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.

Modeling of α‐MSH conformations with implicit solvent

“…In addition, the regions around φ=60°, and near ψ=120° and ψ=−120°, are some what populated. The regions, α L andC ax 7 , are well populated when the peptides are in the gaseous environment but, except in the case of glycine, become relatively unstable in aqueous solution (42).…”

Application of HMM to the Study of Three-Dimensional Protein Structure

“…The polypeptide chains were scanned in overlapping windows that encompassed four successive α-carbons (C α ), thereby producing a succession of short-backbone chain fragments. As in some previous studies (Pavone et al, 1996;Rackovsky, 1993;Rooman et al, 1990;Smith et al, 1997), we used four-residue lengths, which contain enough information to find basic structural elements: four-residue turns for α-helices, bridges for β-sheets and undefined loop structures. Moreover, a four-residue segment is small enough to keep the number of SL categories reasonable.…”