title: Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.
abstract: Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.
authors: Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors: Loïc
authors: L
authors: Salmon
authors: Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States.
authors: George M
authors: GM
authors: Giambaşu
authors: Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States.
authors: Evgenia N
authors: EN
authors: Nikolova
authors: Department of Medical Biochemistry and Biophysics, Karolinska Institute , SE-171 77 Stockholm, Sweden.
authors: Katja
authors: K
authors: Petzold
authors: The University of Texas Health Science Center , San Antonio, Texas 78229, United States.
authors: Akash
authors: A
authors: Bhattacharya
authors: Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States.
authors: David A
authors: DA
authors: Case
authors: Department of Biochemistry and Chemistry, Duke University School of Medicine , Durham, North Carolina 27710, United States.
authors: Hashim M
authors: HM
authors: Al-Hashimi
mesh_terms: D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA