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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Diffusion of tRNA inside the ribosome is position-dependent

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Author(s):
Yang, Huan [1] ; Bandarkar, Prasad [1] ; Horne, Ransom [1] ; Leite, Vitor B. P. [2] ; Chahine, Jorge [2] ; Whitford, Paul C. [1]
Total Authors: 6
Affiliation:
[1] Northeastern Univ, Dept Phys, Dana Res Ctr 111, 360 Huntington Ave, Boston, MA 02115 - USA
[2] Sao Paulo State Univ UNESP, IBILCE, Sao Jose Do Rio Preto - Brazil
Total Affiliations: 2
Document type: Journal article
Source: Journal of Chemical Physics; v. 151, n. 8 AUG 28 2019.
Web of Science Citations: 0
Abstract

In recent years, there has been a growing interest to quantify the energy landscape that governs ribosome dynamics. However, in order to quantitatively integrate theoretical predictions and experimental measurements, it is essential that one has a detailed understanding of the associated diffusive properties. Here, all-atom explicit-solvent simulations (50 mu s of aggregate sampling) predict that the diffusion coefficient of a tRNA molecule will depend on its position within the ribosome. Specifically, during aa-tRNA accommodation (i.e., the process by which tRNA enters the ribosome), the apparent diffusion coefficient decreases by approximately an order of magnitude. By comparing these to values obtained with an energetically ``smooth{''} model, we show that the observed nonuniform behavior likely arises from electrostatic and solvation interactions between the tRNA and ribosome. These calculations also reveal the hierarchical character of ribosomal energetics, where steric interactions induce a large-scale free-energy barrier, and short-scale roughness determines the rate of diffusive movement across the landscape. Published under license by AIP Publishing. (AU)

FAPESP's process: 16/19766-1 - Biological macromolecules energy landscapes with applications in biotechnology and in biomedicine
Grantee:Vitor Barbanti Pereira Leite
Support type: Regular Research Grants
FAPESP's process: 14/50739-5 - Elucidating the role of disorder during biomolecular fuction
Grantee:Vitor Barbanti Pereira Leite
Support type: Regular Research Grants
FAPESP's process: 18/18668-1 - Biological macromolecules energy landscapes visualization
Grantee:Vitor Barbanti Pereira Leite
Support type: Scholarships abroad - Research