Non-bulk-like solvent behavior in the ribosome exit tunnel.
As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-10-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC2958802?pdf=render |
| _version_ | 1818920026265092096 |
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| author | Del Lucent Christopher D Snow Colin Echeverría Aitken Vijay S Pande |
| author_facet | Del Lucent Christopher D Snow Colin Echeverría Aitken Vijay S Pande |
| author_sort | Del Lucent |
| collection | DOAJ |
| description | As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities. |
| first_indexed | 2024-12-20T01:15:12Z |
| format | Article |
| id | doaj.art-cb1ff10704e04eacaa78971523d2be9f |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-20T01:15:12Z |
| publishDate | 2010-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-cb1ff10704e04eacaa78971523d2be9f2022-12-21T19:58:36ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582010-10-01610e100096310.1371/journal.pcbi.1000963Non-bulk-like solvent behavior in the ribosome exit tunnel.Del LucentChristopher D SnowColin Echeverría AitkenVijay S PandeAs nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.http://europepmc.org/articles/PMC2958802?pdf=render |
| spellingShingle | Del Lucent Christopher D Snow Colin Echeverría Aitken Vijay S Pande Non-bulk-like solvent behavior in the ribosome exit tunnel. PLoS Computational Biology |
| title | Non-bulk-like solvent behavior in the ribosome exit tunnel. |
| title_full | Non-bulk-like solvent behavior in the ribosome exit tunnel. |
| title_fullStr | Non-bulk-like solvent behavior in the ribosome exit tunnel. |
| title_full_unstemmed | Non-bulk-like solvent behavior in the ribosome exit tunnel. |
| title_short | Non-bulk-like solvent behavior in the ribosome exit tunnel. |
| title_sort | non bulk like solvent behavior in the ribosome exit tunnel |
| url | http://europepmc.org/articles/PMC2958802?pdf=render |
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