Premium
A simple two‐dimensional representation for the common secondary structural elements of polypeptides and proteins
Author(s) -
Smith Paul E.,
Blatt Herb D.,
Pettitt B. Montgomery
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19970201)27:2<227::aid-prot9>3.0.co;2-c
Subject(s) - simple (philosophy) , protein secondary structure , molecular dynamics , scalar (mathematics) , dihedral angle , surface (topology) , crystallography , representation (politics) , chemistry , biological system , mathematics , physics , computational chemistry , geometry , molecule , biology , philosophy , biochemistry , epistemology , hydrogen bond , organic chemistry , politics , political science , law
A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C α atoms onto a simple two‐dimensional surface. A new set of two degrees of freedom is defined, a pseudo‐dihedral involving four sequential C α 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 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.