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 Thermus thermophilus 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 TtGlnRS 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 tRNAGln specific for GlnRS was docked into the active site of the TtGlnRS 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 TtGlnRS was further proved by isothermal titration calorimetry.
AbbreviationsaaRSs
aminoacyl-tRNA synthetases
AMPadenosine monophosphate
ATPadenosine triphosphate
GlideGrid-based LIgand Docking with Energetic
GlnRSglutaminyl-tRNA synthetase
GRAVYGRand AVerage of hydropathicitY
GROMACSGROingen Machine for Chemical Simulations
HADDOCKHigh Ambiguity Driven protein–protein DOCKing
ITCisothermal titration calorimetry
2MA2-methyladenosine 5'-(dihydrogen phosphate)
MDSmolecular dynamics simulation
5MU5-methyluridine 5'-monophosphate
NPTnumber of particles, pressure and temperature
NVTnumber of particles, volume and temperature
OPLS-AAoptimized potential for liquid simulation all atom
PDBBrookhaven Protein Databank
PMEParticle-Mesh Ewald
QSI5'-o-[n-(l-Glutaminyl)-sulfamoyl]adenosine
Rgradius of gyration
RMSDroot mean square deviation
RMSFroot mean square fluctuation
4SU4-thiouracil 5'-monophosphate
SPCsimple point charge
tRNAtransfer ribo nucleic acid
TtThermus thermophilus
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'-o-[n-(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
Thermus thermophilus
extra precision
Communicated by Ramaswamy H. Sarma