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Free energy perturbation and molecular dynamics calculations of copper binding to azurin
Author(s) -
Pappalardo Matteo,
Milardi Danilo,
Grasso Domenico M.,
La Rosa Carmelo
Publication year - 2003
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10213
Subject(s) - azurin , copper , molecular dynamics , chemistry , free energy perturbation , force field (fiction) , copper protein , ion , binding energy , perturbation (astronomy) , computational chemistry , chemical physics , thermodynamics , atomic physics , physics , quantum mechanics , organic chemistry
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. © 2003 Wiley Periodicals, Inc. J Comput Chem 6: 779–785, 2003