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Topology and structural self-organization in folded proteins
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2013 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 88, no 4, 042709- p.Article in journal (Refereed) Published
Abstract [en]

Topological methods are indispensable in theoretical studies of particle physics, condensed matter physics, and gravity. These powerful techniques have also been applied to biological physics. For example, knowledge of DNA topology is pivotal to the understanding as to how living cells function. Here, the biophysical repertoire of topological methods is extended, with the aim to understand and characterize the global structure of a folded protein. For this, the elementary concept of winding number of a vector field on a plane is utilized to introduce a topological quantity called the folding index of a crystallographic protein. It is observed that in the case of high resolution protein crystals, the folding index, when evaluated over the entire length of the crystallized protein backbone, has a very clear and strong propensity towards integer values. The observation proposes that the way how a protein folds into its biologically active conformation is a structural self-organization process with a topological facet that relates to the concept of solitons. It is proposed that the folding index has a potential to become a useful tool for the global, topological characterization of the folding pathways.

Place, publisher, year, edition, pages
2013. Vol. 88, no 4, 042709- p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-211445DOI: 10.1103/PhysRevE.88.042709ISI: 000326163800009OAI: oai:DiVA.org:uu-211445DiVA: diva2:667591
Available from: 2013-11-27 Created: 2013-11-25 Last updated: 2017-12-06Bibliographically approved

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Niemi, Antti J.

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