Parameters for molecular dynamics simulations of iron-sulfur proteins

• Type: Article in International Scientific Journal
• Date: 2013

Authors

Alexandra T P Carvalho (Author) Other; Ana F S Teixeira (Author) Other; Maria J Ramos (Author) FCUP

Journal

Title: Journal of Computational Chemistry

Vol. 34

Pages: 1540-1548

ISSN: 0192-8651

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 22 Citations

Scopus - 23 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-004-ZSB

DOI: 10.1002/jcc.23287

Abstract (EN): 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. (c) 2013 Wiley Periodicals, Inc.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 9