Simulation of multihaem cytochromes.
This article presents an overview of the simulation studies of the behaviour of multihaem cytochromes using theoretical/computational methodologies, with an emphasis on cytochrome c(3). It starts with the first studies using rigid molecules and continuum electrostatic models, where protonation and redox events were treated as independent. The gradual addition of physical details is then described, from the inclusion of proton isomerism, to the proper treatment of the thermodynamics of electron-proton coupling, to the explicit inclusion of the solvent and protein structural reorganization into the models, culminating with the method for molecular dynamics simulations at constant pH and reduction potential, where the solvation, conformational, protonation and redox features are all simulated in a fully integrated and coupled way. We end with a discussion of the strategies used to study the interaction between multihaem cytochromes, taking into account the further coupling effect introduced by the molecular association.
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal. claudio@itqb.unl.pt
Cláudio M
CM
Soares
António M
AM
Baptista
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D003580:Cytochromes / Q000737:chemistry* / Q000378:metabolism; D006418:Heme / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
D001426:Bacterial Proteins; D003580:Cytochromes; D012997:Solvents; D006418:Heme