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.

Tuesday, June 16, 2009

More catching up

Changes in my circumstances have delayed this one, and of course the longer I delay, the worse it gets. I bring things somewhat up to date here, but there’s still more to come.

First, an ad: there is an RSC Faraday Discussion on ‘Wetting Dynamics of Hydrophobic and Structured Surfaces’ in Richmond, Virginia on 12-14 April 2010. Given the list of organizers and invited speakers, it is sure to be very good. Details are here.

More on water flow inside carbon nanotubes, which is attracting increasing interest because of the possibilities for water purification and desalination. John Thomas and Alan McGaughey at Carnegie Mellon find in MD simulations that the water structure changes significantly for tubes of 0.83 to 1.39 nm – from single chains to stacked pentagons and hexagons and finally to bulk-like (Phys. Rev. Lett. 102, 184502; 2009 – paper here). This seems to significantly affect the (pressure-driven) flow velocity in a non-monotonic way, particularly when the liquid has a layer-like profile.

Thomas Angel and his coworkers have looked at the roles of water molecules in photosensitive rhodopsin-like G protein-coupled receptors (T. E. Angel et al., PNAS 10.1073/pnas.0903545106 – paper here). They find that waters associated with highly conserved residues seem to be crucial to function, in particular providing the plasticity needed to transmit a signal from the retinal binding pocket to the intracellular surface.

Sow-Hsin Chen and coworkers find, using QENS, that lysozyme remains flexible (‘soft’) at low temperatures (210-240 K) when moderate pressure (around 1 kbar) is applied (X.-q. Chu et al., J. Phys. Chem. B 10.1021/jp900557w – paper here). Surprisingly, the dynamics under these conditions are actually faster than those under ambient conditions, and reflect those of the hydration water.

And speaking of low-temperature environments, David Wharton and Craig Marshall have outlined some of the survival strategies of Antarctic organisms in a nice brief review in J. Biol. 8, 39; 2009 – paper here. And Todd Sformo at the University of Alaska at Fairbanks has told me about a very interesting paper reporting an Arctic gnat that simultaneously uses freeze tolerance and freeze avoidance in different parts of its body – these strategies are usually mutually exclusive (T. Sformo et al., J. Compar. Physiol. B: Biochem. System. Envir. Physiol. 10.1007/s00360-009-0369-x; 2009 - paper here. (You see, this is the kind of nice stuff I fear I’m missing all the time…)

Huib Bakker’s group has used THz and femtosecond IR spectroscopy to study proton hydration (K. J. Tielrooij et al., Phys. Rev. Lett. 102, 198303; 2009 – paper here). They find that protons induce a drop in dielectric constant corresponding to an effect on 19 water molecules per proton. Four of these are involved in direct solvation, being irrotationally bound to the proton, but the others are perturbed by becoming implicated in proton motion.

Staying with proton transport, Greg Voth and colleagues have used the MS-EVB method to look at proton transfer in human carbonic anhydrase II (C. M. Maupin et al., JACS 10.1021/ja8091938 – paper here). The proton transfer here, between a zinc-bound OH group and the His64 residue, is the rate-limiting step, and involves a water cluster in the active site. There are some insights here into the ways proteins may use hydrophobic interfaces to control and facilitate proton transport. And Ana-Nicoleta Bondar at the University of California at Irvine and colleagues have studied how protons achieve long-distance transport in bacteriorhodopsin from the acceptor residue Asp85 to the extracellular proton release group (P. Phatak et al., JACS 10.1021/ja809767v – paper here). Bound water molecules in the active site are again implicated.

Prashanth Athri and W. David Wilson at Georgia State University show how interfacial water can help the DNA-binding agent DB921 to bind in the minor groove despite an imperfect geometric match (JACS 10.1021/ja809249h – paper here). These results might offer clues to exploiting water mediation in designing DNA-binding molecules.

More on urea and denaturation: Frank Gabel at the Institut de Biologie Structurale in Grenoble and colleagues have used SANS and SAXS to study the binding of urea to denatured ubiquitin (JACS 10.1021/ja9013248 – paper here). They find that acid-induced denaturation recruits about 20 urea molecules from solution to bind to the protein, supporting the view that these direct interactions between protein and denaturant are the cause of denaturation.

