Wednesday, March 12, 2014

Weird antifreeze


The oddest finding I’ve seen recently has to be the crystal structure of the fish antifreeze protein Maxi reported by Peter Davies of the Queen’s University in Kingston, Canada, and colleagues (T. Sun et al., Science 343, 795; 2014 – paper here). This is a four-helix bundle with an interior, mostly hydrophobic channel filled with more than 400 water molecules, crystallographically ordered into a clathrate-like network of mostly five-membered rings. It seems that this ordered network extends outward through the gaps between the helices, helping to create an ordered later of water molecules on the outer surface that enables Maxi to bind to ice crystals and hinder their growth. Commenting on this work, Gerhard Hummer has called the water network a kind of molecular Velcro that holds the coils together. I have described this work in more detail in a news story for Chemistry World.

Water molecules buried deep within a protein’s interior can have extremely slow dynamics. That fact acquires functional significance in potassium channels, according to Marc Baldus of Utrecht University and coworkers (M. Weingarth et al., JACS 136, 2000; 2014 – paper here). These channels have remarkably slow recovery rates from the non-conductive to the conductive form, especially given that the macromolecular rearrangements involved don’t appear to be large. Using NMR and MD simulations, Baldus et al. find that there are several buried, ordered waters with long residence times behind the selectivity filter region of the channel, and that the recovery pathway involves exchange of these with bulk water.

Warren Beck and colleagues at Michigan State have used guanidinium as a probe of the coupling of a protein – here zinc-substituted cytochrome c – to its hydration shell (J. Tripathy et al., J. Phys. Chem. B 117, 14589; 2013 – paper here). They attribute the fluorescence Stokes shift response in the presence of Gdm ions to the enhanced flexibility of the protein-solvent network caused by direct binding of Gdm+ to the protein surface.

A far more idealized case of osmolyte effects on hydration is reported by Jens Smiatek of the University of Stuttgart, who considers how the hydration of charged model spheres is altered by urea and hydroxyectoine (J. Phys. Chem. B 118, 771; 2014 – paper here). The agenda here is the molecular mechanisms of so-called chaotropic and kosmotropic influences of osmolytes – whether, for example, these involve direct solute-cosolute or indirect (‘structure-making/breaking’) effects. It’s hard to generalize, however, about the results, other than perhaps to say that indirect effects seem to be minor and that the direct interactions of the cosolutes depends on the nature (here charge) of the solute surface. Smiatek concludes that the interactions are more complex than has often been assumed, and that “a general theory for kosmotropic and chaotropic behavior is far from being fully understood… [o]ne reason is the observed specific dependence on the considered solute surface characteristics.”

Similar issues are also explored by Abani Bhuyan and coworkers at the University of Hyderabad (P. Sashi et al., J. Phys. Chem. B 118, 717; 2014 – paper here). They use methanol titration to look at cosolvent effects on the alcohol-induced unfolding of cytochrome c at different pH, and thus differing degrees of side-chain ionization. They find that, with increasing protein charge, increasing amounts of water molecules are associated with the peptide chain, presumably because charge repulsion causes expansion of the folded state. Correspondingly larger amounts of hydration water are thus excluded by the methanol as the unfolding proceeds.

Specific ion (Hofmeister) effects on the diffusion of water at the hydration surface of a lipid bilayer are reported by Songi Han and colleagues at UCSB (J. Song et al., JACS 136, 2642; 2014 – paper here). They use Overhauser nuclear dynamic polarization to monitor water diffusion in the 2-3 layers close to the surface of a lipid vesicle, and find that various ions can have an accelerating or retarding effect that is in line with the Hofmeister series. They put the case nicely: “The concept of ions generally altering the bulk water structure, in the absence of molecular surfaces, does not seem plausible in explaining the effects of ions at the molecular level on surfaces in electrolyte solutions. However, it has been discussed in the literature that the ion’s effect on the local hydration water structure directly surrounding the ions can differ depending on the ion type”. That’s the case they make, and moreover propose a general mechanism: “This suggests that the origin of the Hofmeister ions may be the balancing between macromolecule−water and macromolecule− macromolecule interaction through the modulation of the effective surface hydrophilicity and hydrophobicity mediated by specific ions in dilute solution.”

Why, though, are water molecules generally retarded at lipid membrane surfaces in the first place? It has been suggested that the water molecules might form bridges between the lipid head groups that stabilize the membrane. This ideas is explored by Eiji Yamamoto and colleagues at Keio University in a preprint http://www.arxiv.org/abs/1401.7776. Their MD simulations indicate that water undergoes subdiffusion at a membrane surface due to binding and unbinding of the molecules in bridging conformations. The authors point out that these retarded dynamics of water might be biologically efficacious in increasing the efficiency of biomolecular binding reactions at the membrane.

In a water monolayer confined between two parallel graphene sheets, ions can induce the formation of long fluctuating chains of hydrogen-bonded molecules that can extend for up to 30 or so molecules, according to simulations by Petr Král and colleagues at the University of Illinois at Chicago (I. Strauss et al., JACS 136, 1170; 2014 – paper here). These chains can bridge two ions of opposite charge, and remain locked in place even at room temperature.

Water passing through carbon nanotubes has been found previously to have a high, almost frictionless flow rate and collective dynamics. Thomas Sisan and Seth Lichter at Northwestern now argue from MD simulations that, when the nanotubes are particularly narrow, this flow can occur in the form of solitons (Phys. Rev. Lett. 112, 044501; 2014 – paper here). The solitons are composed of defects in the single-file water chain that convect mass.

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