Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.
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(2+) rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg(2+), the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg(2+), 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.
Réblová
Kamila
K
National Center for Biomolecular Research, Brno, Czech Republic.
Spacková
Nad'a
N
Stefl
Richard
R
Csaszar
Kristina
K
Koca
Jaroslav
J
Leontis
Neocles B
NB
Sponer
Jirí
J
D020137:Base Pair Mismatch; D020029:Base Pairing; D001665:Binding Sites; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry; D046911:Macromolecular Substances; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012329:RNA, Bacterial / Q000737:chemistry*; D018749:RNA, Plant / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013045:Species Specificity; D018724:Spinacia oleracea / Q000737:chemistry; D014867:Water / Q000737:chemistry*
D046911:Macromolecular Substances; D012329:RNA, Bacterial; D018749:RNA, Plant; D012341:RNA, Ribosomal, 5S; D012997:Solvents; D014867:Water; D012964:Sodium; D008274:Magnesium