Verification of protein structures: Patterns of nonbonded atomic interactions
Tóm tắt
A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interactions is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods.
Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise interactions from nine‐residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded interactions from each window.
Từ khóa
Tài liệu tham khảo
Curmi P.M.G., 1992, Crystal structure of the unactivated form of ribulose‐1,5‐bisphosphate carboxylase/oxygenase from tobacco refined at 2.0‐Å resolution, J. Biol. Chem., 267, 16980, 10.1016/S0021-9258(18)41881-9
Fitzgerald P.M.D., 1990, Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl‐pepstain at 2.0 Å resolution, J. Biol. Chem., 265, 14209, 10.1016/S0021-9258(18)77288-8
Schreuder H.A., 1990, The RuBisCO saga—Accuracy and reliability of macromolecular crystal structures, Proc. CCP4 Study Weekend, 26–27 January, 1990, 73
Wilmanns M(1990). Ph.D. Thesis University of Basel Basel Switzerland.