title: A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins.
abstract: A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C alpha atoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudodihedral involving four sequential C alpha atoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple phi,psi pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor.
authors.affiliation: Department of Chemistry, University of Houston, Texas 77204-5641, USA.
authors.forename: P E
authors.initials: PE
authors.lastname: Smith
authors.forename: H D
authors.initials: HD
authors.lastname: Blatt
authors.forename: B M
authors.initials: BM
authors.lastname: Pettitt
mesh_terms: D007611:Aprotinin / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008432:Mathematical Computing; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry
chemical_list: D010455:Peptides; D011506:Proteins; D007611:Aprotinin