Tuesday, March 13, 2007

Why are hot spots hot?

In protein-protein interactions, some residues do nearly all the work. These 'hot spots' are apparently responsible for most of the binding energy, something that becomes apparent if they are mutated to alanine. It has been suggested that hot spots rely on being dry – sheltered from water by a surrounding ring of protective residues, called the O ring. But that idea hasn't been well tested. Now Maria Ramos and coworkers at the University of Porto in Portugal have studied it using MD simulations (see paper here). They find that indeed hot (and 'warm') spots in the interaction of an immunoglobulin and a lysozyme do seem to be relatively inaccessible to water. Moreover, the water molecules that do get past the O ring have relatively short residence times, much the same as those of bulk water – they don't particularly want to be there.

Greg Voth and his coworkers have a paper in JACS looking at proton transport in cytochrome c oxidase. It has been suggested that a proton is held in a 'trap' in the bovine form of this enzyme before being transported once a residue elsewhere is deprotonated. Voth and colleagues show that this process happens for a bacterial cytochrome c oxidase (Rhodobacter sphaeroides) too, and that it depends on a hydrogen-bonded network of about five water molecules that is somewhat comparable to the proton-release and transport complex found in bacteriorhodopsin (see Garczarek & Gerwert, Nature 439, 109; 2006).

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