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Original Articles

Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues

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Pages 929-938 | Received 19 Oct 2009, Accepted 09 May 2010, Published online: 02 Nov 2010

References

  • Batey , R.T. 2006 . Structures of regulatory elements in mRNAs . Curr. Opin. Struct. Biol. , 16 : 299 – 306 .
  • Mandal , M. and Breaker , R.R. 2004 . Gene regulation by riboswitches . Nat. Rev. Mol. Cell Biol. , 5 : 451 – 463 .
  • Winkler , W.C. and Breaker , R.R. 2003 . Genetic control by metabolite-binding riboswitches . Chem. Bio. Chem. , 4 : 1024 – 1032 .
  • Serganov , A. , Huang , L. and Patel , D.J. 2008 . Structural insights into amino acid binding and gene control by a lysine riboswitch . Nature , 455 : 1263 – 1268 .
  • Mandal , M. , Lee , M. , Barrick , J.E. , Weinberg , Z. , Emilsson , G.M. , Ruzzo , W.L. and Breaker , R.R. 2004 . A glycine-dependent riboswitch that uses cooperative binding to control gene expression . Science , 306 : 275 – 279 .
  • Winkler , W. , Nahvi , A. and Breaker , R.R. 2002 . Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression . Nature , 419 : 952 – 956 .
  • Stoddard , C.D. , Gilbert , S.D. and Batey , R.T. 2008 . Ligand-dependent folding of the three-way junction in the purine riboswitch . RNA , 14 : 675 – 684 .
  • Gilbert , S.D. , Stoddard , C.D. , Wise , S.J. and Batey , R.T. 2006 . Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain . J. Mol. Biol. , 359 : 754 – 768 .
  • Brantl , S. 2007 . Metal sensing by RNA in bacteria: Exception or rule? . ACS Chem. Biol. , 2 : 656 – 660 .
  • Kim , J.N. and Breaker , R.R. 2008 . Purine sensing by riboswitches . Biol. Cell , 100 : 1 – 11 .
  • Edwards , A.L. and Batey , R.T. 2009 . A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch . J. Mol. Biol. , 385 : 938 – 948 .
  • Gilbert , S.D. , Mediatore , S.J. and Batey , R.T. 2006 . Modified pyrimidine specifically bind the purine riboswitch . J. Am. Chem. Soc. , 128 : 14214 – 14215 .
  • Gilbert , S.D. , Love , C.E. , Edwards , A.L. and Batey , R.T. 2007 . Mutational analysis of the purine riboswitch aptamer domain . Biochemistry , 46 : 13297 – 13309 .
  • Mulhbacher , J. and Lafontaine , D.A. 2007 . Ligand recognition determinants of guanine riboswitches . Nucleic Acids Res. , 35 : 5568 – 5580 .
  • Mandal , M. , Boese , B. , Barrick , J.E. , Winkler , W.C. and Breaker , R.R. 2003 . Riboswitches control fundamental biochemical pathways in bacillus subtilis and other bacteria . Cell , 113 : 577 – 586 .
  • Khalili-Araghi , F. , Gumbart , J. , Wen , P.C. , Sotomayor , M. , Tajkhorshid , E. and Schulten , K. 2009 . Molecular dynamics simulations of membrane channels and transporters . Curr. Opin. Struct. Biol. , 19 : 128 – 137 .
  • Klepeis , J.L. , Lindorff-Larsen , K. , Dror , R.O. and Shaw , D.E. 2009 . Long-timescale molecular dynamics simulations of protein structure and function . Curr. Opin. Struct. Biol. , 19 : 120 – 127 .
  • Alonso , H. , Bliznyuk , A.A. and Gready , J.E. 2006 . Combining docking and molecular dynamics simulations in drug design . Med. Res. Rev. , 26 : 531 – 568 .
  • Hashem , Y. and Auffinger , P. 2009 . A short guide for molecular dynamics simulations of RNA systems . Methods , 47 : 187 – 197 .
  • Sharma , M. , Bulusu , G. and 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 : 1673 – 1692 .
  • Villa , A. , Wöhnert , J. and Stock , G. 2009 . Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch . Nucleic Acids Res. , 37 : 4774 – 4786 .
  • Ling , B. , Wang , Z. , Zhang , R. , Meng , X. , Liu , Y. , Zhang , C. and Liu , C. 2009 . Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch . J. Mol. Graph. Model. , 28 : 37 – 45 .
