Protein dynamics and molecular motions study in relation to molecular interaction between proteins from sulfur oxidizing proteobacteria Allochromatium vinosum

Abstract

The gamma-proteobacteria Allochromatium vinosum DSM 180^T (A. vinosum) encodes the sulfur oxidizing dsr operon comprising of 15 genes. Dsr proteins are involved in oxidation of sulfur globules produced as an obligatory intermediate during the sulfur oxidation process. The dsrA and dsrB gene products are known to function as a α₂β₂ hetero-tetramer and the protein complex plays the catalytic role in sulfur oxidation process. DsrC has a highly conserved C-terminal domain that forms a flexible arm, where two strictly conserved cysteines were found to act as a substrate donating residue for DsrAB instead of being a subunit of this redox enzyme. Therefore, to elucidate the molecular mechanism of the sulfur oxidation process here an attempt was made to study the dynamics, stability and binding mechanisms of DsrAB and DsrC proteins through computational docking and molecular dynamics (MD) simulations. This structure function relationship investigation revealed that the C-terminal domain of DsrC interacts with DsrA of DsrAB protein complex for catalytic functions. Some basic amino acid residues of DsrC are found to form the catalytic pockets along with DsrAB protein complex where the sulfur anions bind to get oxidized. Structural dynamics and fluctuations as well as the secondary structural alterations study revealed the possible regions responsible for protein-protein interactions. Principal Component Analysis (PCA) of protein motions displayed that the collective motions of DsrAB-DsrC complex was higher and more anti-correlated than the unbound DsrAB form. The present molecular insight study would therefore help researchers to predict the plausible biochemical mechanism of sulfur oxidation process in sulfur metabolic pathways in near future.

Communicated by Ramaswamy H. Sarma

Keywords:

• Reverse dissimilatory sulfite reductase
• sulfur oxidation mechanism
• structure–dynamics–function relationship
• PCA analysis of molecular motion
• free energy landscape

Disclosure statement

We declare no conflict of interest.

Additional information

Funding

The authors would like to thank the Department of Biotechnology (DBT) funded Bioinformatics Infrastructure Facility, the Department of Science and Technology-Promotion of University Research and Scientific Excellence (DST-PURSE) program going on in the Department of Biochemistry and Biophysics, University of Kalyani for the infrastructural support. Ms. Semanti Ghosh is thankful to the University of Kalyani, West Bengal, India for the fellowship support. Authors are thankful to the project of DBT, Government of India (BT/PR7843/BID/7/436/2013) and Indian Council of Medical Research (ICMR) [Grant No. BIC/12(02)/2014] for the instrumental support.