Structural insights into the interactions of xpt riboswitch with novel guanine analogues: a molecular dynamics simulation study

References

• Allner, O., Nilsson, L., & Villa, A. (2013). Loop-loop interaction in an adenine-sensing riboswitch: A molecular dynamics study. RNA, 19, 916–926.
   Google Scholar
• Banas, P., Walter, N. G., Sponer, J., & Otyepka, M. (2010). Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. Journal of Physical Chemistry B, 114, 8701–8712.
   PubMed Web of Science ®Google Scholar
• Batey, R. T., Gilbert, S. D., & Montange, R. K. (2004). Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411–415.
   PubMed Web of Science ®Google Scholar
• 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, 3684–3690.
   Web of Science ®Google Scholar
• Blount, K. F., & Breaker, R. R. (2006). Riboswitches as antibacterial drug targets. Nature Biotechnology, 24, 1558–1564.
   PubMed Web of Science ®Google Scholar
• Breaker, R. R. (2011). Prospects for riboswitch discovery and analysis. Molecular Cell, 43, 867–879.
   PubMed Web of Science ®Google Scholar
• Brenner, M. D., Scanlan, M. S., Nahas, M. K., Ha, T., & Silverman, S. K. (2010). Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry, 49, 1596–1605.
   PubMedGoogle Scholar
• Buck, J., Furtig, B., Noeske, J., Wohnert, J., & Schwalbe, H. (2007). Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America, 104, 15699–15704.
   Google Scholar
• Case, D. A., Darden, T. A., Cheatham III, T. E., Simmerling, C. L., Wang, J., Duke R. E., & Luo, R. (2008). AMBER 10. San Francisco, CA: University of California San Francisco Press.
   Google Scholar
• Cheatham, T. E., & Kollman, P. A. (1997). Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. Journal of the American Chemical Society, 119, 4805–4825.
   Web of Science ®Google Scholar
• Daldrop, P., Reyes, F. E., Robinson, D. A., Hammond, C. M., Lilley, D. M., Batey, R. T., & Brenk, R. (2011). Novel ligands for a purine riboswitch discovered by RNA-ligand docking. Chemistry & Biology, 18, 324–335.
   PubMed Web of Science ®Google Scholar
• Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971). Self consistent molecular orbital methods.9. An extended Gaussian-type basis for molecular orbital studies of organic molecules. The Journal of Chemical Physics, 54, 724–728.
   Web of Science ®Google Scholar
• Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., & Yang, R. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24, 1999–2012.
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., & Montgomery, J. A. (2004). Gaussian 03. (Version C.02). Wallingsford, CT: Gaussian.
   Google Scholar
• Fuchs, R. T., Grundy, F. J., & Henkin, T. M. (2006). The S-MK box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nature Structural & Molecular Biology, 13, 226–233.
   PubMed Web of Science ®Google Scholar
• Hehre, W. J., Ditchfield, R., & Pople, J. A. (1972). Self-consistent molecular orbital methods. xii. Further extensions of gaussian-type basis sets for use in molecular orbital studies of organic molecules. The Journal of Chemical Physics, 56, 2257–2261.
   Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics & Modelling, 14, 33–38.
   Web of Science ®Google Scholar
• Jain, N., Zhao, L., Liu, J. D., & Xia, T. (2010). Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches. Biochemistry, 49, 3703–3714.
   PubMedGoogle Scholar
• 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, 926–935.
   Web of Science ®Google Scholar
• Kim, J. N., Blount, K. F., Puskarz, I., Lim, J., Link, K. H., & Breaker, R. R. (2009). Design and antimicrobial action of purine analogues that bind guanine riboswitches. ACS Chemical Biology, 4, 915–927.
   PubMed Web of Science ®Google Scholar
• Kumar, V., Endoh, T., Murakami, K., & Sugimoto, N. (2012). Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch. Chemical Communications, 48, 9693–9695.
