A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins.
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.
Smith
P E
PE
Department of Chemistry, University of Houston, Texas 77204-5641, USA.
Blatt
H D
HD
Pettitt
B M
BM
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
D010455:Peptides; D011506:Proteins; D007611:Aprotinin