A Molecular Dynamics Simulation Study of Coaxial Stacking in RNA

Schneider, Christoph; Sühnel, Jürgen

doi:10.1080/07391102.2000.10506671

Cited by 11 publications

(7 citation statements)

References 29 publications

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“…Simulations involving RNA are accumulating rapidly, although the size, charge, and structural variety of these molecules continue to pose significant challenges. Several studies have addressed the dynamics of the basic motifs found in folded RNA, including mispairs such as flexible water-bridged UC pairs, or coaxial stacking, where the absence of backbone continuity causes kinking and untwisting but does not enhance flexibility . Studies of stem loops show that nanosecond dynamics maintain stable conformations but cannot sample extensively enough to identify conformational substates .…”

Section: Rna and Rna Complexesmentioning

confidence: 99%

Simulations of Nucleic Acids and Their Complexes

2002

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Recent years have seen considerable progress in simulations of nucleic acids. Improvements in force fields, simulation techniques and protocols, and increasing computer power have all contributed to making nanosecond-scale simulations of both DNA and RNA commonplace. The results are already helping to explain how nucleic acids respond to their environment and to their base sequence and to reveal the factors underlying recognition processes by probing biologically important nucleic acid-protein interactions and medically important nucleic acid-drug complexation. This Account summarizes methodological progress and applications of molecular dynamics to nucleic acids over the past few years and tries to identify remaining challenges.

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Section: Rna and Rna Complexesmentioning

confidence: 99%

Simulations of Nucleic Acids and Their Complexes

2002

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“…X-ray crystallography, solution experiments, and simulations have distinct areas of application and provide complementary views on the structure and dynamics of K-turns. Although limited by force field approximations and the timescale of the simulations, MD is capable of providing qualitative insights into RNA structure and dynamics (Auffinger et al, 1999(Auffinger et al, , 2004Westhof, 1998, 2000;Beveridge and McConnell, 2000;Cheatham and Kollman, 1997;Csaszar et al, 2001;Giudice and Lavery, 2002;Guo et al, 2000;Guo and Gmeiner, 2001;Hermann et al, 1998;Nagan et al, 1999Nagan et al, , 2000Norberg and Nilsson, 2002;Razga et al, 2004;Reblova et al, 2003aReblova et al, ,b, 2004Sanbonmatsu and Joseph, 2003;Sarzynska et al, 2000;Schneider et al, 2001;Schneider and Suhnel, 2000;Stagg et al, 2003;Williams and Hall, 2000;Zacharias, 2000).…”

Section: Introductionmentioning

confidence: 99%

Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases

Rázga

Koča²,

Šponer

et al. 2005

Biophysical Journal

192

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Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent molecular dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in domain III, and for the K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

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“…Besides the experimental approaches, molecular interactions in RNA molecules can be studied by a variety of advanced molecular modeling tools Westhof, 1998, 2001;Beveridge and McConnell, 2000;Brandl et al, 2000;Cheatham and Kollman, 2000;Cheatham and Young, 2000;Chin et al, 1999;Guo et al, 2000;Hermann et al, 1997;Lahiri and Nilsson, 2000;Nagan et al, 1999Nagan et al, , 2000Sarzynska et al, 2000;Schneider and Suhnel, 2000;Schneider et al, 2001;Sponer et al, 2001;Williams and Hall, 1999;Zacharias, 2000). This reflects the enormous progress of computer hardware and software in the last decade, during which the actual performance of computers increased by at least three orders of magnitude.…”

Section: Introductionmentioning

confidence: 99%

Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E

Réblová¹,

Špačková

Štefl³

et al. 2003

Biophysical Journal

111

160

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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 Mg 21 rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg 21 , the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg 21 , 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 1 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.

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A Molecular Dynamics Simulation Study of Coaxial Stacking in RNA

Cited by 11 publications

References 29 publications

Simulations of Nucleic Acids and Their Complexes

Simulations of Nucleic Acids and Their Complexes

Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases

Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E

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