TY - JOUR
T1 - Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture
AU - Penner, Robert
AU - Andersen, Ebbe Sloth
AU - Jensen, Jens Ledet
AU - Kantcheva, Adriana Krassimirova
AU - Bublitz, Maike
AU - Nissen, Poul
AU - Rasmussen, Anton Michael Havelund
AU - Svane, Katrine Louise
AU - Hammer, Bjørk
AU - Rezazadegan, Reza
AU - Nielsen, Niels Christian
AU - Nielsen, Jakob Toudahl
AU - Andersen, Jørgen Ellegaard
PY - 2014/12/17
Y1 - 2014/12/17
N2 - 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.
AB - 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.
KW - Databases, Protein
KW - Hydrogen Bonding
KW - Models, Molecular
KW - Protein Structure, Secondary
KW - Protein Structure, Tertiary
KW - Proteins/chemistry
KW - Quantum Theory
KW - Rotation
KW - Terminology as Topic
U2 - 10.1038/ncomms6803
DO - 10.1038/ncomms6803
M3 - Journal article
C2 - 25517704
SN - 2041-1723
VL - 5
SP - 5803
JO - Nature Communications
JF - Nature Communications
M1 - 5803
ER -