ISSN:
0887-3585
Keywords:
peptide conformation
;
ramachandran plot
;
PDB search
;
peptide dynamics
;
BPTI
;
Chemistry
;
Biochemistry and Biotechnology
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Medicine
Notes:
A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four Cαatoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudo-dihedral involving four sequential Cαatoms, 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 φ,ψ 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. © 1997 Wiley-Liss, Inc.
Additional Material:
5 Ill.
Type of Medium:
Electronic Resource
