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 and Jørgen E. Andersen ()
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Robert C. Penner: Centre for Quantum Geometry of Moduli Spaces, Aarhus University
Ebbe S. Andersen: Interdisciplinary Nanoscience Center, Aarhus University
Jens L. Jensen: Aarhus University
Adriana K. Kantcheva: Aarhus University
Maike Bublitz: Aarhus University
Poul Nissen: Interdisciplinary Nanoscience Center, Aarhus University
Anton M. H. Rasmussen: Interdisciplinary Nanoscience Center, Aarhus University
Katrine L. Svane: Interdisciplinary Nanoscience Center, Aarhus University
Bjørk Hammer: Interdisciplinary Nanoscience Center, Aarhus University
Reza Rezazadegan: Centre for Quantum Geometry of Moduli Spaces, Aarhus University
Niels Chr. Nielsen: Interdisciplinary Nanoscience Center, Aarhus University
Jakob T. Nielsen: Interdisciplinary Nanoscience Center, Aarhus University
Jørgen E. Andersen: Centre for Quantum Geometry of Moduli Spaces, Aarhus University

Nature Communications, 2014, vol. 5, issue 1, 1-14

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms6803

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