Correlation between protein secondary structure, backbone bond angles, and side-chain orientations
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, Vol. 86, no 2, 021904- p.Article in journal (Refereed) Published
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C-alpha 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-beta carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C-alpha-C-beta structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 angstrom in root-mean-square distance from the experimental x-ray structure.
Place, publisher, year, edition, pages
2012. Vol. 86, no 2, 021904- p.
IdentifiersURN: urn:nbn:se:uu:diva-180273DOI: 10.1103/PhysRevE.86.021904ISI: 000307280200004OAI: oai:DiVA.org:uu-180273DiVA: diva2:549147