Getting up to date

I don’t like to do this, but a combination of holidays and a glut of papers means that, in order to have any chance of getting this blog up to date, I am going to have to provide a mere listing of relevant papers here, without further comment or explanation. I hope that the titles will speak for themselves; there is a wealth of nice stuff here. Normal service will be resumed as the days draw in.

1. PNAS advance online publication
Burst analysis spectroscopy: A versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies
Jason Puchalla, Kelly Krantz, Robert Austin and Hays Rye
(Paper here).

2. J. Phys. Chem. B 112, 11106–11111, 2008. 10.1021/jp803956s
Hydrophobic Interactions in Urea_Trimethylamine-N-oxide Solutions
Sandip Paul and G. N. Patey
(Paper here).

3. J. Am. Chem. Soc. 10.1021/ja8021297
Interfacial structure of acidic and basic aqueous solutions
C. Tian et al.
(Paper here).

4. J. Phys. Chem. B 112, 11440-11445, 2008. 10.1021/jp803819a
Anomalously increased lifetimes of biological complexes at zero force due to the protein-water interface.
Y. V. Pereverzev et al.
(Paper here).

5. J. Phys. Chem. B 112, 11396-11401, 2008. 10.1021/jp8015886
Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding
Y. Ding et al.
(Paper here).

6. J. Am. Chem. Soc. 130, 11854-11855, 2008. 10.1021/ja803972g
Chemical denaturants inhibit the onset of dewetting.
J. L. England et al.
(Paper here).

7. J. Am. Chem. Soc. 10.1021/ja8034027
Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations.
D. R. Nutt & J. C. Smith.
(Paper here).

8. J. Phys. Chem. B 112, 10786–10790, 2008. 10.1021/jp804694u
Polarization of Water in the First Hydration Shell of K+ and Ca2+ Ions
Denis Bucher and Serdar Kuyucak
(Paper here).

9. ASAP J. Phys. Chem. B ASAP Article, 10.1021/jp802795a
Hydration Water and Bulk Water in Proteins Have Distinct Properties in Radial Distributions Calculated from 105 Atomic Resolution Crystal Structures
Xianfeng Chen, Irene Weber and Robert W. Harrison
(Paper here).

10. ASAP J. Phys. Chem. B ASAP Article, 10.1021/jp711924f
Trapped Water Molecule in the Charge Separation of a Bacterial Reaction Center
Nikolai Ivashin and Sven Larsson
(Paper here).

11. J. Am. Chem. Soc. 130, 11582–11583, 2008. 10.1021/ja803274p
Specific Ion Binding to Nonpolar Surface Patches of Proteins
Mikael Lund, Lubos_ Vrbka and Pavel Jungwirth
(Paper here).

12. J. Am. Chem. Soc. 130, 11578–11579, 2008. 10.1021/ja802341q
Dissecting Entropic Coiling and Poor Solvent Effects in Protein Collapse
Frauke Gräter, Pascal Heider, Ronen Zangi and B. J. Berne
(Paper here).

13. ASAP J. Am. Chem. Soc. ASAP Article, 10.1021/ja8022434
Electron Capture by a Hydrated Gaseous Peptide: Effects of Water on Fragmentation and Molecular Survival
James S. Prell, Jeremy T. O’Brien, Anne I. S. Holm, Ryan D. Leib, William A. Donald and Evan R. Williams
(Paper here).

14. ASAP J. Chem. Theory Comput. ASAP Article, 10.1021/ct800121e
Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach
Fabio Sterpone, Leonardo Spanu, Luca Ferraro, Sandro Sorella and Leonardo Guidoni
(Paper here).

15. J. Am. Chem. Soc. 129, 2504 -2510, 2007. 10.1021/ja0659370 S0002-7863(06)05937-3
Effect of Field Direction on Electrowetting in a Nanopore
Dusan Bratko, Christopher D. Daub, Kevin Leung and Alenka Luzar
(Paper here).

16. J. Chem. Phys. 127, 174515 (2007); DOI:10.1063/1.2784555
Investigations on the structure of dimethyl sulfoxide and acetone in aqueous solution
S. E. McLain, A. K. Soper and A. Luzar
(Paper here).

(These latter two are older ones I’ve just discovered.)

