Search for the stable state of a short chain in a molecular field

A. V. Finkelstein, B. A. Reva

Research output: Contribution to journalArticlepeer-review

33 Scopus citations

Abstract

A general approach is developed to search for stable structures of short chain fragments (e.g. of loops or bound oligopeptides) in a given molecular field. This molecular field is produced by the remaining part of a globule or by any other surface with a defined spatial structure. The fragment must be short enough to have no pronounced long-range interactions within itself. The method is illustrated by calculation of the 3-D structures of two loops of bovine pancreatic trypsin inhibitor (BPTI). Computations are based on a lattice model of conformational space and on strict and fast algorithms of 1-D statistical mechanics and dynamic programming (which are very similar in essence). This makes a search of oligopeptide structures only several times (and not several orders of magnitude) longer than that of a dipeptide.

Original languageEnglish
Pages (from-to)617-624
Number of pages8
JournalProtein Engineering, Design and Selection
Volume5
Issue number7
DOIs
StatePublished - Oct 1992
Externally publishedYes

Keywords

  • Chain conformation
  • Dynamic programming
  • Lattice model
  • Molecular field
  • Surface binding

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