Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.
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.
Dal Peraro
Matteo
M
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
Ruggerone
Paolo
P
Raugei
Simone
S
Gervasio
Francesco Luigi
FL
Carloni
Paolo
P
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
D000970:Antineoplastic Agents; D004798:Enzymes; D008024:Ligands; D008667:Metalloproteins; D017671:Platinum Compounds