Abstract
The radial distributions of the Calpha and side-chain atoms in a sample of 13 native proteins have been examined. It is found that there are substantial differences in behavior between different atoms of the same amino acid. In particular, the Calpha atoms of polar residues show no particular preference for being far from the center of mass. In light of these results, a new criterion for hydrophobicity and hydrophilicity is proposed--namely, the orientational preference of the side chain. The distribution of this property is shown, and it is suggested that this provides a basis for incorporating hydrophobic interactions into a protein folding algorithm.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature. 1974 Mar 22;248(446):338–339. doi: 10.1038/248338a0. [DOI] [PubMed] [Google Scholar]
- Chothia C. Structural invariants in protein folding. Nature. 1975 Mar 27;254(5498):304–308. doi: 10.1038/254304a0. [DOI] [PubMed] [Google Scholar]
- Chothia C. The nature of the accessible and buried surfaces in proteins. J Mol Biol. 1976 Jul 25;105(1):1–12. doi: 10.1016/0022-2836(76)90191-1. [DOI] [PubMed] [Google Scholar]
- Kuntz I. D., Crippen G. M., Kollman P. A., Kimelman D. Calculation of protein tertiary structure. J Mol Biol. 1976 Oct 5;106(4):983–994. doi: 10.1016/0022-2836(76)90347-8. [DOI] [PubMed] [Google Scholar]
- Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
- Némethy G., Scheraga H. A. Protein folding. Q Rev Biophys. 1977 Aug;10(3):239–252. doi: 10.1017/s0033583500002936. [DOI] [PubMed] [Google Scholar]
- Shrake A., Rupley J. A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol. 1973 Sep 15;79(2):351–371. doi: 10.1016/0022-2836(73)90011-9. [DOI] [PubMed] [Google Scholar]
- Tanaka S., Scheraga H. A. Hypothesis about the mechanism of protein folding. Macromolecules. 1977 Mar-Apr;10(2):291–304. doi: 10.1021/ma60056a015. [DOI] [PubMed] [Google Scholar]
- Tanaka S., Scheraga H. A. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules. 1976 Nov-Dec;9(6):945–950. doi: 10.1021/ma60054a013. [DOI] [PubMed] [Google Scholar]