uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Gauge field theory of chirally folded homopolymers with applications to 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.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2010 (English)In: Physical Review E, ISSN 1539-3755, Vol. 82, no 2, 021910- p.Article in journal (Refereed) Published
Abstract [en]

We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase the model is in the same universality class with proteins that are deposited in the Protein Data Bank, in the sense of the compactness index. We apply the model to analyze various statistical aspects of folded proteins. Curiously we find that it can produce results that are a very good good match to the data in the Protein Data Bank.

Place, publisher, year, edition, pages
2010. Vol. 82, no 2, 021910- p.
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-134959DOI: 10.1103/PhysRevE.82.021910ISI: 000280826800006OAI: oai:DiVA.org:uu-134959DiVA: diva2:375147
Available from: 2010-12-07 Created: 2010-12-03 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

Open Access in DiVA

No full text

Other links

Publisher's full text
By organisation
Theoretical Physics
Physical Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 883 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf