Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.
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.
Rázga
Filip
F
National Centre for Biomolecular Research, Brno, Czech Republic.
Koca
Jaroslav
J
Sponer
Jirí
J
Leontis
Neocles B
NB
D000225:Adenine / Q000737:chemistry; D020816:Amino Acid Motifs; D020029:Base Pairing; D001483:Base Sequence; D001703:Biophysics / Q000379:methods*; D002384:Catalysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000737:chemistry; D046911:Macromolecular Substances; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009991:Oscillometry; D020653:Peptide Elongation Factor G / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry; D012342:RNA, Small Nuclear / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry; D012984:Software; D013997:Time Factors; D014965:X-Rays
D046911:Macromolecular Substances; D020653:Peptide Elongation Factor G; D012338:RNA, Ribosomal, 23S; D012342:RNA, Small Nuclear; C405482:U4 small nuclear RNA; D012313:RNA; D003596:Cytosine; D012343:RNA, Transfer; D000225:Adenine
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