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

Robert Penner, Ebbe Sloth Andersen, Jens Ledet Jensen, Adriana Krassimirova Kantcheva, Maike Bublitz, Poul Nissen, Anton Michael Havelund Rasmussen, Katrine Louise Svane, Bjørk Hammer, Reza Rezazadegan, Niels Christian Nielsen, Jakob Toudahl Nielsen, Jørgen Ellegaard Andersen

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C 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.

Original languageEnglish
Article number5803
JournalNature Communications
Volume5
Pages (from-to)5803
Number of pages12
ISSN2041-1723
DOIs
Publication statusPublished - 17. Dec 2014
Externally publishedYes

Keywords

  • Databases, Protein
  • Hydrogen Bonding
  • Models, Molecular
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins/chemistry
  • Quantum Theory
  • Rotation
  • Terminology as Topic

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