Why cell fluid is lumpy

How homogeneous is the cytoplasm? There is increasing evidence that proteins in concentrated solution form relatively long-lived clusters. Wilson Poon and his colleagues showed in 2004 that this effect, previously rather anecdotal, is real and general, applying to colloidal particles as well as proteins (Stradner et al., Nature 432, 492; 2004). They showed using small-angle X-ray and neutron scattering that lysozyme forms clusters of about 3-10 molecules at volume fractions of between 0.05 and 0.2, which they say are equilibrium structures resulting from the interplay of short-ranged attractive (van de Waals) and electrostatic repulsive forces. Now Peter Vekilov at Houston and his coworkers broadly support that notion by looking at concentrated solution of bacterial lumazine synthase using light scattering (Gliko et al., J. Phys. Chem. B 111, 3106; 2007). They see clusters with lifetimes of around 10 s and a mean radius of about 350 nm (individual molecules are bout 15.6 nm in diameter). Changing the protein concentration changes the cluster concentration (which can reach a volume fraction of 0.001), but not the cluster size. But Velikov et al. say that cluster formation and size is dominated by kinetics, not thermodynamics: these clusters are metastable with respect to both protein crystals (i.e. in supersaturated solution) and to well-dispersed solution.

All of this recalls the flurry of interest in clustering excited by the work of Geckeler and Samal on C60 (Chem. Comm. 2001, 2224), which was rather breathlessly touted as a possible mechanism for homeopathy. That work was truly odd, as it seemed to suggest that the cluster size increased with increasing dilution. I’m not aware that the result has been reproduced. Needless to say, the homeopathy connection makes no sense (at best, you get a few ‘active’ bottles and the vast majority containing just water); but at the very least, there’s no reason to regard clustering per se as perplexing or odd.

The question of a vapour gap at the interface of water and a hydrophobic surface, and its relation to the long-ranged hydrophobic attraction, seems to be resolving itself. It seems now that a very thin depletion layer exists. But the role of dissolved gases in forming nanobubbles remains to be fully resolved (see ‘Why does water do that’ below). They have been seen by various methods, but with the proviso that they could possibly be an artefact of the probe technique, and that they haven’t been shown definitively to be gaseous anyway. Also, small nanobubbles should have a small radius of curvature and thus a large Laplace pressure, promoting their dissolution. William Ducker and colleagues at the University of Melbourne have now shown that flat gas bubbles, about 5-80 nm thick and 4 microns across, can exist at such a hydrophobic interface for over an hour (Phys. Rev. Lett. 98, 136101; 2007). This size means that the internal pressure is barely above atmospheric. But the bubbles form only when a particular protocol is followed for introducing the gas layer (carbon dioxide): in other words, “the presence of the gas phase depends on the previous history of the interface.”

Ivan Brovchenko and colleagues recently linked the low-hydration polymorphic transitions of B-DNA to the presence (or not) of a fully connected (percolating) network of water molecules in the hydration sphere (Brovchenko et al., Phys. Rev. Lett. 97, 137801; 2006). They’ve now extended that work by looking at the percolation transition for both B- and A-DNA (Brovchenko et al., J. Phys. Chem. B 111, 3258; 2007). Although the percolation thresholds (that is, the surface coverage of water on the DNA molecules) are virtually identical, the mechanisms are quite different in each case: the threshold corresponds to the appearance of a spanning water network in the major groove of B-DNA, but the minor groove of A-DNA. It isn’t clear, then, whether the near-coincidence of the two thresholds is indeed just coincidence or has some deeper physical cause. In any event, there are also insights here into how ions can alter the hydrogen-bonding patterns and thus shift the thresholds.

Water seems to play an important role in electron transfer between some protein redox centres – this was discussed nicely by Gray & Winkler recently (PNAS 102, 3534; 2005). They enumerated the various ways, direct and indirect, that water might facilitate electron hopping. Agostino Migliore and colleagues in Modena have now used ab initio calculations for the copper active sites of azurin to figure out how water-mediated pathways are functioning in this case (Migliore et al., J. Phys. Chem. B, advance online publication, doi:10.1021/jp068773i). But it’s a complicated picture that emerges, in which no one physical pathway seems to be responsible for what is observed. Sorry, but it’s hard to put this one into more of a nutshell than that.

Finally, and perhaps even more cryptically, I want to flag up a paper by Bruce Berne and colleagues in JACS ASAP (doi:10.1021/ja068305m) on the effect of ions on the hydrophobic interaction between two plates. This complements Berne’s recent study of much the same thing for hydrophobic particles (J. Phys. Chem. B 110, 22736; 2006). The phenomenon is of course intimately related to salting-in/out and Hofmeister effects, and as such, contains a lot of important information on the effect of electrolytes on protein aggregation and folding. So there’s a lot of good stuff here to digest, and I’m not going to manage that in a hurry without risking indigestion (or more probably, misapprehension). Worth spending time on.