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

References

• Amala, M., Rajamanikandan, S., Prabhu, D., Kanagarajan, S., & Jeyakanthan, J. (2019). Identification of anti-filarial leads against aspartate semialdehyde dehydrogenase of wolbachia endosymbiont of Brugia malayi: Combined molecular docking and molecular dynamics approaches. Journal of Biomolecular Structure and Dynamics, 37(2), 394–410. doi: 10.1080/07391102.2018.1427633
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. doi:10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Choubey, S. K., Prabhu, D., Nachiappan, M., Biswal, J., & Jeyakanthan, J. (2017). Molecular modeling, dynamics studies and density functional theory approaches to identify potential inhibitors of SIRT4 protein from Homo sapiens: A novel target for the treatment of type 2 diabetes. Journal of Biomolecular Structure and Dynamics, 35(15), 3316–3329. doi:10.1080/07391102.2016.1254117
   PubMed Web of Science ®Google Scholar
• Cusack, S. (1995). Eleven down and nine to go. Nature Structural Biology, 2(10), 824–831.
   PubMedGoogle Scholar
• Cusack, S., Hartlein, M., & Leberman, R. (1991). Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Research, 19(13), 3489–3498. doi:10.1093/nar/19.13.3489
   PubMed Web of Science ®Google Scholar
• De Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. doi:10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). PyMOL (p. 700). San Carlos, CA: DeLano Scientific.
   Google Scholar
• Delarue, M., & Moras, D. (1993). The aminoacyl-tRNA synthetase family: Modules at work. Bioessays. News and Reviews in Molecular, Cellular and Developmental Biology, 15(10), 675–687. doi:10.1002/bies.950151007
   PubMed Web of Science ®Google Scholar
• Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003). HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society, 125(7), 1731–1737. doi:10.1021/ja026939x
   PubMed Web of Science ®Google Scholar
• Eriani, G., Delarue, M., Poch, O., Gangloff, J., & Moras, D. (1990). Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature, 347(6289), 203–206. doi:10.1038/347203a0
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., … Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for proteinis–ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196.
   PubMed Web of Science ®Google Scholar
• (2014). Glide. New York, NY: Schrödinger, LLC.
   Google Scholar
• Guru Raj Rao, R., Biswal, J., Prabhu, D., Sureka, K., & Jeyakanthan, J. (2017). Identification of Potential Inhibitors for AIRS from de novo purine biosynthesis pathway through Molecular modeling Studies – A Computational approach. Journal of Biomolecular Structure and Dynamics, 34(10), 2199–2213. doi:10.1080/07391102.2015.1110833
   Web of Science ®Google Scholar
• Halgren, T. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. doi:10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. doi:10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1998). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
   Web of Science ®Google Scholar
• Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. doi:10.1021/ja9621760
   Web of Science ®Google Scholar
• Kawata, M., & Nagashima, U. (2001). Particle mesh Ewald method for three-dimensional systems with two-dimensional periodicity. Chemical Physics Letters, 340(1–2), 165–172. doi:10.1016/S0009-2614(01)00393-1
   Web of Science ®Google Scholar
• Krissinel, E., & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology, 372(3), 774–797. doi:10.1016/j.jmb.2007.05.022
   PubMed Web of Science ®Google Scholar
• Kumar, A., Manimekalai, M. S. S., Balakrishna, A. M., Priya, R., Biuković, G., Jeyakanthan, J., & Grüber, G. (2010). The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding. Journal of Molecular Biology, 401(5), 892–905. doi:10.1016/j.jmb.2010.06.070
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A. (2001). PDBsum: summaries and analyses of PDB structures. Nucleic Acids Research, 29(1), 221–222. doi:10.1093/nar/29.1.221
   PubMed Web of Science ®Google Scholar
• (2018). LigPrep. New York, NY: Schrödinger, LLC.
