title: Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture.
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(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.
authors.affiliation: 1] Centre for Quantum Geometry of Moduli Spaces, Aarhus University, DK-8000 Aarhus C, Denmark [2] Departments of Mathematics and Theoretical Physics, Caltech, Pasadena, California 91125, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Penner
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark [3] Centre for DNA nanotechnology, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Ebbe S
authors.initials: ES
authors.lastname: Andersen
authors.affiliation: Department of Mathematics, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Jens L
authors.initials: JL
authors.lastname: Jensen
authors.affiliation: 1] Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark [2] Centre for Membrane Pumps in Cells and Disease, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Adriana K
authors.initials: AK
authors.lastname: Kantcheva
authors.affiliation: 1] Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark [2] Centre for Membrane Pumps in Cells and Disease, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Maike
authors.initials: M
authors.lastname: Bublitz
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark [3] Centre for Membrane Pumps in Cells and Disease, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Poul
authors.initials: P
authors.lastname: Nissen
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Anton M H
authors.initials: AM
authors.lastname: Rasmussen
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Katrine L
authors.initials: KL
authors.lastname: Svane
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Bjørk
authors.initials: B
authors.lastname: Hammer
authors.affiliation: Centre for Quantum Geometry of Moduli Spaces, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Reza
authors.initials: R
authors.lastname: Rezazadegan
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark [3] Center for Insoluble Protein Structures, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Niels Chr
authors.initials: NC
authors.lastname: Nielsen
authors.affiliation: 1] Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark [2] Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark [3] Center for Insoluble Protein Structures, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Jakob T
authors.initials: JT
authors.lastname: Nielsen
authors.affiliation: 1] Centre for Quantum Geometry of Moduli Spaces, Aarhus University, DK-8000 Aarhus C, Denmark [2] Departments of Mathematics and Theoretical Physics, Caltech, Pasadena, California 91125, USA [3] Department of Mathematics, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Jørgen E
authors.initials: JE
authors.lastname: Andersen
mesh_terms: D030562:Databases, Protein; D006860:Hydrogen Bonding; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012399:Rotation; D009626:Terminology as Topic
chemical_list: D011506:Proteins