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Volumn 17, Issue 11, 2011, Pages 2895-2906

A molecular dynamics study of a miRNA:mRNA interaction

Author keywords

miRNA; Molecular dynamics; Simulation performance; Thermodynamic integration

Indexed keywords

MESSENGER RNA; MICRORNA;

EID: 80255140294     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-0991-x     Document Type: Article
Times cited : (13)

References (26)
  • 1
    • 77957575165 scopus 로고    scopus 로고
    • Pumilio turns on microRNA function
    • 10.1038/ncb1010-928 1:CAS:528:DC%2BC3cXht1aktb7L
    • R Triboulet RI Gregory 2010 Pumilio turns on microRNA function Nat Cell Biology 12 10 928 929 10.1038/ncb1010-928 1:CAS:528:DC%2BC3cXht1aktb7L
    • (2010) Nat Cell Biology , vol.12 , Issue.10 , pp. 928-929
    • Triboulet, R.1    Gregory, R.I.2
  • 2
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, Biogenesis, Mechanism, and Function
    • DOI 10.1016/S0092-8674(04)00045-5
    • DP Bartel 2004 MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 116 2 281 297 10.1016/S0092-8674(04)00045-5 1:CAS:528:DC%2BD2cXhtVals7o%3D (Pubitemid 38167318)
    • (2004) Cell , vol.116 , Issue.2 , pp. 281-297
    • Bartel, D.P.1
  • 3
    • 77951953262 scopus 로고    scopus 로고
    • Got target?: Computational methods for microRNA target prediction and their extension
    • 10.3858/emm.2010.42.4.032 1:CAS:528:DC%2BC3cXlvFyntr8%3D
    • H Min S Yoon 2010 Got target?: computational methods for microRNA target prediction and their extension Exp Mol Med 42 4 233 244 10.3858/emm.2010.42.4. 032 1:CAS:528:DC%2BC3cXlvFyntr8%3D
    • (2010) Exp Mol Med , vol.42 , Issue.4 , pp. 233-244
    • Min, H.1    Yoon, S.2
  • 5
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • DOI 10.1016/j.sbi.2004.05.001, PII S0959440X04000752
    • TE Cheatham III 2004 Simulation and modelling of nucleic acid structure, dynamics and interactions Curr Opin Struct Biol 14 3 360 367 10.1016/j.sbi.2004.05.001 1:CAS:528:DC%2BD2cXkvV2ntrw%3D (Pubitemid 38749065)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.3 , pp. 360-367
    • Cheatham III, T.E.1
  • 6
    • 33749244630 scopus 로고    scopus 로고
    • A Potential Protein-RNA Recognition Event along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA
    • DOI 10.1016/j.str.2006.08.009, PII S0969212606003595
    • Y-R Yuan Y Pei H-Y Chen T Tuschi DJ Patel 2006 A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA Structure 14 10 1557 1565 10.1016/j.str.2006.08.009 1:CAS:528:DC%2BD28XhtVCrtrbM (Pubitemid 44486815)
    • (2006) Structure , vol.14 , Issue.10 , pp. 1557-1565
    • Yuan, Y.-R.1    Pei, Y.2    Chen, H.-Y.3    Tuschl, T.4    Patel, D.J.5
  • 7
    • 10644253787 scopus 로고    scopus 로고
    • Architecture of a validated microRNA::target interaction
    • DOI 10.1016/j.chembiol.2004.09.010, PII S1074552104002947
    • MC Vella K Reinert FJ Slack 2004 Architecture of a validate microRNA: target interaction Chem Biol 11 1619 1623 10.1016/j.chembiol.2004.09.010 1:CAS:528:DC%2BD2cXhtVyqtr7J (Pubitemid 39651295)
    • (2004) Chemistry and Biology , vol.11 , Issue.12 , pp. 1619-1623
    • Vella, M.C.1    Reinert, K.2    Slack, F.J.3
  • 8
    • 0036280718 scopus 로고    scopus 로고
    • Molecular dynamics applied to nucleic acids
    • 10.1021/ar010026a 1:CAS:528:DC%2BD38XjtFahtrs%3D
    • J Norberg L Nilsson 2002 Molecular dynamics applied to nucleic acids Acc Chem Res 35 465 472 10.1021/ar010026a 1:CAS:528:DC%2BD38XjtFahtrs%3D
    • (2002) Acc Chem Res , vol.35 , pp. 465-472
    • Norberg, J.1    Nilsson, L.2
  • 9
    • 0346882954 scopus 로고    scopus 로고
    • Altered structural fluctuations in duplex RNA versus DNA: A conformational switch involving base pair opening
