Diffusion of tRNA inside the ribosome is position-dependent
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1063/1.5113814 http://hdl.handle.net/11449/190631 |
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 μs 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. |
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Repositório Institucional da UNESP |
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Diffusion of tRNA inside the ribosome is position-dependentIn 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 μs 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.National Science FoundationDepartment of Physics Northeastern University Dana Research Center 111, 360 Huntington Ave.São Paulo State University (UNESP) IBILCE São José Do Rio PretoSão Paulo State University (UNESP) IBILCE São José Do Rio PretoNational Science Foundation: 16-19629National Science Foundation: MCB-1350312National Science Foundation: MCB-1915843Dana Research Center 111Universidade Estadual Paulista (Unesp)Yang, HuanBandarkar, PrasadHorne, RansomLeite, Vitor B. P. [UNESP]Chahine, Jorge [UNESP]Whitford, Paul C.2019-10-06T17:19:39Z2019-10-06T17:19:39Z2019-08-28info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1063/1.5113814Journal of Chemical Physics, v. 151, n. 8, 2019.0021-9606http://hdl.handle.net/11449/19063110.1063/1.51138142-s2.0-85071781382Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal of Chemical Physicsinfo:eu-repo/semantics/openAccess2021-10-23T20:19:32Zoai:repositorio.unesp.br:11449/190631Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:12:08.197805Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Diffusion of tRNA inside the ribosome is position-dependent |
title |
Diffusion of tRNA inside the ribosome is position-dependent |
spellingShingle |
Diffusion of tRNA inside the ribosome is position-dependent Yang, Huan |
title_short |
Diffusion of tRNA inside the ribosome is position-dependent |
title_full |
Diffusion of tRNA inside the ribosome is position-dependent |
title_fullStr |
Diffusion of tRNA inside the ribosome is position-dependent |
title_full_unstemmed |
Diffusion of tRNA inside the ribosome is position-dependent |
title_sort |
Diffusion of tRNA inside the ribosome is position-dependent |
author |
Yang, Huan |
author_facet |
Yang, Huan Bandarkar, Prasad Horne, Ransom Leite, Vitor B. P. [UNESP] Chahine, Jorge [UNESP] Whitford, Paul C. |
author_role |
author |
author2 |
Bandarkar, Prasad Horne, Ransom Leite, Vitor B. P. [UNESP] Chahine, Jorge [UNESP] Whitford, Paul C. |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Dana Research Center 111 Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Yang, Huan Bandarkar, Prasad Horne, Ransom Leite, Vitor B. P. [UNESP] Chahine, Jorge [UNESP] Whitford, Paul C. |
description |
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 μs 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. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-06T17:19:39Z 2019-10-06T17:19:39Z 2019-08-28 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1063/1.5113814 Journal of Chemical Physics, v. 151, n. 8, 2019. 0021-9606 http://hdl.handle.net/11449/190631 10.1063/1.5113814 2-s2.0-85071781382 |
url |
http://dx.doi.org/10.1063/1.5113814 http://hdl.handle.net/11449/190631 |
identifier_str_mv |
Journal of Chemical Physics, v. 151, n. 8, 2019. 0021-9606 10.1063/1.5113814 2-s2.0-85071781382 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Journal of Chemical Physics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128331096260608 |