title: How the Ribosomal A-Site Finger Can Lead to tRNA Species-Dependent Dynamics.
abstract: Proteins are synthesized by the joint action of the ribosome and tRNA molecules, where the rate of synthesis can be affected by numerous factors, such as the concentration of tRNA, the binding affinity of tRNA for the ribosome, or post-transcriptional modifications. Here, we expand this range of contributors by demonstrating how differences in tRNA structure can give rise to tRNA species-specific dynamics in the ribosome. To show this, we perform simulations of A/P hybrid-state formation for two tRNA species (tRNAPheand tRNALeu), which differ in the size of their variable loops (VLs). These calculations reveal that steric interactions between the VL and the ribosomal A-site finger (ASF, i.e., H38 of 23S rRNA) can directly modulate the free-energy landscape for each tRNA species. We also find that tRNA and ASF motions are highly correlated, where fluctuations of the ASF are predictive of tRNA transition events. Finally, by introducing perturbations to the model, we demonstrate that ASF flexibility is a determinant of the rate of A/P hybrid-state formation.
authors.affiliation: Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Kien
authors.identifier: 0000-0003-0038-5601
authors.initials: K
authors.lastname: Nguyen
authors.affiliation: Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Huan
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Physics, Northeastern University , Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Paul C
authors.identifier: 0000-0001-7104-2265
authors.initials: PC
authors.lastname: Whitford
mesh_terms: D056004:Molecular Dynamics Simulation; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*
chemical_list: D012338:RNA, Ribosomal, 23S; D012343:RNA, Transfer