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Experimentally observed conformation‐dependent geometry and hidden strain in proteins
Author(s) -
Karplus P. Andrew
Publication year - 1996
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560050719
Subject(s) - peptide , energy minimization , thermostability , geometry , chemistry , protein structure , function (biology) , crystallography , computational chemistry , mathematics , biology , evolutionary biology , enzyme , biochemistry
A database has been compiled documenting the peptide conformations and geometries from 70 diverse proteins refined at 1.75 Å or better. Analysis of the well‐ordered residues within the database shows ϕ, Ψ‐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‐Cα‐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.