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Backbone covalent bond dynamical symmetry breaking and side-chain geometry of folded proteins
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.
(English)Article in journal (Other academic) Submitted
National Category
Condensed Matter Physics Structural Biology
Identifiers
URN: urn:nbn:se:uu:diva-172357OAI: oai:DiVA.org:uu-172357DiVA: diva2:514151
Available from: 2012-04-05 Created: 2012-04-05 Last updated: 2012-08-01Bibliographically approved
In thesis
1. Bending, Twisting and Turning: Protein Modeling and Visualization from a Gauge-Invariance Viewpoint
Open this publication in new window or tab >>Bending, Twisting and Turning: Protein Modeling and Visualization from a Gauge-Invariance Viewpoint
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteins in nature fold to one dominant native structure. Despite being a heavily studied field, predicting the native structure from the amino acid sequence and modeling the folding process can still be considered unsolved problems. In this thesis I present a new approach to this problem with methods borrowed from theoretical physics. In the first part I show how it is possible to use a discrete Frenet frame to define the discrete curvature and torsion of the main chain of the protein. This method is then extended to the side chains as well. In particular I show how to use the discrete Frenet frame to produce a statistical distribution of angles that works in similar fashion as the commonly used Ramachandran plot and side chain rotamers. The discrete Frenet frame displays a gauge symmetry, in the choice of basis vectors on the normal plane, that is reminiscent of features of Abelian-Higgs theory. In the second part of the thesis I show how this similarity with Abelian-Higgs theory can be translated into an effective energy for a protein. The loops of the proteins are shown to correspond to solitons so that the whole protein can be constructed by gluing together any number of solitons. I present results of simulating proteins by minimizing the energy, starting from a real line or straight helix, where the correct native fold is attained. Finally the model is shown to display the same phase structure as real proteins.

 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 68 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 921
Keyword
protein folding, discrete frenet frame, solitons, protein visualization
National Category
Physical Sciences
Research subject
Physics and Astronomy specializing in Theoretical Physics
Identifiers
urn:nbn:se:uu:diva-172358 (URN)978-91-554-8338-8 (ISBN)
Public defence
2012-05-25, Å80101, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2012-05-04 Created: 2012-04-05 Last updated: 2012-08-01Bibliographically approved

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