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Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation

Bernado, Pau ; Modig, Kristofer LU orcid ; Grela, Przemyslaw ; Svergun, Dmitri I. ; Tchorzewski, Marek ; Pons, Miquel and Akke, Mikael LU orcid (2010) In Biophysical Journal 98(10). p.2374-2382
Abstract
Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its... (More)
Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the N-15 relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome. (Less)
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author
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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biophysical Journal
volume
98
issue
10
pages
2374 - 2382
publisher
Cell Press
external identifiers
  • wos:000277858400040
  • scopus:77951645923
  • pmid:20483347
ISSN
1542-0086
DOI
10.1016/j.bpj.2010.02.012
language
English
LU publication?
yes
id
a9128d50-bf53-4a7b-9ad5-018488036889 (old id 1617599)
date added to LUP
2016-04-01 10:02:44
date last changed
2022-04-27 17:57:16
@article{a9128d50-bf53-4a7b-9ad5-018488036889,
  abstract     = {{Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the N-15 relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome.}},
  author       = {{Bernado, Pau and Modig, Kristofer and Grela, Przemyslaw and Svergun, Dmitri I. and Tchorzewski, Marek and Pons, Miquel and Akke, Mikael}},
  issn         = {{1542-0086}},
  language     = {{eng}},
  number       = {{10}},
  pages        = {{2374--2382}},
  publisher    = {{Cell Press}},
  series       = {{Biophysical Journal}},
  title        = {{Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation}},
  url          = {{https://lup.lub.lu.se/search/files/1510790/1670407.pdf}},
  doi          = {{10.1016/j.bpj.2010.02.012}},
  volume       = {{98}},
  year         = {{2010}},
}