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Berkholz DS , Shapovalov MV , Dunbrack RL , Karplus PA
Conformation Dependence of Backbone Geometry in Proteins
Structure. 2009 Oct;17(10) :1316-1325
PMID: 19836332    PMCID: PMC2810841    URL: https://www.ncbi.nlm.nih.gov/pubmed/19836332
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Protein structure determination and predictive modeling have long been guided by the paradigm that the peptide backbone has a single, context-independent ideal geometry. Both quantum-mechanics calculations and empirical analyses have shown this is an incorrect simplification in that backbone covalent geometry actually varies systematically as a function of the Phi and Psi backbone dihedral angles. Here, we use a nonredundant set of ultrahigh-resolution protein structures to define these conformation-dependent variations. The trends have a rational, structural basis that can be explained by avoidance of atomic clashes or optimization of favorable electrostatic interactions. To facilitate adoption of this paradigm, we have created a conformation-dependent library of covalent bond lengths and bond angles and shown that it has improved accuracy over existing methods without any additional variables to optimize. Protein structures derived from crystallographic refinement and predictive modeling both stand to benefit from incorporation of the paradigm.
Berkholz, Donald S. Shapovalov, Maxim V. Dunbrack, Roland L., Jr. Karplus, P. Andrew Cell press Cambridge 509vs