CaltechAUTHORS
  A Caltech Library Service

Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

Penner, Robert C. and Andersen, Ebbe S. and Jensen, Jens L. and Kantcheva, Adriana K. and Bublitz, Maike and Nissen, Poul and Rasmussen, Anton M. H. and Svane, Katrina L. and Hammer, Bjørk and Rezazadegan, Reza and Nielsen, Niels Chr. and Nielsen, Jakob T. and Andersen, Jørgen E. (2014) Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture. Nature Communications, 5 (12). Art. No. 5803. ISSN 2041-1723. http://resolver.caltech.edu/CaltechAUTHORS:20150213-073851159

[img] PDF - Supplemental Material
See Usage Policy.

7Mb

Use this Persistent URL to link to this item: http://resolver.caltech.edu/CaltechAUTHORS:20150213-073851159

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/ncomms6803DOIArticle
http://www.nature.com/ncomms/2014/141217/ncomms6803/full/ncomms6803.htmlPublisherArticle
http://dx.doi.org/10.1038/ncomms7209DOIErratum
http://www.nature.com/ncomms/2015/150203/ncomms7209/full/ncomms7209.htmlPublisherErratum
http://rdcu.be/cmnlPublisherFree ReadCube access
http://rdcu.be/cmnkErrataFree ReadCube access
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/ncomms7209
Funders:
Funding AgencyGrant Number
Danish National Research Foundation Centre for Quantum Geometry of Moduli SpacesUNSPECIFIED
Danish National Research Foundation Centre for DNA nanotechnologyUNSPECIFIED
Danish National Research Foundation Centre for Membrane Pumps in Cells and DiseaseUNSPECIFIED
Danish National Research Foundation Center for Insoluble Protein StructuresUNSPECIFIED
Record Number:CaltechAUTHORS:20150213-073851159
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20150213-073851159
Official Citation: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, + et al. Nature Communications 5, doi:10.1038/ncomms6803
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:54810
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:14 Feb 2015 00:22
Last Modified:19 Mar 2015 18:58

Repository Staff Only: item control page