Diffusion of tRNA inside the ribosome is position-dependent

Autor(es)

Yang, Huan ^[1] ; Bandarkar, Prasad ^[1] ; Horne, Ransom ^[1] ; Leite, Vitor B. P. ^[2] ; Chahine, Jorge ^[2] ; Whitford, Paul C. ^[1]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: Journal of Chemical Physics; v. 151, n. 8 AUG 28 2019.
• Citações Web of Science: 0

Resumo

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)

• Processo FAPESP: 16/19766-1 - Relevo de superfícies de energia de macromoléculas biológicas com aplicações em biotecnologia e em biomedicina
• Beneficiário: Vitor Barbanti Pereira Leite
• Linha de fomento: Auxílio à Pesquisa - Regular
• Processo FAPESP: 14/50739-5 - Elucidating the role of disorder during biomolecular fuction
• Beneficiário: Vitor Barbanti Pereira Leite
• Linha de fomento: Auxílio à Pesquisa - Regular
• Processo FAPESP: 18/18668-1 - Visualização do relevo de superfícies de energia de macromoléculas biológicas
• Beneficiário: Vitor Barbanti Pereira Leite
• Linha de fomento: Bolsas no Exterior - Pesquisa