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On Ramachandran angles, closed strings and knots in protein structure
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Univ Tours, Lab Math & Phys Theor, Federat Denis Poisson, CNRS UMR 6083, Parc Grandmont, F-37200 Tours, France.;Beijing Inst Technol, Dept Phys, Beijing 100081, Peoples R China..
2016 (English)In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 49, no 31, 315401Article in journal (Refereed) Published
Abstract [en]

The Ramachandran angles (phi, psi) of a protein backbone form the vertices of a piecewise geodesic curve on the surface of a torus. When the ends of the curve are connected to each other similarly, by a geodesic, the result is a closed string that in general wraps around the torus a number of times both in the meridional and the longitudinal directions. The two wrapping numbers are global characteristics of the protein structure. A statistical analysis of the wrapping numbers in terms of crystallographic x-ray structures in the protein data bank (PDB) reveals that proteins have no net chirality in the phi direction but in the psi direction, proteins prefer to display chirality. A comparison between the wrapping numbers and the concept of folding index discloses a non-linearity in their relationship. Thus these three integer valued invariants can be used in tandem, to scrutinize and classify the global loop structure of individual PDB proteins, in terms of the overall fold topology.

Place, publisher, year, edition, pages
2016. Vol. 49, no 31, 315401
Keyword [en]
Ramachandran angles, knots in protein, topological classification
National Category
Physical Sciences Engineering and Technology
Identifiers
URN: urn:nbn:se:uu:diva-305939DOI: 10.1088/0022-3727/49/31/315401ISI: 000384003000016OAI: oai:DiVA.org:uu-305939DiVA: diva2:1044916
Funder
Carl Tryggers foundation Swedish Research Council
Available from: 2016-11-07 Created: 2016-10-24 Last updated: 2016-11-08Bibliographically approved

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Chen, SiNiemi, Antti J
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