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

Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C α effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around...

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Bibliographic Details
Published in:Nature communications 2014-12, Vol.5 (1), p.5803-5803, Article 5803
Main Authors: Penner, Robert C., Andersen, Ebbe S., Jensen, Jens L., Kantcheva, Adriana K., Bublitz, Maike, Nissen, Poul, Rasmussen, Anton M. H., Svane, Katrine L., Hammer, Bjørk, Rezazadegan, Reza, Nielsen, Niels Chr, Nielsen, Jakob T., Andersen, Jørgen E.
Format: Article
Language:English
Subjects:
119/118
631/45/535
631/57/2272/2273
82
Databases, Protein
Humanities and Social Sciences
Hydrogen Bonding
Models, Molecular
multidisciplinary
Protein Structure, Secondary
Protein Structure, Tertiary
Proteins - chemistry
Quantum Theory
Rotation
Science
Terminology as Topic
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Summary:Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C α 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. Ramachandran plots are a convenient means of describing protein backbone conformation by depicting the distribution of Ca bond rotations. Here, the authors devise an alternative descriptor based on hydrogen bond rotations, and apply it to describe protein structures using a vocabulary of 30 hydrogen-bonding motifs.
ISSN:2041-1723
2041-1723
DOI:10.1038/ncomms6803