A SIMPLE 2-DIMENSIONAL REPRESENTATION FOR THE COMMON SECONDARY STRUCTURAL ELEMENTS OF POLYPEPTIDES AND PROTEINS

A simple method is presented for projecting the conformation of extend ed secondary structure elements of peptides and proteins that extend o ver four C-alpha atoms onto a simple two-dimensional surface, A new se t of two degrees of freedom is defined, a pseudo-dihedral involving fo ur sequential C-alpha atoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptid e 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 i mportant elements. The new two dimensional surface is explored by refe rence to 63 selected protein crystal structures together with a compar ison of model built peptides representing the common secondary structu ral elements, Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor . (C) 1997 Wiley-Liss, Inc.