Breaker RR: Riboswitches and the RNA world. Cold Spring Harbor Perspectives in Biology. 2012, 4 (2): a003566-
Article
PubMed Central
PubMed
Google Scholar
Serganov A, Nudler E: A decade of riboswitches. Cell. 2013, 152 (1-2): 17-24. 10.1016/j.cell.2012.12.024.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barrick JE, Breaker RR: The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biology. 2007, 8 (11): R239-10.1186/gb-2007-8-11-r239.
Article
PubMed Central
PubMed
Google Scholar
Garst AD, Batey RT: A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta. 2009, 1789 (9-10): 584-591. 10.1016/j.bbagrm.2009.06.004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Porter EB, Marcano-Velázquez JG, Batey RT: The purine riboswitch as a model system for exploring RNA biology and chemistry. Biochim Biophys Acta. 2014, 1839 (10): 919-930. 10.1016/j.bbagrm.2014.02.014.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mandal M, Breaker RR: Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol. 2004, 11 (1): 29-35. 10.1038/nsmb710.
Article
CAS
PubMed
Google Scholar
Serganov A, Yuan Y-R, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, et al: Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs. Chem Biol. 2004, 11 (12): 1729-1741. 10.1016/j.chembiol.2004.11.018.
Article
CAS
PubMed
Google Scholar
Mandal M, Breaker RR: Gene regulation by riboswitches. Nature Reviews Molecular Cell Biology. 2004, 5 (6): 451-463. 10.1038/nrm1403.
Article
CAS
PubMed
Google Scholar
Forsdyke DR: A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Mol Biol Evol. 1995, 12 (5): 949-958.
CAS
PubMed
Google Scholar
Nowakowski J, Tinoco I: RNA structure and stability. Seminars in Virology. 1997, 8 (3): 153-165. 10.1006/smvy.1997.0118.
Article
CAS
Google Scholar
Rieder R, Lang K, Graber D, Micura R: Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. Chembiochem. 2007, 8 (8): 896-902. 10.1002/cbic.200700057.
Article
CAS
PubMed
Google Scholar
Lee MK, Gal M, Frydman L, Varani G: Real-time multidimensional NMR follows RNA folding with second resolution. Proc Natl Acad Sci U S A. 2010, 107 (20): 9192-9197. 10.1073/pnas.1001195107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Neupane K, Yu H, Foster DA, Wang F, Woodside MT: Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism. Nucleic Acids Res. 2011, 39 (17): 7677-7687. 10.1093/nar/gkr305.
Article
PubMed Central
CAS
PubMed
Google Scholar
Leipply D, Draper DE: Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA. Biochemistry. 2011, 50 (14): 2790-2799. 10.1021/bi101948k.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sharma M, Bulusu G, Mitra A: MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch. RNA. 2009, 15 (9): 1673-1692. 10.1261/rna.1675809.
Article
PubMed Central
CAS
PubMed
Google Scholar
Priyakumar UD, MacKerell AD: Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. Journal of Molecular Biology. 2010, 396 (5): 1422-1438. 10.1016/j.jmb.2009.12.024.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gong Z, Zhao Y, Chen C, Xiao Y: Role of ligand binding in structural organization of add A-riboswitch aptamer: A molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics. 2011, 29 (2): 403-416. 10.1080/07391102.2011.10507394.
Article
CAS
PubMed
Google Scholar
Lin JC, Hyeon C, Thirumalai D: Sequence-dependent folding landscapes of adenine riboswitch aptamers. Phys Chem Chem Phys. 2014, 16 (14): 6376-6382. 10.1039/C3CP53932F.
Article
CAS
PubMed
Google Scholar
Lin J-C, Thirumalai D: Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. Journal of the American Chemical Society. 2008, 130 (43): 14080-14081. 10.1021/ja8063638.
Article
CAS
PubMed
Google Scholar
Allnér O, Nilsson L, Villa A: Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. RNA. 2013, 19 (7): 916-926. 10.1261/rna.037549.112.
Article
PubMed Central
PubMed
Google Scholar
Di Palma F, Colizzi F, Bussi G: Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. RNA. 2013, 19 (11): 1517-1524. 10.1261/rna.040493.113.
Article
PubMed Central
CAS
PubMed
Google Scholar
Foloppe N, MacKerell AD: All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. Journal of Computational Chemistry. 2000, 21 (2): 86-104. 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G.
Article
CAS
Google Scholar
MacKerell AD, Banavali NK: All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. Journal of Computational Chemistry. 2000, 21 (2): 105-120. 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P.
Article
CAS
Google Scholar
Zgarbová M, Otyepka M, Mládek A, Banáš P, Cheatham TE, Jurečka P: Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. Journal of Chemical Theory and Computation. 2011, 7 (9): 2886-2902. 10.1021/ct200162x.
Article
PubMed Central
PubMed
Google Scholar
Abrams C, Bussi G: Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration. Entropy. 2014, 16 (1): 163-199.
Article
Google Scholar
Torrie GM, Valleau JP: Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. Journal of Computational Physics. 1977, 23 (2): 187-199. 10.1016/0021-9991(77)90121-8.