17. Faraday Discussions 141, 1-12, 2008
Water-mediated ordering of nanoparticles in an electric field
D. Bratko, C. D. Daub & A. Luzar
Not yet on the web; doi:10.1039/b809135h

18. Biophysical Journal 95, 2916-2923, 2008
Hydration Affects Both Harmonic and Anharmonic Nature of Protein Dynamics
H. Nakagawa , Y. Joti , A. Kitao and M. Kataoka
(Paper here).

19. Langmuir 24, 9183–9188, 2008. 10.1021/la8014578
Teflon is Hydrophilic. Comments on Definitions of Hydrophobic, Shear versus Tensile Hydrophobicity, and Wettability Characterization
Lichao Gao and Thomas J. McCarthy
(Paper here).

20. PNAS 105, 12725-12729, 2008
NMR evidence of a sharp change in a measure of local order in deeply supercooled confined water
F. Mallamace, C. Corsaro, M. Broccio, C. Branca, N. González-Segredo, J. Spooren, S.-H. Chen & H. E. Stanley
(Paper here).

21. PNAS 105, 13391-13396, 2008
Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy
T. Kimura, A. Maeda, S. Nishiguchi, K. Ishimori, T. Konno, Y. Goto & S. Takahashi
(Paper here).

22. J. Chem. Phys. 129, 034504, 2008
POLIR: Polarizable, flexible, transferable water potential optimized for IR spectroscopy
P. K. Mankoo & T. Keyes
(Paper here).

23. JACS 130, 9025-9030, 2008
Combined electrostatics and hydrogen bonding determine intermolecular interactions between polyphosphoinositides
I. Levental, A. Cebers & P. A. Janmey
(Paper here).

24. J. Phys. Chem. B 112, 5500-5511, 2008
Operation of the proton wire in green fluorescent protein. A quantum dynamics simulation
O. Vendrell, R. Gelabert, M. Moreno & J. M. Lluch
(Paper here).

25. PNAS 105, 9233-9237, 2008
A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function
A. E. Kister & J. C. Phillips
(Paper here).

26. J. Phys. Chem. B 112, 9532-9539, 2008
Effect of the air-water interface on the structure of lysozyme in the presence of guanidinium chloride
A. W. Perriman, M. J. Henderson, C. R. Evenhuis, D. J. McGillivray & J. W. White
(Paper here).

27. JACS 130, 10939-10946, 2008
Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides
A. Valiaev, D. W. Lim, S. Schmidler, R. L. Clark, A. Chilkoti & S. Zauscher
(Paper here).

28. J. Phys. Chem. B 112, 10158-10164, 2008
Do probe molecules influence water in confinement?
B. Baruah, L. A. Swafford, D. C. Crans & N. E. Levinger
(Paper here).

29. J. Phys. Chem. B 112, 7702-7705, 2008
Stepwise hydration of protonated proline
C. Michaux, J. Wouters, E. A. Perpète & D. Jacquemin
(Paper here).

30. J. Phys. Chem. B 112, 7157-7161, 2008
Anion fractionation and reactivity at air/water:methanol interfaces. Implications for the origin of Hofmeister effects.
J. Cheng, M. R. Hoffmann & A. J. Colussi
(Paper here).

31. J. Phys. Chem. B 112, 7810-7815, 2008
Two-particle entropy and structural ordering in liquid water
J. Zielkiewicz
(Paper here).

32. PNAS 105, 7456-7461, 2008
Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
C.-E. A. Chang, W. A. McLaughlin, R. Baron, W. Wang & J. A. McCammon
(Paper here).

33. Mol. Phys. 106, 485-495, 2008
The distribution of acceptor and donor hydrogen-bonds in bulk liquid water
O. Markovitch & N. Agmon
(Paper here).

Some meeting news:
Alenka Luzar is organizing a session at Pacifichem 2010 that hits the bullseye of all the topics I try to cover here; see here.

And finally, a real oddity:
Geophys. Res. Lett. 35, L16710, doi:10.1029/2008GL034288, 2008
Magnetic effect on CO2 solubility in seawater: A possible link between geomagnetic field variations and climate
Alexander Pazur& Michael Winklhofer
(Paper here).
This looks at face value irrelevant to water in biology, except that if these weak-field effects are seen for seawater, would one not expect them for blood and cytoplasm? And in that case, would significant changes in air and CO2 solubility not be expected to have profound physiological implications? And am I therefore right to be deeply sceptical?