| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
pa
ková 
tefl *
a *
í poner
* National Center for Biomolecular Research, Kotláská 2, 611 37 Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic and National Center for Biomolecular Research, Královopolská 135, 612 65, Brno, Czech Republic; and Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
Correspondence: Address reprint requests to Jií poner, Institute of Biophysics, Academy of Sciences of the Czech Republic and National Center for Biomolecular Research, Královopolská 135, 612 65, Brno, Czech Republic. E-mail: sponer{at}ibp.cz or Neocles B. Leontis, Chemistry Department, Bowling Green State University, Bowling Green, OH 43403. E-mail: leontis{at}bgnet.bgsu.edu.
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg2+ rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg2+, the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg2+, penetrate into the most negative regions inside the deep groove. The spinach chloroplast Loop E shows a marked tendency to compress its deep groove compared with the bacterial consensus. Structures with a narrow deep groove essentially collapse around a string of Na+ cations with long coordination times. The Loop E non-Watson-Crick basepairing is complemented by highly specific hydration sites ranging from water bridges to hydration pockets hosting 2 to 3 long-residing waters. The ordered hydration is intimately connected with RNA local conformational variations.
This article has been cited by other articles:
 |
|
 |
|
  K. Reblova, E. Fadrna, J. Sarzynska, T. Kulinski, P. Kulhanek, E. Ennifar, J. Koca, and J. Sponer Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics Biophys. J., December 1, 2007; 93(11): 3932 - 3949. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. V. Krasovska, J. Sefcikova, K. Reblova, B. Schneider, N. G. Walter, and J. Sponer Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme Biophys. J., July 15, 2006; 91(2): 626 - 638. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Spackova and J. Sponer Molecular dynamics simulations of sarcin-ricin rRNA motif Nucleic Acids Res., February 2, 2006; 34(2): 697 - 708. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. R. Stefan, R. Zhang, A. G. Levitan, D. K. Hendrix, S. E. Brenner, and S. R. Holbrook MeRNA: a database of metal ion binding sites in RNA structures Nucleic Acids Res., January 1, 2006; 34(suppl_1): D131 - D134. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Cojocaru, R. Klement, and T. M. Jovin Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif Nucleic Acids Res., June 13, 2005; 33(10): 3435 - 3446. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Razga, J. Koca, J. Sponer, and N. B. Leontis Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases Biophys. J., May 1, 2005; 88(5): 3466 - 3485. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. COJOCARU, S. NOTTROTT, R. KLEMENT, and T. M. JOVIN The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study RNA, February 1, 2005; 11(2): 197 - 209. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Reblova, N. Spackova, J. Koca, N. B. Leontis, and J. Sponer Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex Biophys. J., November 1, 2004; 87(5): 3397 - 3412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Varnai and K. Zakrzewska DNA and its counterions: a molecular dynamics study Nucleic Acids Res., August 10, 2004; 32(14): 4269 - 4280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Rueda, E. Cubero, C. A. Laughton, and M. Orozco Exploring the Counterion Atmosphere around DNA: What Can Be Learned from Molecular Dynamics Simulations? Biophys. J., August 1, 2004; 87(2): 800 - 811. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Fadrna, N. Spackova, R. Stefl, J. Koca, T. E. Cheatham 3rd, and J. Sponer Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations Biophys. J., July 1, 2004; 87(1): 227 - 242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Reblova, N.'a Spackova, J. E. Sponer, J. Koca, and J. Sponer Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets Nucleic Acids Res., December 1, 2003; 31(23): 6942 - 6952. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