Some studies of water at lipid membranes. M. D. Fayer and colleagues at Stanford look at the hydration of AOT reverse micelles, compared to the lamellar phase, using ultrafast IR spectroscopy, and conclude that short-range, direct interactions with the head groups, rather than more general nanoconfinement effects, seen to be responsible for the orientiation retardation of water molecules (D. E. Moilanen et al., JACS 131, 8318; 2009 – paper here). And Zhancheng Zhang and Max Berkowitz at UNC have looked at the slowing of water orientational relaxation in the hydration layer of phospholipids bilayers using MD (J. Phys. Chem. B 113, 7676; 2009 – paper here). Berkowitz and Changsun Eun have also looked (via MD) at the hydration of lipid headgroups attached to two parallel graphene plates, as a model for interactions between bilayers (J. Phys. Chem. B 10.1021/jp901747s – paper here). They find a repulsive interaction between the plates that has three regimes, dependent on the plate separation. At small distances (0.75-1 nm) the repulsion is steric. At intermediate distances (1-1.6 nm) it results from dehydration of the head groups, and at large separations (1.7-2.4 nm) – well, I must be missing something in my rapid reading here, but all I can glean is that this is water-mediated too.

Alenka Luzar and colleagues have compared MD simulations of the hydration of monosodium glutamate with the recent neutron data from Sylvia McLain et al. (J. Phys. Chem. B 110, 21251; 2006). They find that the simulations could not reproduce the reduction in water-water correlations seen experimentally, pointing to some of the shortcomings of the classical potentials used (C. D. Daub et al., J. Phys. Chem. B. 113, 7687; 2009 – paper here). And Janusz Stangret and colleagues have characterized the hydration of carboxylate ions using FTIR spectroscopy (E. Gojlo et al., J. Phys. Chem. B 10.1021/jp811346x – paper here). They find that two water molecules induce symmetry-breaking of the carboxylate group, providing non-equivalent proton donors to the oxygen atoms.

Jacob Petrich and colleagues at Iowa State describe a new method for probing the dynamics of proteins – specifically, measuring the solvation correlation function – by monitoring the fluorescence from two coumarins with different lifetimes (S. Bose et al., J. Phys. Chem. B 10.1021/jp9004345 – paper here).

Benoît Roux at Chicago and coworkers consider the ‘topological control hypothesis’ for selective ion binding to proteins, which postulates that selectivity is controlled primarily by the number of ligands coordinating the ion – which can in turn be predicted from the average coordination structure in bulk water – and not from their chemical nature (H. Yu et al., J. Phys. Chem. B 10.1021/jp901233v – paper here). They find, perhaps not surprisingly, that this hypothesis has some serious limitations in predicting binding free energies.

Kelly Gaffney and coworkers at Stanford use ultrafast IR spectroscopy to look at hydrogen-bond dynamics in sodium perchlorate solution (S. Park et al., J. Phys. Chem. B 10.1021/jp9016739 – paper here). They find that the dynamics support an orientational jump model in which the making and breaking of H-bonds is the predominant control on reorientation times. MD simulations also indicate that the anion hydration shells have two distinct shells, and that the molecules in the inner shell donate one H-bond each to the perchlorate ion.

Nicolas Giovambattista, Peter rossky and Pablo Debenedetti have been trying to map out the phase behaviour of water confined between hydropholic, hydrophobic and heterogeneous plates at various temperatures and pressures (Phys. Rev. E 73, 041604; 2006 and J. Phys. Chem. C 11, 1323; 2007). They have now extended this work by looking at the effects of varying the T and P simultaneously between 220-300 K and –0.2 to 0.2 GPa (J. Phys. Chem. B 10.1021/jp9018266 – paper here). It’s hard to summarize all the information in this rich paper, but one general conclusion is that the plates become effectively less hydrophobic (the vapour phase is suppressed) as the temperature drops. An underlying motive for this work is to understand the pressure- and cold-denaturation of proteins and how this is tied up with invasion of hydrophobic cavities by water.