Molecular dynamics simulation study on Thermotoga maritima EngA: GTP/GDP bound state of the second G-domain influences the domain–domain interface interactions

Abstract

EngA, a GTPase involved in the late steps of ribosome maturation, consists of two GTP binding domains (G-domains) [GD1, GD2] and a C-terminal domain. The combination of GTP/GDP in G-domains dictates its binding to the ribosomal subunits by altering its conformation. Studies and comparisons on the available structures of EngA enable us to understand the correlation between nucleotide bound states and its conformation. Using all-atom molecular dynamics (MD) simulations, we have explored the conformational behavior of EngA from Thermotoga maritima (TmDer) upon binding the various combinations of GTP and GDP. Analyses of Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) emphasize the importance of the second G-domain nucleotide bound state. RMSD and Rg exhibit slightly lower values when GTP is embedded in GD2 compared to GDP. These lower values are due to Sw-II of GD2, which has been observed from RMSF plot. Further investigation on the effects of GD2 nucleotide bound state using Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis manifests an allosteric connection between GD2 nucleotide bound state and the GD1–KH interface. This is further validated by extracting electrostatic interactions and H-bonds at the GD1–KH interface. In silico mutations at the GD1 interface of KH domain affect the Sw-II mobility of GD2 by showing inverted behavior. This suggests using the second G-domain as an antibacterial target and further simulation studies on different species of EngA are to be explored.

Communicated by Ramaswamy H. Sarma

Keywords:

• Molecular dynamics
• GTPase
• EngA
• Thermotoga maritima
• GD1–KH interface

Acknowledgements

We thank University of Mysore for providing all the facilities and sanctioning minor research project. Author U.N. thank UGC for providing BSR-RFSMS fellowship for financial assistance. We acknowledge Prof. Balaji Prakash, Former Senior Principal Scientist, Department of Molecular Nutrition, CSIR-CFTRI, Mysuru and Dr. Lalitha R Gowda, Former Chief Scientist, CSIR-CFTRI for all support and useful discussions to carry out this work.

Disclosure statement

No potential conflict of interest was reported by the authors.