Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation
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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 (15)N 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.
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The L12 conformational ensemble shows that its two C-terminal domains sample a large volume and extend farther from the ribosomal anchor than expected for a random-chain linker, indicating residual order in the flexible linker.
“The ensemble of L12 conformations reveals that the two C-terminal domains sample a large volume and extend further away from the ribosomal anchor than expected for a random-chain linker, indicating that the flexible linker has residual order.”
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- Authors
- Bernadó, P., Modig, K., Grela, P., Svergun, D. I., Tchorzewski, M., Pons, M., & Akke, M.
- Affiliations
- Institute for Research in Biomedicine (ES)
- Lund University (SE)
- Maria Curie-Skłodowska University (PL)
- Russian Academy of Sciences (RU)
- Corresponding author
- Bernadó, Pau
- Akke, Mikael
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2010-05
- Volume
- 98
- Issue
- 10
- Pages
- 2374-2382
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC2872255
- OpenAlex
- W2038084867
- Cited by
- 77
- References
- 48
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2023: 1 · 2021: 2 · 2020: 1 · 2019: 9 · 2018: 3 · 2017: 5 · 2016: 4 · 2015: 8 · 2014: 9 · 2013: 9 · 2012: 10
- FWCI
- 4.04
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Desy Publications Database (Deutsches Elektronen-Synchrotron DESY) (publishedVersion)
- Lund University Publications (Lund University) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- ribosomal protein L12, ensemble learning, domain reorientation, flexible linkers, conformational dynamics, correlation time, 15N relaxation, ribosome, translation (biology), protein dimerization
- MeSH terms
- Magnetic Resonance Spectroscopy, Protein Conformation, Ribosomal Proteins, Ribosomes, X-Rays, Protein Structure, Tertiary, Protein Folding, Nuclear Magnetic Resonance, Biomolecular, Escherichia coli Proteins, Prokaryotic Initiation Factor-2, Scattering, Small Angle
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