On the design and analysis of protein folding potentials

Dror Tobi, Gil Shafran, Nathan Linial, Ron Elber*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

102 Scopus citations

Abstract

Pairwise interaction models to recognize native folds are designed and analyzed. Different sets of parameters are considered but the focus was on 20 x 20 contact matrices. Simultaneous solution of inequalities and minimization of the variance of the energy find matrices that recognize exactly the native folds of 572 sequences and structures from the protein data bank (PDB). The set includes many homologous pairs, which present a difficult recognition problem. Significant recognition ability is recovered with a small number of parameters (e.g., the H/P model). However, full recognition requires a complete set of amino acids. In addition to structures from the PDB, a folding program (MONSSTER) was used to generate decoy structures for 75 proteins. It is impossible to recognize all the native structures of the extended set by contact potentials. We therefore searched for a new functional form. An energy function U, which is based on a sum of general pairwise interactions limited to a resolution of 1 angstrom, is considered. This set was infeasible too. We therefore conjecture that it is not possible to find a folding potential, resolved to 1 angstrom, which is a sum of pair interactions. (C) 2000 Wiley-Liss, Inc.

Original languageAmerican English
Pages (from-to)71-85
Number of pages15
JournalProteins: Structure, Function and Genetics
Volume40
Issue number1
DOIs
StatePublished - 1 Jul 2000

Keywords

  • Contact matrices
  • Decoy structures
  • Linear programming
  • Optimization

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