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

Matteo Dal Peraro, Paolo Ruggerone, Simone Raugei, Francesco Luigi Gervasio, Paolo Carloni

Research output: Contribution to journalArticle

81 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)149-156
Number of pages8
JournalCurrent Opinion in Structural Biology
Volume17
Issue number2
DOIs
Publication statusPublished - Apr 2007

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Molecular Dynamics Simulation
Mechanics
Molecular Evolution
Platinum
Oxidation-Reduction
Metals
Electrons
DNA
Pharmaceutical Preparations
Proteins

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. / Dal Peraro, Matteo; Ruggerone, Paolo; Raugei, Simone; Gervasio, Francesco Luigi; Carloni, Paolo.

In: Current Opinion in Structural Biology, Vol. 17, No. 2, 04.2007, p. 149-156.

Research output: Contribution to journalArticle

Dal Peraro, Matteo ; Ruggerone, Paolo ; Raugei, Simone ; Gervasio, Francesco Luigi ; Carloni, Paolo. / Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. In: Current Opinion in Structural Biology. 2007 ; Vol. 17, No. 2. pp. 149-156.
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