Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations

M. Dal Peraro, Katrin Spiegel, Guillaume Lamoureux, Marco De Vivo, William F. DeGrado, Michael L. Klein

Research output: Contribution to journalArticlepeer-review

41 Scopus citations

Abstract

Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the intrinsic difficulty of handling polarization and charge transfer contributions. In order to improve the description of metalloproteins, a simple reparameterization strategy is proposed herein that does not involve artificial constraints. Specifically, a non-bonded quantum mechanical-based model is used to capture the mean polarization and charge transfer contributions to the interatomic forces within the metal site. The present approach is demonstrated to provide enough accuracy to maintain the integrity of the metal pocket for a variety of metalloproteins during extended (multi-nanosecond) molecular dynamics simulations. The method enables the sampling of small conformational changes and the relaxation of local frustrations in NMR structures.

Original languageEnglish (US)
Pages (from-to)444-453
Number of pages10
JournalJournal of Structural Biology
Volume157
Issue number3
DOIs
StatePublished - Mar 2007
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology

Keywords

  • Bader charges (AIM)
  • Charge distribution
  • Charge transfer
  • DueFerri four-helix bundle
  • Metal ions
  • Metal site
  • Metalloproteins
  • Mn-Catalase
  • RNase H
  • Thermolysin

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