A theoretical databank of transferable aspherical atoms and its application to electrostatic interaction energy calculations of macromolecules

Paulina M. Dominiak, Anatoliy Volkov, Xue Li, Marc Messerschmidt, Philip Coppens

Research output: Contribution to journalArticle

116 Scopus citations

Abstract

A comprehensive version of the theoretical databank of transferable aspherical pseudoatoms is described, and its first application to protein-ligand interaction energies is discussed. The databank contains all atom types present in natural amino acid residues and other biologically relevant molecules. Each atom type results from averaging over a family of chemically unique pseudoatoms, taking into account both first and second neighbors. The spawning procedure is used to ensure that close transferability is obeyed. The databank is applied to the syntenin PDZ2 domain complexed with four-residue peptides and to the PDZ2 dimer. Analysis of the electrostatic interactions energies calculated by the exact-potential/multipole-moment-databank method stresses the importance of the P0 and P-2 residues of the peptide in establishing the interaction, whereas the P-1 residue is shown to play a much smaller role. Unexpectedly, the charged P-3 residue contributes significantly to the interaction. The class I and II peptides are bound with the same strength by the syntenin PDZ2 domain, though the electrostatic interaction energy of the P-2 residue is smaller for class I peptides. There is no difference between the interaction energies of the peptides with PDZ2 domains from single-domain protein fragments and those from PDZ1-PDZ2 tandems.

Original languageEnglish (US)
Pages (from-to)232-247
Number of pages16
JournalJournal of Chemical Theory and Computation
Volume3
Issue number1
DOIs
StatePublished - Jan 1 2007
Externally publishedYes

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ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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