Abstract
It is shown that most present empirical prediction algorithms provide information about the conformational states of individual residues, but give little information about the three-dimensional structure of a protein. It is necessary to predict the conformational state of every residue before the resulting structure can serve as a starting conformation to compute the native structure. It is also shown that even a perfect five-state algorithm (which does not include long-range interactions from disulifide loop closing or solvation) will not lead to a globular structure resembling the native one. However, starting from the results of a perfect prediction algorithm, it appears that conformational energy minimization (with long-range interactions included) can lead to a structure having the general features of the native protein.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Chou P. Y., Fasman G. D. Prediction of protein conformation. Biochemistry. 1974 Jan 15;13(2):222–245. doi: 10.1021/bi00699a002. [DOI] [PubMed] [Google Scholar]
- Gibson K. D., Scheraga H. A. Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide. Proc Natl Acad Sci U S A. 1967 Aug;58(2):420–427. doi: 10.1073/pnas.58.2.420. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lim V. I. Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins. J Mol Biol. 1974 Oct 5;88(4):873–894. doi: 10.1016/0022-2836(74)90405-7. [DOI] [PubMed] [Google Scholar]
- Ponnuswamy P. K., Warme P. K., Scheraga H. A. Role of medium-range interactions in proteins. Proc Natl Acad Sci U S A. 1973 Mar;70(3):830–833. doi: 10.1073/pnas.70.3.830. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Robson B., Pain R. H. Analysis of the code relating sequence to conformation in globular proteins. Development of a stereochemical alphabet on the basis of intra-residue information. Biochem J. 1974 Sep;141(3):869–882. doi: 10.1042/bj1410869. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rühlmann A., Schramm H. J., Kukla D., Huber R. Pancreatic trypsin inhibitor (Kunitz). II. Complexes with proteinases. Cold Spring Harb Symp Quant Biol. 1972;36:148–150. [PubMed] [Google Scholar]