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A comparison of reduced coordinate sets for describing protein structure
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Uppsala University, Science for Life Laboratory, SciLifeLab.
2013 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 12, 124115- p.Article in journal (Refereed) Published
Abstract [en]

In all-atom molecular simulation studies of proteins, each atom in the protein is represented by a point mass and interactions are defined in terms of the atomic positions. In recent years, various simplified approaches have been proposed. These approaches aim to improve computational efficiency and to provide a better physical insight. The simplified models can differ widely in their description of the geometry and the interactions inside the protein. This study explores the most fundamental choice in the simplified protein models: the choice of a coordinate set defining the protein structure. A simplified model can use fewer point masses than the all-atom model and/or eliminate some of the internal coordinates of the molecule by setting them to an average or ideal value. We look at the implications of such choices for the overall protein structure. We find that care must be taken for angular coordinates, where even very small variations can lead to significant changes in the positions of far away atoms. In particular, we show that the phi/psi torsion angles are not a sufficient coordinate set, whereas another coordinate set with two degrees of freedom per residue, virtual C-alpha backbone bond, and torsion angles performs satisfactorily.

Place, publisher, year, edition, pages
2013. Vol. 139, no 12, 124115- p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-210724DOI: 10.1063/1.4821598ISI: 000325392000049OAI: oai:DiVA.org:uu-210724DiVA: diva2:664345
Available from: 2013-11-14 Created: 2013-11-14 Last updated: 2017-12-06Bibliographically approved

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Niemi, Antti J.

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