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
Protein loops, solitons and side-chain visualization with applications to the left-handed helix region
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.
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, no 6, 061909- p.Article in journal (Refereed) Published
Abstract [en]

Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha helices and beta strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C-alpha atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C-beta carbons on the two-sphere. We show that the residue independent localization extends to C gamma and C-delta carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed beta turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

Place, publisher, year, edition, pages
2012. Vol. 85, no 6, 061909- p.
National Category
Condensed Matter Physics Structural Biology
Identifiers
URN: urn:nbn:se:uu:diva-172355DOI: 10.1103/PhysRevE.85.061909ISI: 000305128000007OAI: oai:DiVA.org:uu-172355DiVA: diva2:514149
Available from: 2012-04-05 Created: 2012-04-05 Last updated: 2017-12-07Bibliographically 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

Authority records BETA

Lundgren, MartinNiemi, AnttiSha, Fan

Search in DiVA

By author/editor
Lundgren, MartinNiemi, AnttiSha, Fan
By organisation
Theoretical Physics
In the same journal
Physical Review E. Statistical, Nonlinear, and Soft Matter Physics
Condensed Matter PhysicsStructural Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 400 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