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Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations
Author(s) -
Jiang Zhongming,
Biczysko Malgorzata,
Moriarty Nigel W.
Publication year - 2018
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25451
Subject(s) - ramachandran plot , plot (graphics) , orientation (vector space) , quantum chemical , energy landscape , computation , chemistry , crystallography , computational chemistry , geometry , quantum , space (punctuation) , molecular geometry , physics , molecular physics , chemical physics , protein structure , molecule , quantum mechanics , thermodynamics , mathematics , algorithm , computer science , biochemistry , statistics , operating system
Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly‐peptide molecular models can predict accurate geometries for any well‐defined backbone Ramachandran orientation. For conformations along transition regions—ϕ from −60 to 60°—a very good agreement with representative high‐resolution experimental X‐ray (≤1.5 Å) protein structures is obtained for both backbone C −1 ‐N‐C α angle and the nonbonded O −1 …C distance, while “standard geometry” leads to the “clashing” of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high‐energy or unusual regions.