    • DOI 10.1093/nar/gkg941
    • Y Pan AD Mackerell Jr 2003 Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening Nucleic Acids Res 31 24 7131 7140 10.1093/nar/gkg941 1:CAS:528:DC%2BD3sXps1Shs70%3D (Pubitemid 38016159)
    • (2003) Nucleic Acids Research , vol.31 , Issue.24 , pp. 7131-7140
    • Pan, Y.1    MacKerell Jr., A.D.2
  • 10
    • 67650495212 scopus 로고    scopus 로고
    • λ-dynamics free energy simulation methods
    • 10.1002/jcc.21295 1:CAS:528:DC%2BD1MXnsFCiur4%3D
    • JL Knight CL Brooks III 2009 λ-dynamics free energy simulation methods J Comput Chem 30 11 1692 1700 10.1002/jcc.21295 1:CAS:528: DC%2BD1MXnsFCiur4%3D
    • (2009) J Comput Chem , vol.30 , Issue.11 , pp. 1692-1700
    • Knight, J.L.1    Brooks Iii, C.L.2
  • 11
    • 65249136476 scopus 로고    scopus 로고
    • Independent-trajectories thermodynamic-integration free-energy changes for biomolecular system: Determinants of N5HN1 avian influenza virus neuraminidase inhibition by Peramivir
    • 10.1021/ct800559d 1:CAS:528:DC%2BD1MXjs1ahtrw%3D
    • M Lawrenz R Baron JA McCammon 2009 Independent-trajectories thermodynamic-integration free-energy changes for biomolecular system: determinants of N5HN1 avian influenza virus neuraminidase inhibition by Peramivir J Chem Theory Comput 5 4 1106 1116 10.1021/ct800559d 1:CAS:528:DC%2BD1MXjs1ahtrw%3D
    • (2009) J Chem Theory Comput , vol.5 , Issue.4 , pp. 1106-1116
    • Lawrenz, M.1    Baron, R.2    McCammon, J.A.3
  • 12
    • 41949124146 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acid-protein complexes
    • 10.1016/j.sbi.2007.12.012 1:CAS:528:DC%2BD1cXkvFCls7w%3D
    • AD MacKerell Jr L Nilsson 2008 Molecular dynamics simulations of nucleic acid-protein complexes Curr Opin Struct Biol 18 2 194 199 10.1016/j.sbi.2007.12. 012 1:CAS:528:DC%2BD1cXkvFCls7w%3D
    • (2008) Curr Opin Struct Biol , vol.18 , Issue.2 , pp. 194-199
    • MacKerell Jr., A.D.1    Nilsson, L.2
  • 13
    • 42449094162 scopus 로고    scopus 로고
    • Solution structure of a let-7 miRNA: Lin-41 mRNA complex from C. elegans
    • DOI 10.1093/nar/gkn088
    • M Cevec C Thibaudeau J Plavec 2008 Solution structure of a let-7 miRNA:lin41 mRNA complex from C. elegans Nucleic Acids Res 36 2330 2337 10.1093/nar/gkn088 1:CAS:528:DC%2BD1cXkvFGgsLY%3D (Pubitemid 351567006)
    • (2008) Nucleic Acids Research , vol.36 , Issue.7 , pp. 2330-2337
    • Cevec, M.1    Thibaudeau, C.2    Plavec, J.3
  • 14
    • 0036570589 scopus 로고    scopus 로고
    • Why do miRNAs live in the miRNP?
    • DOI 10.1101/gad.992502
    • DS Schwarz PD Zamore 2002 Why do miRNAs live in the miRNP Genes Dev 16 1025 1031 10.1101/gad.992502 1:CAS:528:DC%2BD38XjvV2kurk%3D (Pubitemid 34507192)
    • (2002) Genes and Development , vol.16 , Issue.9 , pp. 1025-1031
    • Schwarz, D.S.1    Zamore, P.D.2
  • 15
    • 14644393684 scopus 로고    scopus 로고
    • Perspective: Machines for RNAi
    • DOI 10.1101/gad.1284105
    • Y Tomari PD Zamore 2005 Perspective: machines for RNAi Genes Dev 19 5 517 529 10.1101/gad.1284105 1:CAS:528:DC%2BD2MXitFOksrc%3D (Pubitemid 40314984)
    • (2005) Genes and Development , vol.19 , Issue.5 , pp. 517-529
    • Tomari, Y.1    Zamore, P.D.2
  • 16
    • 26444581314 scopus 로고    scopus 로고
    • Structure and function of argonaute proteins
    • DOI 10.1016/j.str.2005.08.005, PII S0969212605003059
    • TM Tanaka Hall 2005 Structure and function of Argonaute proteins Structure 13 1403 1408 10.1016/j.str.2005.08.005 (Pubitemid 41427580)
    • (2005) Structure , vol.13 , Issue.10 , pp. 1403-1408
    • Hall, T.M.T.1
  • 17
    • 57749206034 scopus 로고    scopus 로고
    • Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    • 10.1038/nature07666 1:CAS:528:DC%2BD1cXhsFWmsLnJ