  • Frisch , M.J. , Trucks , G.W. , Schlegel , H.B. , Scuseria , G.E. , Robb , M.A. , Cheeseman , J.R. , Montgomery , J.A. Jr. , Vreven , T. , Kudin , K.N. , Burant , J.C. , Millam , J.M. , Iyengar , S.S. , Tomasi , J. , Barone , V. , Mennucci , B. , Cossi , M. , Scalmani , G. , Rega , N. , Petersson , G.A. , Nakatsuji , H. , Hada , M. , Ehara , M. , Toyota , K. , Fukuda , R. , Hasegawa , J. , Ishida , M. , Nakajima , T. , Honda , Y. , Kitao , O. , Nakai , H. , Klene , M. , Li , X. , Knox , J.E. , Hratchian , H.P. , Cross , J.B. , Bakken , V. , Adamo , C. , Jaramillo , J. , Gomperts , R. , Stratmann , R.E. , Yazyev , O. , Austin , A.J. , Cammi , R. , Pomelli , C. , Ochterski , J.W. , Ayala , P.Y. , Morokuma , K. , Voth , G.A. , Salvador , P. , Dannenberg , J.J. , Zakrzewski , V.G. , Dapprich , S. , Daniels , A.D. , Strain , M.C. , Farkas , O. , Malick , D.K. , Rabuck , A.D. , Raghavachari , K. , Foresman , J.B. , Ortiz , J.V. , Cui , Q. , Baboul , A.G. , Clifford , S. , Cioslowski , J. , Stefanov , B.B. , Liu , G. , Liashenko , A. , Piskorz , P. , Komaromi , I. , Martin , R.L. , Fox , D.J. , Keith , T. , Al-Laham , M.A. , Peng , C.Y. , Nanayakkara , A. , Challacombe , M. , Gill , P.M.W. , Johnson , B. , Chen , W. , Wong , M.W. , Gonzalez , C. and Pople , J.A. 2004 . “ Gaussian 03 ” . In Revision C. 02 , Wallingford, CT : Gaussian, Inc. .
  • Morris , G.M. , Goodsell , D.S. , Halliday , R.S. , Huey , R. , Hart , W.E. , Belew , R.K. and Olson , A.J. 1998 . Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function . J. Comput. Chem. , 19 : 1639 – 1662 .
  • Guilbert , C. and James , T.L. 2008 . Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets . J. Chem. Inf. Model. , 48 : 1257 – 1268 .
  • Holt , P.A. , Chaires , J.B. and Trent , J.O. 2008 . Molecular docking of intercalators and groove-binders to nucleic acids using autodock and surflex . J. Chem. Inf. Model. , 48 : 1602 – 1615 .
  • Moitessier , N. , Westhof , E. and Hanessian , S. 2006 . Docking of aminoglycosides to hydrated and flexible RNA . J. Med. Chem. , 49 : 1023 – 1033 .
  • Yan , Z. , Sikri , S. , Beveridge , D.L. and Baranger , A.M. 2007 . Identification of an aminoacridine derivative that binds to RNA tetraloops . J. Med. Chem. , 50 : 4096 – 4104 .
  • Chen , D. , Menche , G. , Power , T.D. , Sower , L. , Peterson , J.W. and Schein , C.H. 2007 . Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins . Proteins , 67 : 593 – 605 .
  • Huey , R. , Morris , G.M. , Olson , A.J. and Goodsell , D.S. 2007 . Software news and update a semiempirical free energy force field with charge-based desolvation . J. Comput. Chem. , 28 : 1145 – 1152 .
  • Odžak , R. , Čalić , M. , Hrenar , T. , Primožič , I. and Kovarik , Z. 2007 . Evaluation of monoquaternary pyrimidium oximes potency to reactive tabun-inhibited human acetylcholinesterase . Toxicology , 233 : 85 – 96 .
  • Van Der Spoel , D. , Lindahl , E. , Hess , B. , Groenhof , G. , Mark , A.E. and Berendsen , H.J.C. 2005 . GROMACS: Fast, flexible and free . J. Comput. Chem. , 26 : 1701 – 1718 .
  • Wang , J. , Cieplak , P. and Kollman , P.A. 2000 . How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? . J. Comput. Chem. , 21 : 1049 – 1074 .
  • Wang , J. , Wang , W. , Kollman , P.A. and Case , D.A. 2006 . Automatic atom type and bond type perception in molecular mechanical calculations . J. Mol. Graph. Model. , 25 : 247 – 260 .
  • Wang , J. , Wolf , R.M. , Caldwell , J.W. , Kollman , P.A. and Case , D.A. 2004 . Development and testing of a general amber force field . J. Comput. Chem. , 25 : 1157 – 1174 .
  • Mobley , D.L. , Chodera , J.D. and Dill , K.A. 2006 . On the use of orientational restraints and symmetry corrections in alchemical free energy calculations . J. Chem. Phys. , 125 : 084902
  • Berrera , M. , Pantano , S. and Carloni , P. 2007 . Catabolite activator protein in aqueous solution: A molecular simulation study . J. Phys. Chem. B , 111 : 1496 – 1501 .
  • Pettersen , E.F. , Goddard , T.D. , Huang , C.C. , Couch , G.S. , Greenblatt , D.M. , Meng , E.C. and Ferrin , T.E. 2004 . UCSF chimera – A visualization system for exploratory research and analysis . J. Comput. Chem. , 25 : 1605 – 1612 .
  • Batey , R.T. , Gilbert , S.D. and Montange , R.K. 2004 . Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine . Nature , 432 : 411 – 415 .
  • Kim , J.N. , Roth , A. and Breaker , R.R. 2007 . Guanine riboswitch variants from mesoplasma florum selectively recognize 2′-deoxyguanosine . Proc. Natl Acad. Sci. USA , 104 : 16092 – 16097 .
  • Gilbert , S.D. , Reyes , F.E. , Edward , A.L. and Batey , R.T. 2009 . Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs . Structure , 17 : 857 – 868 .

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