417
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Structural insights into the interactions of flavin mononucleotide (FMN) and riboflavin with FMN riboswitch: a molecular dynamics simulation study

ORCID Icon, ORCID Icon & ORCID Icon
Pages 3856-3866 | Received 20 Jun 2019, Accepted 03 Sep 2019, Published online: 15 Sep 2019

References

  • Abraham, E. P. (1946). Discovery and development of penicillin. Dental Record, 66, 1-10. doi: 10.1016/j.athoracsur.2014.06.054
  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. doi: 10.1016/j.softx.2015.06.001
  • Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. doi: 10.1063/1.448118
  • Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. doi: 10.1016/0010-4655(95)00042-E
  • Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., … Zardecki, C. (2002). The protein data bank. Acta Crystallographica Section D Biological Crystallography, 58(6), 899–907. doi: 10.1107/S0907444902003451
  • D’Costa, V. M. (2006). Sampling the antibiotic resistome. Science, 311(5759), 374–377. doi: 10.1126/science.1120800
  • Gilbert, S. D., Stoddard, C. D., Wise, S. J., & Batey, R. T. (2006). Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. Journal of Molecular Biology, 359(3), 754–768. doi: 10.1016/j.jmb.2006.04.003
  • Guy, A. T., Piggot, T. J., & Khalid, S. (2012). Single-stranded DNA within nanopores: Conformational Dynamics and implications for sequencing; a molecular dynamics simulation study. Biophysical Journal, 103, 1028–1036. (September). doi: 10.1016/j.bpj.2012.08.012
  • Helmling, C., Klötzner, D.-P., Sochor, F., Mooney, R. A., Wacker, A., Landick, R., … Schwalbe, H. (2018). Life times of metastable states guide regulatory signaling in transcriptional riboswitches. Nature Communications, 9(1), 944. doi: 10.1038/s41467-018-03375-w
  • Howe, J. A., Wang, H., Fischmann, T. O., Balibar, C. J., Xiao, L., Galgoci, A. M., … Roemer, T. (2015). Selective small-molecule inhibition of an RNA structural element. Nature, 526(7575), 672–677. doi: 10.1038/nature15542
  • Hu, G., Ma, A., & Wang, J. (2017). Ligand selectivity mechanism and conformational changes in guanine riboswitch by molecular dynamics simulations and free energy calculations. Journal of Chemical Information and Modeling, 57(4), 918–928. doi: 10.1021/acs.jcim.7b00139
  • Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation of high-quality atomic charges. AM1-BCC model. II. Parameterization and validation. Journal of Computational Chemistry, 23(16), 1623–1641. doi: 10.1002/jcc.10128
  • Kesherwani, M., Kutumbarao, N. H. V., & Velmurugan, D. (2018). Conformational dynamics of thiM riboswitch to understand the gene regulation mechanism using Markov state modeling and the residual fluctuation network approach. Journal of Chemical Information and Modeling, 58(8), 1638–1651. doi: 10.1021/acs.jcim.8b00155
  • Kumari, R., Kumar, R., & Lynn, A. (2014). G-MMPBSA – A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. doi: 10.1021/ci500020m
  • Kuppuraj, G., Kruise, D., & Yura, K. (2014). Conformational behavior of flavin adenine dinucleotide: Conserved stereochemistry in bound and free states. The Journal of Physical Chemistry B, 118(47), 13486–13497. doi: 10.1021/jp507629n
  • Lin, J. C., Hyeon, C., & Thirumalai, D. (2014). Sequence-dependent folding landscapes of adenine riboswitch aptamers. Physical Chemistry Chemical Physics, 16(14), 6376–6382. doi: 10.1039/C3CP53932F
  • Luzar, A., & Chandler, D. (1996). Hydrogen bond kinetics in liqiud water. Nature, 379(6560), 55–57. doi: 10.1038/379055a0
