Conformation Dependence of Backbone Geometry in Proteins
Donald S. Berkholz, Maxim V. Shapovalov, Roland L. Dunbrack Jr., P. Andrew Karpluscorrespondenceemail
Accepted:August 20, 2009 Received in revised form:July 20, 2009 Received:July 20, 2009
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 ϕ and Ψ 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.
Received: July 20, 2009; Received in revised form: July 20, 2009; Accepted: August 20, 2009;
© 2009 Elsevier Ltd. Published by Elsevier Inc.
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