Abstract
Conformational potentials of sidechains in the bovine pancreatic trypsin inhibitor have been studied with an empirical energy function. Calculated minimumenergy positions are in excellent agreement with the x-ray structure for sidechains in the core or at the surface of the protein; as expected, angles for sidechains that are directed out into the solvent do not agree with the calculated values. The contributions to the potentials are analyzed and compared with the potentials for the free amino acid. Although there is a large restriction in the available conformational space due to nonbonded interactions, the minimum energy positions in the protein are close to those of the free amino acid; the significance of this result is discussed. To estimate the effective barriers for rotation of the aromatic rings (tyrosine and phenylalanine), calculations are done in which the protein is permitted to relax as a function of the ring orientation. Thr resulting barriers, which are much lowere than the rigid rotation barriers, are used to evaluate the rotation rates; comparison is made with the available nuclear magnetic resonance data.
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Selected References
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- 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]
- 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]
- Huber R., Kukla D., Bode W., Schwager P., Bartels K., Deisenhofer J., Steigemann W. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution. J Mol Biol. 1974 Oct 15;89(1):73–101. doi: 10.1016/0022-2836(74)90163-6. [DOI] [PubMed] [Google Scholar]
- Karplus S., Snyder G. H., Sykes B. D. A nuclear magnetic resonance study of bovine pancreatic trypsin inhibitor. Tyrosine titrations and backbone NH groups. Biochemistry. 1973 Mar 27;12(7):1323–1329. doi: 10.1021/bi00731a012. [DOI] [PubMed] [Google Scholar]
- Levitt M., Lifson S. Refinement of protein conformations using a macromolecular energy minimization procedure. J Mol Biol. 1969 Dec 14;46(2):269–279. doi: 10.1016/0022-2836(69)90421-5. [DOI] [PubMed] [Google Scholar]
- Masson A., Wüthrich K. Proton magnetic resonance investigation of the conformational properties of the basic pancreatic trypsin inhibitor. FEBS Lett. 1973 Apr 1;31(1):114–118. doi: 10.1016/0014-5793(73)80086-9. [DOI] [PubMed] [Google Scholar]
- Pullman B., Pullman A. Molecular orbital calculations on the conformation of amino acid residues of proteins. Adv Protein Chem. 1974;28:347–526. doi: 10.1016/s0065-3233(08)60233-8. [DOI] [PubMed] [Google Scholar]
- Warme P. K., Scheraga H. A. Refinement of the x-ray structure of lysozyme by complete energy minimization. Biochemistry. 1974 Feb 12;13(4):757–767. doi: 10.1021/bi00701a019. [DOI] [PubMed] [Google Scholar]