Conformational changes in glutaminyl-tRNA synthetases upon binding of the substrates and analogs using molecular docking and molecular dynamics approaches

Aminoacyl-tRNA synthetases (aaRSs) are considered as important components in protein translation as they facilitate the attachment of specific transfer RNA (tRNA) to form aminoacyl-tRNAs. Our study focused on understanding the crystal structure of Glutaminyl-tRNA synthetase (GlnRS) from <i>Thermus thermophilus</i> HB8 (PDB ID:5ZDO) and mechanism of formation of enzyme–substrate complex using substrates and its analogs by applying molecular dynamics simulation (MDS) to investigate the conformational changes. Least energy structure of <i>Tt</i>GlnRS was considered to dock the enzyme substrates such as glutamine (Gln), glutamic acid (Glu), adenosine monophosphate (AMP), adenosine triphosphate (ATP), QSI and various substrate analogs (2MA, 4SU and 5MU) onto the active site of the enzyme. We focused on comparative analysis of binding specificity between Gln and Glu; similarly, ATP and AMP. Active site organization as observed by MDS analysis showed interactive changes associated with substrate and catalytically important loops. Study found that when tRNA^Gln specific for GlnRS was docked into the active site of the <i>Tt</i>GlnRS enzyme it interacts with 2' OH on the ribose acceptor end of the tRNA. Upon validation with 50 ns MDS, the maximum deviations and conformational changes of secondary structural elements were observed to be high in the loop regions of enzyme–substrate complexes. Binding affinity of ATP to <i>Tt</i>GlnRS was further proved by isothermal titration calorimetry.
AbbreviationsaaRSsaminoacyl-tRNA synthetasesAMPadenosine monophosphateATPadenosine triphosphateGlideGrid-based LIgand Docking with EnergeticGlnRSglutaminyl-tRNA synthetaseGRAVYGRand AVerage of hydropathicitYGROMACSGROingen Machine for Chemical SimulationsHADDOCKHigh Ambiguity Driven protein–protein DOCKingITCisothermal titration calorimetry2MA2-methyladenosine 5'-(dihydrogen phosphate)MDSmolecular dynamics simulation5MU5-methyluridine 5'-monophosphateNPTnumber of particles, pressure and temperatureNVTnumber of particles, volume and temperatureOPLS-AAoptimized potential for liquid simulation all atomPDBBrookhaven Protein DatabankPMEParticle-Mesh EwaldQSI5'-<i>o</i>-[<i>n</i>-(l-Glutaminyl)-sulfamoyl]adenosineRgradius of gyrationRMSDroot mean square deviationRMSFroot mean square fluctuation4SU4-thiouracil 5'-monophosphateSPCsimple point chargetRNAtransfer ribo nucleic acidTt<i>Thermus thermophilus</i>XPextra precision aminoacyl-tRNA synthetases adenosine monophosphate adenosine triphosphate Grid-based LIgand Docking with Energetic glutaminyl-tRNA synthetase GRand AVerage of hydropathicitY GROingen Machine for Chemical Simulations High Ambiguity Driven protein–protein DOCKing isothermal titration calorimetry 2-methyladenosine 5'-(dihydrogen phosphate) molecular dynamics simulation 5-methyluridine 5'-monophosphate number of particles, pressure and temperature number of particles, volume and temperature optimized potential for liquid simulation all atom Brookhaven Protein Databank Particle-Mesh Ewald 5'-<i>o</i>-[<i>n</i>-(l-Glutaminyl)-sulfamoyl]adenosine radius of gyration root mean square deviation root mean square fluctuation 4-thiouracil 5'-monophosphate simple point charge transfer ribo nucleic acid <i>Thermus thermophilus</i> extra precision Communicated by Ramaswamy H. Sarma