title: Free energy perturbation and molecular dynamics calculations of copper binding to azurin.
abstract: Free energy perturbation/molecular dynamics simulations have been carried out on copper/azurin systems calculating the binding affinities of copper (II) ion to azurin either in the native or in the unfolded state. In order to test the validity of the strategy adopted for the calculations and to establish what force field is suitable for these kinds of calculations, three different force fields, AMBER, CVFF, and CFF, have been alternatively used for the calculations and the results have been compared with experimental data obtained by spectroscopic titrations of copper (II)/azurin solutions and denaturation experiments. Our findings have pointed out that only CFF gives satisfactory results, thus providing a reliable tool for copper binding simulations in copper protein.
authors.affiliation: Dipartimento di Scienze Chimiche, Universita' di Catania, V.le A. Doria 6, 95125 Catania, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pappalardo
authors.forename: Danilo
authors.initials: D
authors.lastname: Milardi
authors.forename: Domenico M
authors.initials: DM
authors.lastname: Grasso
authors.forename: Carmelo
authors.initials: C
authors.lastname: La Rosa
mesh_terms: D000465:Algorithms; D001400:Azurin / Q000737:chemistry*; D001665:Binding Sites; D003300:Copper / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D001400:Azurin; D003300:Copper