Tuesday, September 18, 2007

A(nother) word on urea

I discovered at the 2007 Halophiles meeting at the University of Essex earlier this month that the mechanism of protein denaturation by urea is still a matter of debate. That’s not, perhaps, terribly surprising in view of the fact that even the hydration structure of urea itself is not certain, as earlier posts have mentioned. Jose Manuel Hermida-Ramon at the University of Vigo in Spain and coworkers add a contribution to this debate in J. Phys. Chem. B [doi:10.1021/jp073579x]. They use quantum-chemical calculations to deduce the structure of the hydrated urea molecule, and say that it is ill-defined: the molecule is very floppy, because the transition from a planar to a non-planar structure has an activation energy comparable to the room-temperature thermal energy. However, they say that urea might adopt a fixed, or less flexible, structure, as it approaches a protein surface.

Wayne Bolen and colleagues at the University of Texas Medical Branch at Galveston have attempted to tease out the ways that urea interacts with peptide residues when this happens [M. Auton et al., PNAS doi:10.1073/pnas.0706251104]. Using thermodynamic data, they say that, contrary to some previous views, the key interactions are not with nonpolar side chains, but involve the peptide backbone itself, and that these latter interactions are what drives denaturation. No doubt we’ll be hearing more about this issue.

The question of dewetting of protein surfaces in folding and aggregation also rumbles on. Following on from the Lum/Chandler/Weeks idea of dewetting of large hydrophobes and a consequent crossover length in the mechanism of hydrophobic attraction [K. Lum et al., J. Phys. Chem. B 103, 4570; 1999; D. Chandler, Nature 437, 640; 2005], Jeremy Smith at Heidelberg and colleagues have looked at whether there is ‘dewetting’ around hydrophobic residues of smaller peptides [I. Daidone et al., PNAS doi:10.1073/pnas.0701401104]. They say that for a 14-residue beta-hairpin peptide, conformers that expose significant amounts of hydrophobic surface have a lower hydration density than those that don’t, and that as a consequence, “dehydration-driven solvent exposure of hydrophobic surfaces may be a significant factor determining peptide conformational equilibria.” Which looks fine as far as it goes, but I can’t obviously see if this addresses the question of whether there is an abrupt, cooperative drying transition during folding, as seemed to be a central feature of the LCW model…

Thursday, September 6, 2007

Collapse and cooperation in water

I seem to have missed the recent paper by David Chandler and colleagues on collapse of a hydrophobic polymer chain within a ‘coarse-grained’ model of a water solvent [PNAS 104, 14559]. I was alerted to it by the commentary in the forthcoming issue of PNAS by Gerhard Hummer [doi:10.1073/pnas.0706633104]. David’s paper provides support for his suggestion, with ten Wolde, that hydrophobic polymer collapse happens via a dewetting transition [PNAS 99, 6539; 2002]. In the new simulations, expulsion of water through collective motions is the rate-limiting step of the collapse, and moreover it is the work performed on the solvent in this process that supplies the free-energy barrier – that is, dewetting doesn’t passively accompany the collapse, but drives it.
I’ve talked about this idea a fair bit in previous posts in relation to protein folding and aggregation: Bruce Berne’ studies have suggested that dewetting transitions can happen in this context, but are not the general rule. There doesn’t seem to be any obvious inconsistency between these findings: David is looking simply at hydrophobic chains, whereas it seems that only a few polar groups in the chain, as are generally found in proteins, can be sufficient to suppress dewetting. That, at this point, seems to be the story.

There are two nice illustrations of the roles of hydration water in protein function in the latest ASAP section of JACS. Mario Rivera at the University of Kansas and coworkers have used NMR relaxation to look at the role of a hydrogen-bonded network of waters in the function of a bacterial heme oxygenase [J. C. Rodriguez et al., doi:10.1021/ja072405q]. They find that the network serves three roles. First, it conducts protons to the iron-dioxygen complex during catalysis. Second, it propagates changes in electronic structure at the active site during the course of the reaction to remote parts of the polypeptide. Third, it modulates the conformational freedom of the enzyme, allowing it to accommodate and adapt to the changes in conformation required during the catalytic process. If the hydrogen-bonded network is disrupted in a mutant form, the necessary coordination in dynamics of different parts of the protein is lost and the motions become almost globally chaotic, lowering the efficiency of the enzyme significantly. In short, the enzymatic process simply ‘makes no sense’ without the aid of the waters. As the authors put it, “The information needed to tune the dynamic freedom of the polypeptide is communicated from the active site to the polypeptide via the hydrogen-bonding network.” That’s a wonderful example of the delicate fine-tuning of structure and dynamics that these hydration structures can offer.

Second, Vicent Moliner at the Universitat Jaume I in Castello and colleagues use simulations to confirm the idea that long-distance electron transfer between the metal sites in a dicopper enzyme (peptidylglycine alpha-hydroxylating monooxygenase) is mediated by a bridge of hydrogen-bonded water molecules and peptide residues [de la Lande et al., doi:10.1021.ja070329l] This has been suggested for some cytochromes too.