Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • 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
Intrinsic protein geometry with application to non-proline cis peptide planes
Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Beijing Institute of Technology, People’s Republic of China; Uppsala University, Sweden.
Show others and affiliations
Number of Authors: 62019 (English)In: Journal of Mathematical Chemistry, ISSN 0259-9791, E-ISSN 1572-8897, Vol. 57, no 1, p. 263-279Article in journal (Refereed) Published
Abstract [en]

The shape of a protein can be modeled by the C atoms of its backbone, the mathematical description employing the notion of extrinsic geometry of a discrete piecewise linear chain. We advance differential geometry of a natively framed discrete chain to argue the existence of two additional, independent and intrinsic geometric structures, provided by the peptide planes and side chains, respectively. We develop our general methodology within a case study: analysis of the intrinsic geometry of atoms that are located around a non-proline cis peptide plane. We show that the native peptide plane framing allows for revealing of atomic positions anomalies. That way, we identify a number of entries that display such anomalies around their non-proline cis peptide planes within the ultrahigh-resolution structures in PDB. We propose that our approach can be extended into a visual analysis and refinement tool that is applicable even when resolution is limited or data is incomplete, for example when there are atoms missing in an experimental construct.

Place, publisher, year, edition, pages
2019. Vol. 57, no 1, p. 263-279
Keywords [en]
Protein structure, Backbone geometry, Coordinate frames, Peptide planes
National Category
Chemical Sciences Mathematics Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-166844DOI: 10.1007/s10910-018-0949-7ISI: 000456663400011OAI: oai:DiVA.org:su-166844DiVA, id: diva2:1294448
Available from: 2019-03-07 Created: 2019-03-07 Last updated: 2019-03-07Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full text

Search in DiVA

By author/editor
Dai, JinNiemi, Antti J.
By organisation
Nordic Institute for Theoretical Physics (Nordita)
In the same journal
Journal of Mathematical Chemistry
Chemical SciencesMathematicsPhysical Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 8 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • 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