A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins

✍ Scribed by Paul E. Smith; Herb D. Blatt; B. Montgomery Pettitt

• Publisher: John Wiley and Sons
• Year: 1997
• Tongue: English
• Weight: 184 KB
• Volume: 27
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/(sici)1097-0134(19970201)27:2<227::aid-prot9>3.0.co;2-c

✦ Synopsis

A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four C a atoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudodihedral involving four sequential C a 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 f,c 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.