Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study

Abstract

MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen, Mycobacterium tuberculosis (Mtb), aiding their survival. Though extensively studied, the mode of action between the antitoxin-toxin and DNA of this family remains largely unclear. Here, the important interactions between MazF7 toxin and MazE7 antitoxin, and how MazE7 binds its promoter/operator region have been studied. To elucidate this, molecular dynamics (MD) simulation has been performed on MazE7, MazF7, MazEF7, MazEF7-DNA, and MazE7-DNA complexes to investigate how MazF7 and DNA affect the conformational change and dynamics of MazE7 antitoxin. This study demonstrated that the MazE7 dimer is disordered and one monomer (Chain C) attains stability after binding to the MazF7 toxin. Both the monomers (Chain C and Chain D) however are stabilized when MazE7 binds to DNA. MazE7 is also observed to sterically inhibit tRNA from binding to MazF7, thus suppressing its toxic activity. Comparative structural analysis performed on all the available antitoxins/antitoxin-toxin-DNA structures revealed MazEF7-DNA mechanism was similar to another TA system, AtaRT_E.coli. Simulation performed on the crystal structures of AtaR, AtaT, AtaRT, AtaRT-DNA, and AtaR-DNA showed that the disordered AtaR antitoxin attains stability by AtaT and DNA binding similar to MazE7. Based on these analyses it can thus be hypothesized that the disordered antitoxins enable tighter toxin and DNA binding thus preventing accidental toxin activation. Overall, this study provides crucial structural and dynamic insights into the MazEF7 toxin-antitoxin system and should provide a basis for targeting this TA system in combating Mycobacterium tuberculosis.

Communicated by Ramaswamy H. Sarma

Keywords:

• Mycobacterium tuberculosis
• toxin-antitoxin
• MazEF7 system
• conformational stability
• dynamics

Acknowledgements

RS acknowledges CSIR-HRDG for providing her fellowship. The authors are also thankful to National Supercomputing Machine (NSM) for providing computing resources of ‘PARAM Shakti’ at IIT Kharagpur, implemented by C-DAC and supported by the Ministry of Electronics and Information Technology (MeitY) and Department of Science and Technology (DST), Government of India.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors contributions

RS, GB and AKD conceived the project. RS and GB performed the experiments and analysed the data. SD and AKD supervised the project. All authors wrote and edited the manuscript.

Additional information

Funding

This work was funded by the Department of Biotechnology (DBT), Govt. of India (BT/PR40990/MED/29/1540/2020).