Friday, October 22, 2010

Pores for thought

Two papers in Science look at the mechanics of proton conduction in the M2 pore of influenza viruses (F. Hu et al., Science 330, 505-508; M. Sharma et al., Science 330, 509-512; 2010 – papers here and here). Hu et al. say that the key is whether a complex of histidine groups (His37) in the tetrameric pore is or is not in contact with a water chain threading the pore, which changes in a pH-dependent manner. Previously it has been controversial whether the His37 group participates in an active fashion by protonation/deprotonation or merely alters the channel diameter electrostatically. Hu et al. say that the latter does happen, but is accompanied by increased rotational freedom of the His imidazole group to make contact with the ‘water wire’ and relay a hopping proton. Sharma et al. could be said to refine this picture by considering the interactions between all the His37s in the tetramer and their relation to the adjacent Trp41 residues. They say that the proton-conducting state is activated at low pH by ‘unlocking’ of the imidazole group in a way that is gated by Trp41 via pi-cation interactions.

More pores. Not all aquaporins are selective for water only – some will admit glycerol and other alcohols. David Savage at UCSF and colleagues have determined their X-ray crystal structures to figure out what determines the selectivity (D. Savage et al., PNAS 10.1073/pnas.1009864107 – paper here). The details are complex, but the basic features arguably those one might expect: in the region of the pore’s selectivity filter, the energetics of water transport are controlled by channel hydrophilicity, while selectivity for larger molecules such as glycerol is steric, governed by channel width.

Some other protein pores will also allow water and other small molecules to pass, such as the sodium-glucose cotransporter, which permits water flow in the presence of Na+ or glucose. This class of proteins allows passive water flow in the presence of an osmotic Na+ or glucose gradient, but also flow against such a gradient if Na+ or glucose is present. To what extent, then, is such flow passive, and to what extent actively pumped in the presence of these solutes? Michael Grabe at the University of Pittsburgh and colleagues investigate that question using MD simulations (S. Choe et al., Biophys. J. 99, L56-L58; 2010 – paper here). They find that water will pass through the sodium-dependent galactose cotransporter vSGLT both in the absence and the presence of galactose. In the former case the flow is passive (and occurs through the galactose-binding region), but that in the latter case the release of galactose ‘pushes’ water molecules through the pore in the same direction as its exit – as the authors put it, galactose acts as a Brownian piston that rectifies the passive water motion through the pore.

Comparable rectification of proton motion through a proton pumps such as bacteriorhodopin, resulting in a ‘proton diode’, is described by Klaus Gerwert and colleagues at Bochum (S. Wolf et al., Angew. Chem. Int. Ed. 49, 6889-6893; 2010 – paper here). This team draw on their detailed investigations of bR over recent years, and new studies of point mutations, to explain how conformational changes in a few residues can control access between internally bound and external water molecules in such a way as to bias the direction of proton flow in a general mechanism that they suspect might be more general to other proton pumps.

Biological processes involving proton motion are prime candidates for manifesting quantum-mechanical effects. A rather striking instance of this is claimed by George Reiter of the University of Houston and colleagues, who say that the zero-point motions of protons in are entirely responsible for the binding of water to A-DNA (G. Reiter et al., Phys. Rev. Lett. 105, 148101; 2010 – paper here). Changes in hydration seem to be what drive the A-to-B transition in DNA (the A phase forms in dehydrated conditions), and Reiter et al. say that this is accompanied by a change in the zero-point kinetic energy of the protons in the hydrated B-DNA that is sufficient in itself to motivate the transition. Whether the protons concerned are those of water molecules in the hydration shell or those in the DNA’s H-bonds (or, presumably, a bit of both) is not yet clear.

It’s many years ago now that David Tirrell, now at Caltech, developed ways to incorporate fluorinated amino acids into proteins using recombinant DNA technology – a feat popularized with reference to non-stick fried eggs. David has now teamed up with Ahmed Zewail and colleagues to investigate what fluorinated residues do to the hydration of such proteins, using ultrafast time-dependent fluorescent Stokes shift spectroscopy on fluorinated coiled-coil peptides (O.-H. Kwon et al., PNAS 10.1073/pnas.1011569107 – paper here). They find that the hydration dynamics are retarded around fluorinated residues, in marked contrast to an acceleration of the dynamics for the corresponding cases of hydrogenated residues, which are of comparable size.

Some mini-proteins, such as the villin headpiece domains HP35 and HP36, with just 35 and 36 residues, have an unusual ability to fold quickly into a conformation with a securely buried hydrophobic core despite their small size. Takao Yoda of the Nagahama Institute of Bio-science and Technology and colleagues have used simulations to investigate how this happens (T. Yoda et al., Biophys. J. 99, 1637-1644; 2010 – paper here). The cores in the folded state are fully dehydrated, but some water molecules remain therein until the final stages of folding. This is an unusually large system for which the folding process has been followed in detail from a fully extended state in explicit solvent. Meanwhile, David Cerutti at Rutgers and coworkers have simulated the crystal structures of a scorpion toxin protein to probe the performance of different protein and water force-field models in predicting the observed structure (D. S. Cerutti et al., J. Phys. Chem. B 114, 12811-12824; 2010 – paper here). They find that the results are not very sensitive to the water model, and far more dependent on the protein model (FF99SB does best) in terms of correctly predicting the right contacts in the peptide chain.

