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Research Article

Molecular dynamics simulation study on Bacillus subtilis EngA: the presence of Mg2+ at the active-sites promotes the functionally important conformation

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Pages 9219-9231 | Received 16 Aug 2022, Accepted 20 Nov 2022, Published online: 29 Nov 2022

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
  • Bharat, A., Jiang, M., Sullivan, S. M., Maddock, J. R., & Brown, E. D. (2006). Cooperative and critical roles for both G domains in the GTPase activity and cellular function of ribosome-associated Escherichia coli EngA. Journal of Bacteriology, 188(22), 7992–7996. https://doi.org/10.1128/JB.00959-06
  • Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., & Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications, 180(10), 1961–1972. https://doi.org/10.1016/j.cpc.2009.05.011
  • Bourne, H. R., Sanders, D. A., & McCormick, F. (1990). The GTPase superfamily: A conserved switch for diverse cell functions. Nature, 348(6297), 125–132. https://doi.org/10.1038/348125a0
  • Bourne, H. R., Sanders, D. A., & McCormick, F. (1991). The GTPase superfamily: Conserved structure and molecular mechanism. Nature, 349(6305), 117–127.
  • Britton, R. A. (2009). Role of GTPases in bacterial ribosome assembly. Annual Review of Microbiology, 63, 155–176. https://doi.org/10.1146/annurev.micro.091208.073225
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101.
  • da Silveira Tomé, C., Foucher, A.-E., Jault, J.-M., & Housset, D. (2018). High concentrations of GTP induce conformational changes in the essential bacterial GTPase EngA and enhance its binding to the ribosome. The FEBS Journal, 285(1), 160–177. https://doi.org/10.1111/febs.14333
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Eargle, J., & Luthey-Schulten, Z. (2012). NetworkView: 3D display and analysis of protein· RNA interaction networks. Bioinformatics (Oxford, England), 28(22), 3000–3001.
  • Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., & Scharf, M. (1995). The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. Journal of Computational Chemistry, 16(3), 273–284. https://doi.org/10.1002/jcc.540160303
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Floyd, R. W. (1962). Algorithm 97: Shortest path. Communications of the ACM, 5(6), 345. https://doi.org/10.1145/367766.368168
  • Foucher, A.-E., Reiser, J.-B., Ebel, C., Housset, D., & Jault, J.-M. (2012). Potassium acts as a GTPase-activating element on each nucleotide-binding domain of the essential Bacillus subtilis EngA. PLoS One. 7(10), e46795. https://doi.org/10.1371/journal.pone.0046795
  • Girvan, M., & Newman, M. E. (2002). Community structure in social and biological networks. Proceedings of the National Academy of Sciences, 99(12), 7821–7826. https://doi.org/10.1073/pnas.122653799
  • Glykos, N. M. (2006). Software news and updates carma: A molecular dynamics analysis program. Journal of Computational Chemistry, 27(14), 1765–1768. https://doi.org/10.1002/jcc.20482
  • Goto, S., Muto, A., & Himeno, H. (2013). GTPases involved in bacterial ribosome maturation. The Journal of Biochemistry, 153(5), 403–414. https://doi.org/10.1093/jb/mvt022
  • Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  • Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447.
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38.
  • Hwang, J., & Inouye, M. (2001). An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima. The Journal of Biological Chemistry, 276(33), 31415–31421. https://doi.org/10.1074/jbc.M104455200
  • Hwang, J., & Inouye, M. (2006). The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli. Molecular Microbiology, 61(6), 1660–1672.
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. https://doi.org/10.1002/bip.360221211
  • Karbstein, K. (2007). Role of GTPases in ribosome assembly. Biopolymers, 87(1), 1–11. https://doi.org/10.1002/bip.20762
  • Lamb, H. K., Thompson, P., Elliott, C., Charles, I. G., Richards, J., Lockyer, M., Watkins, N., Nichols, C., Stammers, D. K., Bagshaw, C. R., Cooper, A., & Hawkins, A. R. (2007). Functional analysis of the GTPases EngA and YhbZ encoded by Salmonella typhimurium. Protein Science: A Publication of the Protein Society, 16(11), 2391–2402.
