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Correlation between protein secondary structure, backbone bond angles, and side-chain orientations
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, no 2, 021904- p.Article in journal (Refereed) Published
Abstract [en]

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.
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Physical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-180273DOI: 10.1103/PhysRevE.86.021904ISI: 000307280200004OAI: oai:DiVA.org:uu-180273DiVA: diva2:549147
Available from: 2012-09-03 Created: 2012-09-03 Last updated: 2017-12-07Bibliographically approved

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Lundgren, MartinNiemi, Antti J.

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