Whether we can understand the various forces involved in protein folding sufficiently to design peptides and other heteropolymers to adopt specific conformations is of course one of the big challenges not only for protein design but for polymer chemistry more generally. Shekhar Garde and colleagues at RPI have studied how water-mediated interactions might be exploited in this endeavour (S. N. Jamadagni et al., J. Phys. Chem. B jp104924g – paper here). In particular, they explore the sequence space of model polymers containing one or two pairs of charged monomers, in cases where the other monomers are more or less hydrophobic, and at the effect of adding salt to such systems. The results reveal subtle factors at play: for example, ion pairs among hydrophobic monomers can stabilize hairpin conformations over collapsed globules via water-mediated Coulombic interactions, but this depends on where the charged monomers appear along the chain. And adding salt can open up these hairpins, whereas salt stabilizes the globular forms of hydrophobic homopolymers.

Some membrane-binding proteins induce curvature of the membrane (see H. T. McMahon & J. L. Gallop, Nature 438, 590; 2005) – for example, the so-called BAR domain of amphiphysin will remodel lipid vesicles into tubules. Greg Voth and colleagues have performed MD simulations to try to figure out how this works, and they find that, surprisingly, there is a layer of water intervening between BAR and the membrane even when the protein domain is strongly bound (E. Lyman et al., Biophys. J. 99, 1783-1790; 2010 – paper here). This implies that the charged region of BAR is screened from the lipid headgroups, so that the bending mechanism is not electrostatic.

How homogeneous are solutions of denaturing guanidinium salts? Recently, Mason and coworkers have reported evidence that the cations form nanoscale aggregates (e.g. P. E. Mason et al., PNAS 100, 4557; 2003). Using dielectric relaxation spectroscopy, Richard Buchner of the University of Regensburg question this conclusion (J. Hunger et al., J. Phys. Chem. B jp101520h – paper here). In other words, perhaps after all Gdm+ ions can ‘fit’ comfortably into the structure of bulk water without altering it – which would seem to support the ‘direct’ mechanism of denaturation whereby Gdm+ interacts with the protein backbone rather than loosening up the folded state by influencing hydration.

More evidence for the direct intermediation of water in enzyme action: Sason Shaik at the Hebrew University of Jerusalem and colleagues say that a water cluster in the binding site of heme oxygenase participates in its ring-opening degradation of heme groups (W. Lai et al., JACS 132, 12960-12970; 2010 – paper here). The water cluster organizes the substrate into the proper geometry, serves as a proton shuttle, and stabilizes the hydroxyl nucleophile that attacks the ring. And Dongping Zhong at Ohio State University and colleagues say that flavoproteins, which act as redox coenzymes, contain water networks in the active site with fast relaxation dynamics that probably controls the protein flexibility in a functionally relevant manner (C.-W. Chang et al., JACS 132,12741-12747; 2010 – paper here). Meanwhile, Peter Brzezinski at Stockholm University and colleagues offer evidence that water molecules are involved in proton transport through cytochrome c oxidase, which actively pumps protons across a membrane to sustain a proton-motive force for ATP synthesis (H. J. Lee et al., JACS ja107244g – paper here).

Mischa Bonn of the FOM Institute AMOLF in Amsterdam and colleagues say that the hydration region of lipid headgroups in monolayers contains two populations of water molecules, one with bulk-like relaxation and the other that relaxes faster (M. Bonn et al., JACS ja106194u – paper here). Their VSF spectroscopic measurements thus imply the presence of a group of water molecules that are strongly hydrogen-bonded to the headgroups, decoupled from the bulk, and potentially involved in rapid, in-plane proton transfer, as previous studies have suggested for lipid membranes.

How does the hydration of antifreeze proteins differ from that of regular proteins? Ann McDermott and colleagues at Columbia use NMR methods to study this question by investigating the hydration shells of ubiquitin and an ice-binding (type III) antifreeze protein at cryogenic temperatures (-35 C) (A. B. Siemer et al., PNAS 10.1073/pnas.1009369107 – paper here). They find that the ubiquitin hydration shell remains unfrozen and uncoupled to the ice lattice, whereas this is true of only parts of the AFP III shell: as one might expect, the ice-binding interface establishes direct contact with ice.

The ability of sufficiently narrow carbon nanotubes to admit water but exclude ions has been proposed as a basis for desalination technologies. But Daejoong Kim and coworkers at Sogang University in South Korea show that admission or exclusion of ions can be a subtle business. They say that at certain nanotube diameters, strong sodium hydration can lead to a preferential admission of potassium ions over sodium in mixed ionic solutions, while at other diameters sodium can be preferred, or that both ions can be increasingly excluded even as the tube diameter increases (J. J. Cannon et al., J. Phys. Chem. B jp104609d – paper here). So it is conceivable that selective filtration and separation might be achieved. It seems quite conceivable that Ilan Benjamin’s new analysis of the hydration of alkali-metal halides in hydrophobic environments, and the formation of ion pairs (J. Phys. Chem. B jp1050673 – paper here), might be relevant here to the state inside the nanotubes.

Finally, bulk water, and a suggestion that the structural picture here is still not fully resolved. Peter Hamm at the University of Freiburg and colleagues use the theoretical tools developed for the study of complex networks (such as those in social science) to reveal hidden topological aspects of the H-bonded network in MD simulations of liquid water (F. Rao et al., J. Phys. Chem. B jp1060792 – paper here). They say this approach reveals structural inhomogeneities, extending at least to the second hydration shell, that are not evident from methods that focus on a single scalar order parameter such as tetrahedrality. Needless to say, the same technique might be used to look at solute hydration shells.

2 comments:

Carl said...

Brilliant to read about the Comparable rectification of proton motion,the type of information given in this blog is just magnificent.

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Biology Dissertation

Graduate Dissertation Writing Concerns said...

This is such an ordinary peace of work about water and biology and lots of book have been wrote on it.

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