Počet záznamů: 1

An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods

  1. 1.
    0340907 - BFU-R 2010 RIV US eng J - Článek v odborném periodiku
    Réblová, Kamila - Střelcová, Z. - Kulhánek, P. - Beššeová, Ivana - Mathews, D.H. - Van Nostrand, K. - Yildirim, I. - Turner, D.H. - Šponer, Jiří
    An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods.
    Journal of Chemical Theory and Computation. Roč. 6, č. 3 (2010), s. 910-929 ISSN 1549-9618
    Grant CEP: GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) KJB400040901
    Grant ostatní: GA MŠk(CZ) LC06030; GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476
    Výzkumný záměr: CEZ:AV0Z50040507; CEZ:AV0Z50040702
    Klíčová slova: RNA * internal loop * molecular dynamics
    Kód oboru RIV: AQ - Bezpečnost a ochrana zdraví, člověk-stroj
    Impakt faktor: 5.138, rok: 2010

    Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. We performed 3.1 us of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na+ versus excess salt KCl ion environments.
    Trvalý link: http://hdl.handle.net/11104/0184052