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Posted on 03/16/2009 12:13:21 AM PDT by neverdem
In my previous post I mentioned work by Pablo Debenedetti on ‘toy models’ of water. The places to look are: Buldyrev et al., PNAS 104, 20177 (2007) (here) for the solvation thermodynamics of ‘spherical’ water; and Patel et al., Biophys. J. 93, 4116 (2007) (here) and J. Chem. Phys. 128, 175102 (2008) (here) for water-explicit lattice models of proteins.
And in discussing recent work on the mechanism of urea-induced protein denaturation, I neglected to mention Bruce Berne’s PNAS paper from late last year with Ruhong Zhou, Dave Thirumalai and Lan Hua (105, 16928; paper here). That paper on MD simulations for lysozyme anticipated the more recent work showing that denaturation seems to be caused by direct urea-protein interactions: the urea displaced water from the first hydration shell and penetrates into the hydrophobic core to give a ‘dry globule’.
The notion that protein dynamics are ‘slaved’ to those of the hydration shell has been floating around for some time now. Hans Frauenfelder and colleagues have now brought considerable focus to the idea (PNAS doi:10.1073/pnas.0900336106; paper here) with dynamical measurements using dielectric spectroscopy, Mossbauer and neutron scattering. They find that large-scale protein motions follow the fluctuations of the solvent and are dependent on solvent viscosity. There are two classes of fluctuation in the solvent, alpha and beta, with different timescales. It seems that the former are ‘structural’ in nature and control protein shape; the latter are those to which the protein’s internal motions are slaved.
Jianxing Song at the National University of Singapore, who I met in Hangzhou, has sent me three papers on the intriguing solubilisation of ‘water-insoluble’ proteins in pure water. He and his coworkers found this effect in 2006 for a range of diverse proteins (M. Li et al., Protein Science 15, 1835 (2006) – paper here; M. Li et al., Biophys. J. 91, 4201 (2006) – paper here). They attributed it to the tendency of the ‘insoluble’ proteins to form partially folded states with many exposed hydrophobic residues, such that only a very low ionic strength is sufficient to screen out repulsive interactions and cause aggregation. In pure water, however, those electrostatic interactions remain sufficiently strong to suppress aggregation and precipitation. Jianxing has now provided an overview of this work, expanding on the importance of pH for this effect, in FEBS Letters (doi:10.1016/j.febslet.2009.02.022; paper here).
Roberto Righini at the University of Florence and colleagues have used IR spectroscopy to identify and quantify the various aqueous species that solvate the polar heads of phospholipids in bilayers (V. V. Volkov et al., J. Phys. Chem. B doi:10.1021/jp806650c; paper here). And Davide Donadio and coworkers in California have shown how electronic charge fluctuations show up in the IR spectra of water close to nonpolar surfaces (here graphite) (D. Donadio et al., J. Phys. Chem. B doi:10.1021/jp807709z; paper here). Still in that neck of the woods, Chuan-Shan Tian and Ron Shen have used sum-frequency-IR spectroscopy to sort out the nature of hydrogen-bonding at the air-water interface (JACS 131, 2791 (2009) – paper here). And Heather Allen and colleagues at Ohio State University have used this and other spectroscopic techniques to study hydration structure of the air-water interface for various divalent nitrates (M. Xu et al., J. Phys. Chem. B doi:10.1021/jp806565a; paper here).
Haiping Fang in Shanghai continues his exploration of how water and solutes can be manipulated within the confinement of carbon nanotubes. He and colleagues now show, using MD simulations, how a single charge outside a nanotube can be used to move a hydrated peptide inside it, regardless of whether the peptide itself is charged (P. Xiu et al., JACS 131, 2840 (2009) – paper here). This is due to the dipole-orientational ordering of the water molecules caused by confinement and interaction with the external charge.
There’s more, but later.
If the URL is too long, then right click. Look for "Properties." Click on that. The URL is there.
uhhh, ummm, Huh?
I like cheese.
So familiar...
Yet so strange.
In 2007 the Folding@home team at Stanford completed a molecular dynamics simulation that showed that proteins fold differently in a confined solvent. The paper is here:
http://www.pnas.org/content/104/25/10430.full.pdf+html
Folding@home has recently moved much of its research onto NVidia and ATI graphics cards, and have shown a speedup of 700 times faster. As a result, the total processing accomplished by the 400,000 systems that make up Folding@home has exceeded 5 petaFLOPS, making F@H the fastest computing effort anywhere.
MD simulations are becoming increasingly sophisticated, but the interactions inside a cell dwarf all of our imaginations and techniques.
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