Homology modelling and molecular dynamics simulations of wild type and mutated flavodoxins from Desulfovibrio vulgaris (Miyazaki F): insight into FMN–apoprotein interactions

Abstract

The flavodoxin from Desulfovibrio vulgaris, strain Miyazaki F (FD-DvMF), binds one molecule of flavin mononucleotide (FMN) as a cofactor and is considered to associate with electron transport reactions. However, although the 3D structure of the related FD from D. vulgaris strain Hildenborough has been determined, that for FD-DvMF has not. In this study, we have predicted the protein structures of the wild type and the W59F, Y97F and W59F-Y97F substitutional mutants of FD-DvMF by a homology modelling approach. Subsequently, the dynamic properties of these four FD-DvMF variants were investigated by molecular dynamics simulations. The results revealed that peptide O of Trp59 formed H-bond with Tyr99OH only in Y97F, leading to FMN being buried deeper inside the protein than in the other three variants and reducing the accessibility of water to FMN. The phosphate oxygen atoms formed extensive H-bonds with amino acid residues in the 10-loop region in all variants resulting in the highest degree of stabilisation. The OH groups of the ribityl chain and the isoalloxazine ring formed H-bonds with amino acid residues of the 60- and 90-loop regions, respectively. The decomposition free energy calculations suggest that the greatest contribution come from the 10-loop region, which is compatible with the published data. That the calculated binding and decomposition free energies were both greatest in Y97F is proposed to be due to the H-bond between peptide O of Trp59 and Tyr99OH.

Keywords:

• flavodoxin
• molecular dynamic simulation
• MM-PBSA free energy calculation
• decomposition free energy calculation

Acknowledgements

This study was supported by The Royal Golden Jubilee PhD Program (3.C.CU/50/S.1) from Chulalongkorn University and The Thailand Research Fund (TRF). We would like to thank the reviewers for their useful suggestions on this article. We appreciate the correction of English from Dr Robert Butcher. We thank the Higher Education Research Promotion and National Research University Project of Thailand, Office of the Higher Education Commission (HR 1155A). The Computational Chemistry Unit Cell, Chulalongkorn University, the National Electronics and Computer Technology Center (NECTEC) and the Thai Government Stimulus Package 2 (TKK2555) under the Project for Establishment of Comprehensive Center for Innovative Food, Health Products and Agriculture are acknowledged.