Experimentally observed conformation-dependent geometry and hidden strain in proteins

被引:221
作者
Karplus, PA [1 ]
机构
[1] OREGON STATE UNIV, DEPT BIOCHEM & BIOPHYS, CORVALLIS, OR 97331 USA
关键词
amino acids; conformational energetics; local geometry; peptide geometry; protein folding; protein stability; protein structure; Ramachandran plot;
D O I
10.1002/pro.5560050719
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A database has been compiled documenting the peptide conformations and geometries from 70 diverse proteins refined at 1.75 Angstrom or better. Analysis of the well-ordered residues within the database shows phi,psi-distributions that have more fine structure than is generally observed. Also, clear evidence is presented that the peptide covalent geometry depends on conformation, with the interpeptide N-C alpha-C bond angle varying by nearly +/-5 degrees from its standard value. The observed deviations from standard peptide geometry are greatest near the edges of well-populated regions, consistent with strain occurring in these conformations. Minimization of such hidden strain could be an important factor in thermostability of proteins. These empirical data describing how equilibrium peptide geometry varies as a function of conformation confirm and extend quantum mechanics calculations, and have predictive value that will aid both theoretical and experimental analyses of protein structure.
引用
收藏
页码:1406 / 1420
页数:15
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