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

Paul E. Smith, Herb D. Blatt, Bernard Pettitt

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

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 pseudodihedral 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.

Original languageEnglish (US)
Pages (from-to)227-234
Number of pages8
JournalProteins: Structure, Function and Genetics
Volume27
Issue number2
DOIs
StatePublished - 1997
Externally publishedYes

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Keywords

  • BPTI
  • PDB search
  • peptide conformation
  • peptide dynamics
  • ramachandran plot

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

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