An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

Tanja Kortemme, Alexandre Morozov, David Baker

Research output: Contribution to journalArticle

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Abstract

Hydrogen bonding is a key contributor to the specificity of intramolecular and intermolecular interactions in biological systems. Here, we develop an orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds in high-resolution protein crystal structures, and evaluate it using four tests related to the prediction and design of protein structures and protein-protein complexes. The new potential is superior to the widely used Coulomb model of hydrogen bonding in prediction of the sequences of proteins and protein-protein interfaces from their structures, and improves discrimination of correctly docked protein-protein complexes from large sets of alternative structures.

Original languageEnglish (US)
Pages (from-to)1239-1259
Number of pages21
JournalJournal of molecular biology
Volume326
Issue number4
DOIs
StatePublished - Feb 28 2003

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All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • Electrostatics
  • Free energy function
  • Hydrogen bond
  • Protein design
  • Protein docking

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