title: Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.
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.
authors.affiliation: Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Dal Peraro
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
authors.forename: Simone
authors.initials: S
authors.lastname: Raugei
authors.forename: Francesco Luigi
authors.initials: FL
authors.lastname: Gervasio
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
mesh_terms: D000970:Antineoplastic Agents / Q000737:chemistry; D004563:Electrochemistry; D004579:Electron Transport; D004798:Enzymes / Q000737:chemistry; D008024:Ligands; D008667:Metalloproteins / Q000737:chemistry; D008954:Models, Biological; D008958:Models, Molecular; D010084:Oxidation-Reduction; D017671:Platinum Compounds / Q000737:chemistry; D049490:Systems Biology; D013816:Thermodynamics
chemical_list: D000970:Antineoplastic Agents; D004798:Enzymes; D008024:Ligands; D008667:Metalloproteins; D017671:Platinum Compounds