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- Title
Parameters for molecular dynamics simulations of iron-sulfur proteins.
- Authors
Carvalho, Alexandra T P; Teixeira, Ana F S; Ramos, Maria J
- Abstract
Iron-sulfur proteins involved in electron transfer reactions have finely tuned redox potentials, which allow them to be highly efficient and specific. Factors such as metal center solvent exposure, interaction with charged residues, or hydrogen bonds between the ligand residues and amide backbone groups have all been pointed out to cause such specific redox potentials. Here, we derived parameters compatible with the AMBER force field for the metal centers of iron-sulfur proteins and applied them in the molecular dynamics simulations of three iron-sulfur proteins. We used density-functional theory (DFT) calculations and Seminario's method for the parameterization. Parameter validation was obtained by matching structures and normal frequencies at the quantum mechanics and molecular mechanics levels of theory. Having guaranteed a correct representation of the protein coordination spheres, the amide H-bonds and the water exposure to the ligands were analyzed. Our results for the pattern of interactions with the metal centers are consistent to those obtained by nuclear magnetic resonance spectroscopy (NMR) experiments and DFT calculations, allowing the application of molecular dynamics to the study of those proteins.
- Publication
Journal of computational chemistry, 2013, Vol 34, Issue 18, p1540
- ISSN
1096-987X
- Publication type
Journal Article
- DOI
10.1002/jcc.23287