Genetic interaction mapping informs integrative structure determination of protein complexes
Open accessAbstract
Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.
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Braberg et al. converted similarities between mutational profiles into an upper bound on distance between mutational residues to create multiscale models of protein complex structures.
“In another recent study, similarities between mutational profiles were converted into an upper bound on distance between mutational residues to create multiscale models of protein complex structures (Braberg et al., 2020).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Braberg et al., 2020
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Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Mapping the multiscale structure of biological systems
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- Authors
- Braberg, H., Echeverria, I., Bohn, S., Cimermancic, P., Shiver, A., Alexander, R., Xu, J., Shales, M., Dronamraju, R., Jiang, S., Dwivedi, G., Bogdanoff, D., Chaung, K. K., Hüttenhain, R., Wang, S., Mavor, D., Pellarin, R., Schneidman, D., Bader, J. S., Fraser, J. S., Morris, J., Haber, J. E., Strahl, B. D., Gross, C. A., Dai, J., Boeke, J. D., Sali, A., & Krogan, N. J.
- Affiliations
- University of California, San Francisco (US)
- Gladstone Institutes (US)
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
- University of North Carolina at Chapel Hill (US)
- Chinese Academy of Sciences (CN)
- Brandeis University (US)
- Johns Hopkins University (US)
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
- Corresponding author
- Boeke, Jef D.
- Krogan, Nevan J.
- ORCID
- Braberg, Hannes
- Echeverria, Ignacia
- Bohn, Stefan
- Cimermancic, Peter
- Shiver, Anthony
- Alexander, Richard
- Xu, Jiewei
- Jiang, Shuangying
- Chaung, Kaitlin K.
- Hüttenhain, Ruth
- Wang, Shuyi
- Mavor, David
- Pellarin, Riccardo
- Schneidman, Dina
- Bader, Joel S.
- Fraser, James S.
- Morris, John
- Haber, James E.
- Strahl, Brian D.
- Gross, Carol A.
- Dai, Junbiao
- Boeke, Jef D.
- Sali, Andrej
- Krogan, Nevan J.
- Venue
- Science
- Published
- 2020-12-11
- Volume
- 370
- Issue
- 6522
- Pages
- eaaz4910
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7946025
- OpenAlex
- W3111783782
- Cited by
- 37
- References
- 146
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 3 · 2023: 4 · 2022: 8 · 2021: 13 · 2020: 1
- FWCI
- 2.19
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- HAL (submittedVersion)
- Funders
- National Institutes of Health (R01 GM083960, P50 GM082250, U19 AI135990, S10 OD021596, P41 GM109824, U54 RR020839, P01GM105473, R01 GM084448, GM126900, R01 GM084279, P50 GM081879, R01 GM098101, U54 GM103520, OD009180, GM123159, GM008284, P41 GM103504, P50AI150476, R35GM118061)
- National Natural Science Foundation of China (31800069)
- National Key Research and Development Program of China Stem Cell and Translational Research (2017YFA0505103)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- genetic interaction mapping, protein complex structure, phenotypic profiles, point mutations, gene deletion, environmental disturbance, RNA polymerase II, RNA polymerase, chemical cross-links, yeast
- MeSH terms
- Histones, Mutation, Protein Conformation, Saccharomyces cerevisiae, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins, Multiprotein Complexes, Protein Interaction Maps
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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