The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
Hydrophobicity of protein surfaces: Separating geometry from chemistry
Open accessAbstract
To better understand the role of surface chemical heterogeneity in natural nanoscale hydration, we study via molecular dynamics simulation the structure and thermodynamics of water confined between two protein-like surfaces. Each surface is constructed to have interactions with water corresponding to those of the putative hydrophobic surface of a melittin dimer, but is flattened rather than having its native “cupped” configuration. Furthermore, peripheral charged groups are removed. Thus, the role of a rough surface topography is removed, and results can be productively compared with those previously observed for idealized, atomically smooth hydrophilic and hydrophobic flat surfaces. The results indicate that the protein surface is less hydrophobic than the idealized counterpart. The density and compressibility of water adjacent to a melittin dimer is intermediate between that observed adjacent to idealized hydrophobic or hydrophilic surfaces. We find that solvent evacuation of the hydrophobic gap (cavitation) between dimers is observed when the gap has closed to sterically permit a single water layer. This cavitation occurs at smaller pressures and separations than in the case of idealized hydrophobic flat surfaces. The vapor phase between the melittin dimers occupies a much smaller lateral region than in the case of the idealized surfaces; cavitation is localized in a narrow central region between the dimers, where an apolar amino acid is located. When that amino acid is replaced by a polar residue, cavitation is no longer observed.
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Cites
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Water is an active matrix of life for cell and molecular biology
Ball, P. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1703781114 · Cited by 484
Instantaneous Liquid Interfaces
Willard, A. P., & Chandler, D. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp909219k · Cited by 462
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Snyder, P. W., Mecinović, J., Moustakas, D. T., Thomas, S. W., Harder, M., Mack, E. T., Lockett, M. R., Héroux, A., Sherman, W., & Whitesides, G. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1114107108 · Cited by 357
Water in Cavity−Ligand Recognition
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Metadata
- Authors
- Giovambattista, N., Lopez, C. F., Rossky, P. J., & Debenedetti, P. G.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2008-02-19
- Volume
- 105
- Issue
- 7
- Pages
- 2274-2279
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2029375222
- Cited by
- 260
- References
- 35
- FWCI
- 12.11
- Type
- journal article
- Language
- en
- Open access
- green
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- Giovambattista, N., Lopez, C. F., Rossky, P. J., & Debenedetti, P. G. (2008). Hydrophobicity of protein surfaces: Separating geometry from chemistry. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0708088105
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