this looks like. Xiao-Yang Zhu and colleagues at Minnesota have investigated this with interfacial force microscopy (M. P. Goertz et al., Langmuir 10.1021/la9001994 – paper here). They see a liquid-like layer tens of nanometres thick, but suggest that it is in fact viscoelastic.

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