Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

Curr Opin Struct Biol. 2007 Apr;17(2):149-56. doi: 10.1016/j.sbi.2007.03.018. Epub 2007 Apr 6.

Abstract

Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Antineoplastic Agents / chemistry
  • Electrochemistry
  • Electron Transport
  • Enzymes / chemistry
  • Ligands
  • Metalloproteins / chemistry
  • Models, Biological
  • Models, Molecular
  • Oxidation-Reduction
  • Platinum Compounds / chemistry
  • Systems Biology*
  • Thermodynamics*

Substances

  • Antineoplastic Agents
  • Enzymes
  • Ligands
  • Metalloproteins
  • Platinum Compounds