Cargando…

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that...

Descripción completa

Detalles Bibliográficos
Autores principales: Watson, Zoe L., Knudson, Isaac J., Ward, Fred R., Miller, Scott J., Cate, Jamie H. D., Schepartz, Alanna, Abramyan, Ara M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322701/
https://www.ncbi.nlm.nih.gov/pubmed/37308707
http://dx.doi.org/10.1038/s41557-023-01226-w
_version_ 1785068816427909120
author Watson, Zoe L.
Knudson, Isaac J.
Ward, Fred R.
Miller, Scott J.
Cate, Jamie H. D.
Schepartz, Alanna
Abramyan, Ara M.
author_facet Watson, Zoe L.
Knudson, Isaac J.
Ward, Fred R.
Miller, Scott J.
Cate, Jamie H. D.
Schepartz, Alanna
Abramyan, Ara M.
author_sort Watson, Zoe L.
collection PubMed
description As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers. [Image: see text]
format Online
Article
Text
id pubmed-10322701
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-103227012023-07-07 Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates Watson, Zoe L. Knudson, Isaac J. Ward, Fred R. Miller, Scott J. Cate, Jamie H. D. Schepartz, Alanna Abramyan, Ara M. Nat Chem Article As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers. [Image: see text] Nature Publishing Group UK 2023-06-12 2023 /pmc/articles/PMC10322701/ /pubmed/37308707 http://dx.doi.org/10.1038/s41557-023-01226-w Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Watson, Zoe L.
Knudson, Isaac J.
Ward, Fred R.
Miller, Scott J.
Cate, Jamie H. D.
Schepartz, Alanna
Abramyan, Ara M.
Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates
title Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates
title_full Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates
title_fullStr Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates
title_full_unstemmed Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates
title_short Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates
title_sort atomistic simulations of the escherichia coli ribosome provide selection criteria for translationally active substrates
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322701/
https://www.ncbi.nlm.nih.gov/pubmed/37308707
http://dx.doi.org/10.1038/s41557-023-01226-w
work_keys_str_mv AT watsonzoel atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates
AT knudsonisaacj atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates
AT wardfredr atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates
AT millerscottj atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates
AT catejamiehd atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates
AT schepartzalanna atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates
AT abramyanaram atomisticsimulationsoftheescherichiacoliribosomeprovideselectioncriteriafortranslationallyactivesubstrates