Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated structures. The major groove of LE is a prominent rRNA cation-binding site. Divalent cations rigidify the LE major groove geometry whereas in the absence of divalent cations LE extensively interacts with monovalent cations via inner-shell binding. The HeIV region shows bistability of its major groove explaining the observed differences between x-ray and NMR structures. In agreement with the experiments, the simulations suggest that helix-alpha1 of L25 is the least stable part of the protein. Inclusion of Mg2+ cations into the simulations causes perturbation of basepairing at the LE/HeIV junction, which does not, however, affect the protein binding. The rRNA-protein complex is mediated by a number of highly specific hydration sites with long-residing water molecules and two of them are bound throughout the entire 24-ns simulation. Long-residing water molecules are seen also outside the RNA-protein contact areas with water-binding times substantially enhanced compared to simulations of free RNA. Long-residency hydration sites thus represent important elements of the three-dimensional structure of rRNA.
Réblová
Kamila
K
National Centre for Biomolecular Research, Faculty of Sciences, Masaryk University, Kotlárská 2, 61137 Brno, Czech Republic.
Spacková
Nad'a
N
Koca
Jaroslav
J
Leontis
Neocles B
NB
Sponer
Jirí
J
D001665:Binding Sites; D002412:Cations; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D046912:Multiprotein Complexes / Q000737:chemistry; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012329:RNA, Bacterial / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D002412:Cations; D046912:Multiprotein Complexes; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012269:Ribosomal Proteins; C031127:ribosomal protein L25; D014867:Water