Article
Google Scholar
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM: The weighted histogram analysis method for free-energy calculations on biomolecules. I: the method. Journal of Computational Chemistry. 1992, 13 (8): 1011-1021. 10.1002/jcc.540130812.
Article
CAS
Google Scholar
Pronk S, P´áll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al: GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013, 29 (7): 845-854. 10.1093/bioinformatics/btt055.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tribello GA, Bonomi M, Branduardi D, Camilloni C, Bussi G: PLUMED 2: New feathers for an old bird. Computer Physics Communications. 2014, 185 (2): 604-613. 10.1016/j.cpc.2013.09.018.
Article
CAS
Google Scholar
Wang J, Cieplak P, Kollman PA: How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. Journal of Computational Chemistry. 2000, 21 (12): 1049-1074. 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F.
Article
CAS
Google Scholar
Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M: Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophysical Journal. 2007, 92 (11): 3817-3829. 10.1529/biophysj.106.097782.
Article
PubMed Central
PubMed
Google Scholar
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA: Development and testing of a general amber force field. Journal of Computational Chemistry. 2004, 25 (9): 1157-1174. 10.1002/jcc.20035.
Article
CAS
PubMed
Google Scholar
Bayly CI, Cieplak P, Cornell W, Kollman PA: A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. Journal of Physical Chemistry. 1993, 97 (40): 10269-10280. 10.1021/j100142a004.
Article
CAS
Google Scholar
Frisch M, Trucks G, Schlegel H, Scuseria G, Robb M, Cheeseman J, et al: Gaussian 03, Revision C.02. 2004, Gaussian, Inc., Wallingford, CT
Google Scholar
Darden T, York D, Pedersen L: Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. Journal of Chemical Physics. 1993, 98: 10089-10.1063/1.464397.
Article
CAS
Google Scholar
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM: LINCS: a linear constraint solver for molecular simulations. Journal of Computational Chemistry. 1997, 18 (12): 1463-1472. 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H.
Article
CAS
Google Scholar
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML: Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983, 79: 926-10.1063/1.445869.
Article
CAS
Google Scholar
Allnér O, Nilsson L, Villa A: Magnesium ion-water coordination and exchange in biomolecular simulations. J Chem Theory Comput. 2012, 8 (4): 1493-1502. 10.1021/ct3000734.
Article
Google Scholar
Bussi G, Donadio D, Parrinello M: Canonical sampling through velocity rescaling. Journal of Chemical Physics. 2007, 126 (1): 014101-10.1063/1.2408420.
Article
PubMed
Google Scholar
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR: Molecular dynamics with coupling to an external bath. Journal of Chemical Physics. 1984, 81: 3684-10.1063/1.448118.
Article
CAS
Google Scholar
Grossfield A: WHAM: an Implementation of the Weighted Histogram Analysis Method. Version 2.0.9, [http://membrane.urmc.rochester.edu/content/wham]
Klein DJ, Moore PB, Steitz TA: The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. Journal of Molecular Biology. 2004, 340 (1): 141-177. 10.1016/j.jmb.2004.03.076.
Article
CAS
PubMed
Google Scholar
Gendron P, Lemieux S, Major F: Quantitative analysis of nucleic acid three-dimensional structures. Journal of Molecular Biology. 2001, 308 (5): 919-936. 10.1006/jmbi.2001.4626.
Article
CAS
PubMed
Google Scholar
Bottaro S, Di Palma F, Bussi G: The role of nucleobase interactions in RNA structure and dynamics. Nucleic Acids Research. 2014, 42 (21): 13306-13314. 10.1093/nar/gku972.
Article
PubMed Central
PubMed
Google Scholar
Salim N, Lamichhane R, Zhao R, Banerjee T, Philip J, Rueda D, Feig AL: Thermodynamic and kinetic analysis of an rna kissing interaction and its resolution into an extended duplex. Biophys J. 2012, 102 (5): 1097-1107. 10.1016/j.bpj.2011.12.052.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, et al: The essential role of stacking adenines in a two-base-pair rna kissing complex. Journal of the American Chemical Society. 2013, 135 (15): 5602-5611. 10.1021/ja310820h.
Article
PubMed Central
CAS
PubMed
Google Scholar
Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, et al: Can we accurately describe the structure of adenine tracts in B-DNA? reference quantum-chemical computations reveal overstabilization of stacking by molecular mechanics. Journal of Chemical Theory and Computation. 2012, 8 (7): 2448-2460. 10.1021/ct3001238.
Article
PubMed
Google Scholar
Grubmüller H, Heymann B, Tavan P: Ligand-binding-molecular mechanics calculation of the streptavidin biotin rupture force. Science. 1996, 271 (5251): 997-999. 10.1126/science.271.5251.997.
Article
PubMed
Google Scholar
Minh DD, Adib AB: Optimized free energies from bidirectional single-molecule force spectroscopy. Physical Review Letters. 2008, 100 (18): 180602-
Article
PubMed Central
PubMed
Google Scholar
Do TN, Carloni P, Varani G, Bussi G: RNA/peptide binding driven by electrostatics - Insight from bidirectional pulling simulations. J Chem Theory Comput. 2013, 9 (3): 1720-1730. 10.1021/ct3009914.
Article
CAS
PubMed
Google Scholar