  • Leipe, D. D., Wolf, Y. I., Koonin, E. V., & Aravind, L. (2002). Classification and evolution of P-loop GTPases and related ATPases. Journal of Molecular Biology, 317(1), 41–72. https://doi.org/10.1006/jmbi.2001.5378
  • Lindahl, E., Hess, B., & Van Der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7(8), 306–317. https://doi.org/10.1007/s008940100045
  • Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
  • Majumdar, S., Acharya, A., Tomar, S. K., & Prakash, B. (2017). Disrupting domain-domain interactions is indispensable for EngA-ribosome interactions. Biochimica et Biophysica Acta. Proteins and Proteomics, 1865(3), 289–303. https://doi.org/10.1016/j.bbapap.2016.12.005
  • Muench, S. P., Xu, L., Sedelnikova, S. E., & Rice, D. W. (2006). The essential GTPase YphC displays a major domain rearrangement associated with nucleotide binding. Proceedings of the National Academy of Sciences, 103(33), 12359–12364. https://doi.org/10.1073/pnas.0602585103
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612.
  • Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
  • Robinson, V. L., Hwang, J., Fox, E., Inouye, M., & Stock, A. M. (2002). Domain arrangement of Der, a switch protein containing two GTPase domains. Structure (London, England: 1993), 10(12), 1649–1658.
  • Šali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3), 779–815.
  • Salomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle Mesh Ewald. Journal of Chemical Theory and Computation, 9(9), 3878–3888. https://doi.org/10.1021/ct400314y
  • Schaefer, L., Uicker, W. C., Wicker-Planquart, C., Foucher, A.-E., Jault, J.-M., & Britton, R. A. (2006). Multiple GTPases participate in the assembly of the large ribosomal subunit in Bacillus subtilis. Journal of Bacteriology, 188(23), 8252–8258. https://doi.org/10.1128/JB.01213-06
  • Sethi, A., Eargle, J., Black, A. A., & Luthey-Schulten, Z. (2009). Dynamical networks in tRNA: Protein complexes. Proceedings of the National Academy of Sciences, 106(16), 6620–6625. https://doi.org/10.1073/pnas.0810961106
  • Tomar, S. K., Dhimole, N., Chatterjee, M., & Prakash, B. (2009). Distinct GDP/GTP bound states of the tandem G-domains of EngA regulate ribosome binding. Nucleic Acids Research, 37(7), 2359–2370.
  • Upendra, N., & Krishnaveni, S. (2020). Molecular dynamics simulation study on Thermotoga maritima EngA: GTP/GDP bound state of the second G-domain influences the domain-domain interface interactions. Journal of Biomolecular Structure and Dynamics, 5, 1–13.
  • Upendra, N., & Krishnaveni, S. (2022). Conformational exploration of RbgA using molecular dynamics: Possible implications in ribosome maturation and GTPase activity in different nucleotide bound states. Journal of Molecular Graphics & Modelling, 111, 108087. https://doi.org/10.1016/j.jmgm.2021.108087
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718.
  • Vetter, I. R., & Wittinghofer, A. (2001). The guanine nucleotide-binding switch in three dimensions. Science (New York, N.Y.), 294(5545), 1299–1304. https://doi.org/10.1126/science.1062023
  • Webb, B., & Sali, A. (2014). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 47(1), 5–6. https://doi.org/10.1002/0471250953.bi0506s47
  • Wittinghofer, A., & Vetter, I. R. (2011). Structure-function relationships of the G domain, a canonical switch motif. Annual Review of Biochemistry, 80(1), 943–971. https://doi.org/10.1146/annurev-biochem-062708-134043
  • Yang, Z., Lasker, K., Schneidman-Duhovny, D., Webb, B., Huang, C. C., Pettersen, E. F., Goddard, T. D., Meng, E. C., Sali, A., & Ferrin, T. E. (2012). UCSF Chimera, MODELLER, and IMP: An integrated modeling system. Journal of Structural Biology, 179(3), 269–278.
  • Zhang, X., Yan, K., Zhang, Y., Li, N., Ma, C., Li, Z., Zhang, Y., Feng, B., Liu, J., Sun, Y., Xu, Y., Lei, J., & Gao, N. (2014). Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly. Nucleic Acids Research, 42(21), 13430–13439.

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