   Google Scholar
• Lovell, S. C., Davis, I. W., Arendall, W. B., III, de Bakker, P. I. W., Word, J. M., Prisant, M. G., … Richardson, D. C. (2002). Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins: Structure, Function, and Bioinformatics, 50, 437–450. doi:10.1002/prot.10286
   Web of Science ®Google Scholar
• McClain, W. H., Schneider, J., & Bhattacharya, S. (1998). The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation. Proceedings of the National Academy of Sciences of the United States of America, 95(2), 460–465. doi:10.1073/pnas.95.2.460
   PubMed Web of Science ®Google Scholar
• Nachiappan, M., Jain, V., Sharma, A., Yogavel, M., & Jeyakanthan, J. (2018). Structural and functional analysis of Glutaminyl-tRNA synthetase (TtGlnRS) from Thermus thermophilus HB8 and its complexes. International Journal of Biological Macromolecules, Dec120 (Part B), 1379–1386. doi:10.1016/j.ijbiomac.2018.09.115
   PubMedGoogle Scholar
• Nureki, O., Vassylyev, D. G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., … Morikawa, K. (1995). Architecture of class defining and specific domains of glutamyl-tRNA synthetase. Science, 267(5206), 1958–1964.
   PubMed Web of Science ®Google Scholar
• Perona, J. J., Swanson, R. N., & Rould, M. A. (1989). Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science, 246(4934), 1152–1154.
   PubMed Web of Science ®Google Scholar
• Rodriguez-Hernandez, A., Spears, J. L., Gaston, K. W., Limbach, P. A., Gamper, H., Hou, Y.-M., … Perona, J. J. (2013). Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position. Journal of Molecular Biology, 425(20), 3888–906. doi: 10.1016/j.jmb.2013.05.018
   PubMed Web of Science ®Google Scholar
• Rogers, M. J., Weygand-Durasević, I., Schwob, E. (1993). Selectivity and specificity in the recognition of tRNA by E. coli glutaminyl-tRNA synthetase. Biochimie, 75(12), 1083–1090.
   PubMed Web of Science ®Google Scholar
• Rould, M. A., Perona, J. J., & Steitz, T. A. (1991). Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature, 352(6332), 213–218. doi:10.1038/352213a0
   PubMed Web of Science ®Google Scholar
• Rould, M. A., Perona, J. J., & Söll, D. (1989). Structure of glutaminyl-tRNA synthetase complexed with tRNA Gln and ATP at 2.8 Å resolution. Science, 246(4934), 1135–1142.
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. doi:10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. doi:10.1107/S0907444904011679
   PubMedGoogle Scholar
• Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., & van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation program package. The Journal of Physical Chemistry A, 103(19), 3596–3607. doi:10.1021/jp984217f
   Web of Science ®Google Scholar
• Sherlin, L. D., Bullock, T. L., Newberry, K. J., Lipman, R. S., Hou, Y.-M., Beijer, B., … Erona, J. J. (2000). Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases. Edited by J. Doudna. Journal of Molecular Biology, 299(2), 431–446. doi:10.1006/jmbi.2000.3749
   PubMed Web of Science ®Google Scholar
• Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins: Structure, Function, and Genetics, 17(4), 355–362. doi:10.1002/prot.340170404
   PubMed Web of Science ®Google Scholar
• Surekha, K., Nachiappan, M., Prabhu, D., Choubey, S. K., Biswal, J., & Jeyakanthan, J. (2017). Identification of potential inhibitors for oncogenic target of dihydroorotate dehydrogenase using in silico approaches. Journal of Molecular Structure, 1127, 675–688. doi:10.1016/j.molstruc.2016.08.015
   Web of Science ®Google Scholar
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680. doi:10.1093/nar/22.22.4673
   PubMed Web of Science ®Google Scholar
• Turner, P. J. (2005). XMGRACE, Version 5.1.19. Center for coastal and land-margin research. Beaverton, OR: Oregon Graduate Institute of Science and Technology.
   Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, W407–W410. doi:10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar