title: Correlation between protein secondary structure, backbone bond angles, and side-chain orientations.
abstract: We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C(α) carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C(β) carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C(α)-C(β) structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.
authors.affiliation: Department of Physics and Astronomy, Uppsala University, PO Box 803, S-75108 Uppsala, Sweden. martin.lundgren@physics.uu.se
authors.forename: Martin
authors.initials: M
authors.lastname: Lundgren
authors.forename: Antti J
authors.initials: AJ
authors.lastname: Niemi
mesh_terms: D000818:Animals; D002645:Chickens; D030562:Databases, Protein; D008840:Microfilament Proteins / Q000737:chemistry; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D008840:Microfilament Proteins; D011506:Proteins; C026615:villin