Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture
Creators
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1.
Aarhus University
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2.
California Institute of Technology
Abstract
Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each Cα effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.
Additional Information
© 2014 Macmillan Publishers Limited. Received 06 May 2014. Accepted 07 November 2014. Published 17 December 2014. Updated online 03 February 2015. All researchers in this project were supported by the Danish National Research Foundation through the foundations centre of excellence grants 'Centre for Quantum Geometry of Moduli Spaces', 'Centre for DNA nanotechnology', 'Centre for Membrane Pumps in Cells and Disease' and 'Center for Insoluble Protein Structures' from Danish National Research Foundation. R.C.P. and J.E.A. acknowledge valuable discussions with Alexey Finkelstein during the early stages of this work. We thank Niels Larsen for technical assistance in setting up a web analysis server, and Rikke Schmidt-Kjaergaard for graphical suggestions and assistance and Rasmus Villemoes for assistance with programming.Errata
Erratum: Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture Robert C. Penner, Ebbe S. Andersen, Jens L. Jensen, Adriana K. Kantcheva, Maike Bublitz, Poul Nissen, Anton M.H. Rasmussen, Katrine L. Svane, Bjørk Hammer, Reza Rezazadegan, Niels Chr Nielsen, Jakob T. Nielsen & Jørgen E. Andersen Nature Communications 6, Article number: 6209 doi:10.1038/ncomms7209Attached Files
Supplemental Material - ncomms6803-s1.pdf
Files
ncomms6803-s1.pdf
Additional details
Identifiers
- Eprint ID
- 54810
- Resolver ID
- CaltechAUTHORS:20150213-073851159
Related works
- Describes
- 10.1038/ncomms7209 (DOI)
- http://rdcu.be/cmnk (URL)
Funding
- Danish National Research Foundation
Dates
- Created
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2015-02-14Created from EPrint's datestamp field
- Updated
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2023-06-01Created from EPrint's last_modified field