  • Matzner, D., & Mayer, G. (2015). (Dis)similar analogues of riboswitch metabolites as antibacterial lead compounds. Journal of Medicinal Chemistry, 58(8), 3275–3286. doi: 10.1021/jm500868e
  • Noeske, J., Buck, J., Fürtig, B., Nasiri, H. R., Schwalbe, H., & Wöhnert, J. (2007). Interplay of “induced fit” and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Research, 35(2), 572–583. doi: 10.1093/nar/gkl1094
  • Origin. 2003. Origin 7.5. Northampton, MA: OriginLab Corp.
  • Priyakumar, U. D. (2010). Atomistic details of the ligand discrimination mechanism of S MK/SAM-III riboswitch. The Journal of Physical Chemistry B, 114(30), 9920–9925. doi: 10.1021/jp1042427
  • Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854. doi: 10.1093/bioinformatics/btt055
  • Pueyo, J. J., Curley, G. P., & Mayhew, S. G. (1996).Kinetics and thermodynamics of the binding of riboflavin, riboflavin 5′-phosphate and riboflavin 3′, 5′-bisphosphate by apoflavodoxins.Biochemical journal, 861, 855–861. doi: 10.1042/bj3130855
  • Rawat, N., & Biswas, P. (2014). Hydrogen bond dynamics in intrinsically disordered proteins. The Journal of Physical Chemistry B, 118(11), 3018–3025. doi: 10.1021/jp5013544
  • Rossolini, G. M., Arena, F., Pecile, P., & Pollini, S. (2014). Update on the antibiotic resistance crisis. Current Opinion in Pharmacology, 18, 56–60. doi: 10.1016/j.coph.2014.09.006
  • San Diego, Dassault Systèmes (n.d.). BIOvIA, D. S. discovery studio modeling environment. San Diego, CA: Dassault Systèmes.
  • Schank, R. C. (2010). The pragmatics of learning by doing. Pragmatics and Society, 1(1), 157–172. doi: 10.1261/rna.5090103
  • Schrödinger, LLC. (2015). The PyMOL molecular graphics system, version{\textasciitilde}1.8. New York, NY: Schrödinger, LLC.
  • Serganov, A., Huang, L., & Patel, D. J. (2009). Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature, 458(7235), 233–237. doi: 10.1038/nature07642
  • Sharma, M., Bulusu, G., & Mitra, A. (2009). MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch. RNA, 15(9), 1673–1692. doi: 10.1261/rna.1675809
  • Sousa, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1), 367–368. (doi: 10.1186/1756-0500-5-367
  • Theuretzbacher, U., & Toney, J. H. (2006). Nature’s clarion call of antibacterial resistance: Are we listening? Current Opinion in Investigational Drugs (London, England: 2000), 7(2), 158–166.
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi: 10.1002/jcc.20291
  • Vicens, Q., Mondragón, E., & Batey, R. T. (2011). Molecular sensing by the aptamer domain of the FMN riboswitch: A general model for ligand binding by conformational selection. Nucleic Acids Research, 39(19), 8586–8598. doi: 10.1093/nar/gkr565
  • Wang, H., Mann, P. A., Xiao, L., Gill, C., Galgoci, A. M., Howe, J. A., … Roemer, T. (2017). Dual-targeting small-molecule inhibitors of the Staphylococcus aureus FMN riboswitch disrupt riboflavin homeostasis in an infectious setting. Cell Chemical Biology, 24(5), 576–588.e6. doi: 10.1016/j.chembiol.2017.03.014
  • Wickiser, J. K., Winkler, W. C., Breaker, R. R., & Crothers, D. M. (2005). The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular Cell, 18(1), 49–60. doi: 10.1016/j.molcel.2005.02.032
  • Winkler, W. C., Cohen-Chalamish, S., & Breaker, R. R. (2002). An mRNA structure that controls gene expression by binding FMN. Proceedings of the National Academy of Sciences, 99(25), 15908–15913. doi: 10.1073/pnas.212628899

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.