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@inproceedings{595966, author = {Rázga, Filip and Zacharias, Martin and Réblová, Kamila and Koča, Jaroslav and Šponer, Jiří}, address = {Brno}, booktitle = {Strukturní biofyzika makromolekul}, edition = {prvé}, keywords = {Molecular Dynamics; RNA Kink Turn; Ribosome; RNA flexibility;}, language = {eng}, location = {Brno}, pages = {17-17}, publisher = {Biofyzikálny ústav AVČR a MU v Brne}, title = {RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function}, year = {2005} }
TY - JOUR ID - 595966 AU - Rázga, Filip - Zacharias, Martin - Réblová, Kamila - Koča, Jaroslav - Šponer, Jiří PY - 2005 TI - RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function PB - Biofyzikálny ústav AVČR a MU v Brne CY - Brno KW - Molecular Dynamics KW - RNA Kink Turn KW - Ribosome KW - RNA flexibility; N2 - Explicit-solvent Molecular Dynamics (MD) simulations were carried out for three K-turns (Kt) from 23S rRNA, i.e., Kt-38 located at the A-site finger base, Kt-42 located at the L7/L12 stalk base, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The presence of K-turns at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some K-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. MD simulations demonstrated that the K-turns can act as flexible molecular elbows. The angle between the helical arms is regulated by local variations of the second A-minor (type I) interaction, which mediates the contact between the helical stems, and by conformational change of the single base from the nominally unpaired region. Moreover, K-turns are associated with a unique network of long-residency and dynamical hydration sites that are intimately involved in modulating their conformational dynamics. Variability of A-minor interaction ranges from closed geometries to open ones stabilized by insertion of long-residency waters between the interacting bases. Implicit solvent conformational search confirms the flexibility of K-turns around their x-ray geometries and identifies a second separate low-energy region with more open structures that could correspond to K-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor-binding site shows that elbow-like motion fully propagates beyond the K-turn and could mediate large-scale adjustments of distant RNA regions. ER -
RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA a Jiří ŠPONER. RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function. In \textit{Strukturní biofyzika makromolekul}. prvé. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005, s.~17-17.
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