Abstract
We use molecular dynamics to simulate recent neutron scattering experiments on aqueous solutions of N-acetyl-leucine-amide and N-acetyl-glutamine-amide, and break down the total scattering function into contributions from solute-solute, solute-water, water-water, and intramolecular correlations. We show that the shift of the main diffraction peak to smaller angle that is observed for leucine, but not for glutamine, is attributable primarily to alterations in water-water correlations relative to bulk. The perturbation of the water hydrogen-bonded network extends roughly two solvation layers from the hydrophobic side chain surface, and is characterized by a distribution of hydrogen bonded ring sizes that are more planar and are dominated by pentagons in particular than those near the hydrophilic side chain. The different structural organization of water near the hydrophobic solute that gives rise to the inward shift in the main neutron diffraction peak under ambient conditions may also provide insight into the same directional shift for pure liquid water as it is cooled and supercooled.
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- Caflisch A., Karplus M. Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1746–1750. doi: 10.1073/pnas.91.5.1746. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Daggett V., Levitt M. A model of the molten globule state from molecular dynamics simulations. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):5142–5146. doi: 10.1073/pnas.89.11.5142. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Daggett V., Levitt M. Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol. 1993 Jul 20;232(2):600–619. doi: 10.1006/jmbi.1993.1414. [DOI] [PubMed] [Google Scholar]
- Dill K. A. Dominant forces in protein folding. Biochemistry. 1990 Aug 7;29(31):7133–7155. doi: 10.1021/bi00483a001. [DOI] [PubMed] [Google Scholar]
- Dunbrack R. L., Jr, Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol. 1994 May;1(5):334–340. doi: 10.1038/nsb0594-334. [DOI] [PubMed] [Google Scholar]
- Head-Gordon T. Is water structure around hydrophobic groups clathrate-like? Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8308–8312. doi: 10.1073/pnas.92.18.8308. [DOI] [PMC free article] [PubMed] [Google Scholar]
- KAUZMANN W. Some factors in the interpretation of protein denaturation. Adv Protein Chem. 1959;14:1–63. doi: 10.1016/s0065-3233(08)60608-7. [DOI] [PubMed] [Google Scholar]
- Li A., Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol. 1996 Mar 29;257(2):412–429. doi: 10.1006/jmbi.1996.0172. [DOI] [PubMed] [Google Scholar]
- Pertsemlidis A., Saxena A. M., Soper A. K., Head-Gordon T., Glaeser R. M. Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10769–10774. doi: 10.1073/pnas.93.20.10769. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stillinger F. H. Water revisited. Science. 1980 Jul 25;209(4455):451–457. doi: 10.1126/science.209.4455.451. [DOI] [PubMed] [Google Scholar]
- Stillinger F. H., Weber T. A. Packing structures and transitions in liquids and solids. Science. 1984 Sep 7;225(4666):983–989. doi: 10.1126/science.225.4666.983. [DOI] [PubMed] [Google Scholar]