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A three dimensional visualisation approach to protein heavy-atom structure reconstruction
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.
Department of Biomedicine Faculty of Medicine and Dentistry,UIB.
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2014 (English)In: BMC Structural Biology, ISSN 1472-6807, E-ISSN 1472-6807, Vol. 14, 27- p.Article in journal (Refereed) Published
Abstract [en]

Background

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.

Results

We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the Cα coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.

Conclusions

We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

Place, publisher, year, edition, pages
2014. Vol. 14, 27- p.
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-232508DOI: 10.1186/s12900-014-0027-8ISI: 000348232200001OAI: oai:DiVA.org:uu-232508DiVA: diva2:748489
Available from: 2014-09-19 Created: 2014-09-19 Last updated: 2017-12-05Bibliographically approved

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