    • Y Wang A Juranek H Li G Sheng T Tuschl DJ Patel 2008 Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex Nature 456 921 926 10.1038/nature07666 1:CAS:528:DC%2BD1cXhsFWmsLnJ
    • (2008) Nature , vol.456 , pp. 921-926
    • Wang, Y.1    Juranek, A.2    Li, H.3    Sheng, G.4    Tuschl, T.5    Patel, D.J.6
  • 18
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • DOI 10.1093/nar/gkg599
    • IL Hofacker 2003 Vienna RNA secondary structure server Nucleic Acids Res 31 3429 3431 10.1093/nar/gkg599 1:CAS:528:DC%2BD3sXltVWisrs%3D (Pubitemid 37442172)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3429-3431
    • Hofacker, I.L.1
  • 19
    • 77955817276 scopus 로고    scopus 로고
    • Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
    • 10.1093/nar/gkq134 1:CAS:528:DC%2BC3cXhtVekur3N
    • AJ DePaul EJ Thompson SS Patel K Haldeman EJ Sorin 2010 Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics Nucleic Acids Res 38 4856 4867 10.1093/nar/gkq134 1:CAS:528: DC%2BC3cXhtVekur3N
    • (2010) Nucleic Acids Res , vol.38 , pp. 4856-4867
    • Depaul, A.J.1    Thompson, E.J.2    Patel, S.S.3    Haldeman, K.4    Sorin, E.J.5
  • 21
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • DOI 10.1007/S008940100045
    • E Lindahl B Hess D van der Spoel 2001 GROMACS 3.0: a package for molecular simulation and trajectory analysis J Mol Model 7 306 317 1:CAS:528:DC%2BD3MXnsVGjsL4%3D (Pubitemid 36153547)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.8 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 23
    • 34548661770 scopus 로고    scopus 로고
    • Free energy calculations in biological systems. How useful are they in practice?
    • Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark AE, Schlick T, Schütte C, Skeel R (eds) Springer, Berlin
    • Chipot C (2005) Free energy calculations in biological systems. How useful are they in practice? In: Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark AE, Schlick T, Schütte C, Skeel R (eds) New algorithms for macromolecular simulation, vol 49. Springer, Berlin, pp 183-209
    • (2005) New Algorithms for Macromolecular Simulation , vol.49 , pp. 183-209
    • Chipot, C.1
  • 24
    • 78049314237 scopus 로고    scopus 로고
    • Mechanism of microRNA-target interaction: Molecular dynamics simulations and thermodynamic analysis
    • 10.1371/journal.pcbi.1000866 10.1371/journal.pcbi.1000866
    • Y Wang Y Li Z Ma W Yang A Chunzhi 2010 Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamic analysis PLoS Comput Biol 6 7 e1000866 10.1371/journal.pcbi.1000866 10.1371/journal.pcbi. 1000866
    • (2010) PLoS Comput Biol , vol.6 , Issue.7 , pp. 1000866
    • Wang, Y.1    Li, Y.2    Ma, Z.3    Yang, W.4    Chunzhi, A.5
  • 25
    • 70349961432 scopus 로고    scopus 로고
    • Nucleation, propagation and cleavage of target RNA in Ago silencing complexes
    • 10.1038/nature08434 1:CAS:528:DC%2BD1MXht1CisL3F
    • Y Wang S Juranek H Li G Sheng GS Wardle T Tuschl DJ Patel 2009 Nucleation, propagation and cleavage of target RNA in Ago silencing complexes Nature 461 754 756 10.1038/nature08434 1:CAS:528:DC%2BD1MXht1CisL3F
    • (2009) Nature , vol.461 , pp. 754-756
    • Wang, Y.1    Juranek, S.2    Li, H.3    Sheng, G.4    Wardle, G.S.5    Tuschl, T.6    Patel, D.J.7
  • 26
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • I Bahar AR Atilgan B Erman 1997 Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential Fold Des 2 3 173 181 10.1016/S1359-0278(97)00024-2 1:CAS:528:DyaK2sXktlCis78%3D (Pubitemid 127740467)
    • (1997) Folding and Design , vol.2 , Issue.3 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3


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