   Google Scholar
• Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C., & Breaker, R. R. (2003). Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell, 113, 577–586.
   PubMed Web of Science ®Google Scholar
• Mandal, M., & Breaker, R. R. (2004). Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Structural & Molecular Biology, 11, 29–35.
   PubMed Web of Science ®Google Scholar
• Miller, J. H. (1992). A short course in bacterial genetics. Long Island, NY: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Montange, R. K., & Batey, R. T. (2008). Riboswitches: Emerging themes in RNA structure and function. Annual Review of Biophysics, 37, 117–133.
   PubMed Web of Science ®Google Scholar
• Mulhbacher, J., Brouillette, E., Allard, M., Fortier, L.-C., Malouin, F., & Lafontaine, D. A. (2010). Novel riboswitch ligand analogs as selective inhibitors of Guanine-related metabolic pathways. Plos Pathogens, 6, 1–11.
   Web of Science ®Google Scholar
• Mulhbacher, J., & Lafontaine, D. A. (2007). Ligand recognition determinants of guanine riboswitches. Nucleic Acids Research, 35, 5568–5580.
   PubMed Web of Science ®Google Scholar
• Noeske, J., Buck, J., Furtig, B., Nasiri, H. R., Schwalbe, H., & Wohnert, 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, 572–583.
   PubMed Web of Science ®Google Scholar
• Noeske, J., Richter, C., Grundl, M. A., Nasiri, H. R., Schwalbe, H., & Wohnert, J. (2005). An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proceedings of the National Academy of Sciences of the United States of America, 102, 1372–1377.
   PubMed Web of Science ®Google Scholar
• Ren, A. M., Rajashankar, K. R., & Patel, D. J. (2012). Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature, 486, 85–85-U1501.
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.
   Web of Science ®Google Scholar
• Schill, M., & Koslowski, T. (2013). Sensing organic molecules by charge transfer through aptamer-target complexes: Theory and simulation. Journal of Physical Chemistry B, 117, 475–483.
   PubMed Web of Science ®Google Scholar
• Serganov, A., & Patel, D. J. (2007). Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins. Nature Reviews Genetics, 8, 776–790.
   PubMed Web of Science ®Google Scholar
• Serganov, A., … Patel, D. J. (2004). Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chemistry & Biology, 11, 1729–1741.
   PubMed Web of Science ®Google Scholar
• Sudarsan, N., Barrick, J. E., & Breaker, R. R. (2003). Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA, 9, 644–647.
   PubMed Web of Science ®Google Scholar
• Tucker, B. J., & Breaker, R. R. (2005). Riboswitches as versatile gene control elements. Current Opinion in Structural Biology, 15, 342–348.
   PubMed Web of Science ®Google Scholar
• Villa, A., Wohnert, J., & Stock, G. (2009). Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Research, 37, 4774–4786.
   PubMed Web of Science ®Google Scholar
• Watson, P. Y., & Fedor, M. J. (2012). The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nature Chemical Biology, 8, 963–965.
   PubMed Web of Science ®Google Scholar
• Winkler, W. C. (2005). Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Current Opinion in Chemical Biology, 9, 594–602.
   PubMed Web of Science ®Google Scholar
• Winkler, W. C., & Breaker, R. R. (2005). Regulation of bacterial gene expression by riboswitches. Annual Review of Microbiology, 59, 487–517.
   PubMed Web of Science ®Google Scholar
• Xin, Y., & Hamelberg, D. (2010). Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme. RNA, 16, 2455–2463.
   Google Scholar
• York, D. M., Darden, T. A., & Pedersen, L. G. (1993). The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. The Journal of Chemical Physics, 99, 8345–8348.
   Web of Science ®Google Scholar
• Zaman, G. J., Michiels, P. J., & van Boeckel, C. A. (2003). Targeting RNA: New opportunities to address drugless targets. Drug Discovery Today, 8, 297–306.
   PubMed Web of Science ®Google Scholar