Genetic interaction mapping informs integrative structure determination of protein complexes

Hannes Braberg; Ignacia Echeverria; Stefan Bohn; Peter Cimermancic; Anthony Shiver; Richard Alexander; Jiewei Xu; Michael Shales; Raghuvar Dronamraju; Shuangying Jiang; Gajendradhar Dwivedi; Derek Bogdanoff; Kaitlin K Chaung; Ruth Hüttenhain; Shuyi Wang; David Mavor; Riccardo Pellarin; Dina Schneidman; Joel S Bader; James S Fraser; John Morris; James E Haber; Brian D Strahl; Carol A Gross; Junbiao Dai; Jef D Boeke; Andrej Sali; Nevan J Krogan

doi:10.1126/science.aaz4910

Genetic interaction mapping informs integrative structure determination of protein complexes

Science. 2020 Dec 11;370(6522):eaaz4910. doi: 10.1126/science.aaz4910.

Authors

Hannes Braberg^#^{1

2}, Ignacia Echeverria^#^{1

2

3}, Stefan Bohn^#^{1

2

4}, Peter Cimermancic^#³, Anthony Shiver⁵, Richard Alexander¹, Jiewei Xu^{1

2

4}, Michael Shales^{1

2}, Raghuvar Dronamraju⁶, Shuangying Jiang⁷, Gajendradhar Dwivedi⁸, Derek Bogdanoff⁹, Kaitlin K Chaung⁹, Ruth Hüttenhain^{1

2

4}, Shuyi Wang¹, David Mavor^{2

3}, Riccardo Pellarin³, Dina Schneidman³, Joel S Bader¹⁰, James S Fraser^{2

3}, John Morris¹¹, James E Haber⁸, Brian D Strahl⁶, Carol A Gross¹², Junbiao Dai⁷, Jef D Boeke^{13

14

15

16}, Andrej Sali^{17

3

11}, Nevan J Krogan^{18

2

4

19}

Affiliations

¹ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
² Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
³ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
⁴ Gladstone Institutes, San Francisco, CA 94158, USA.
⁵ Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.
⁶ Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
⁷ CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
⁸ Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA.
⁹ Center for Advanced Technology, Department of Biophysics and Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
¹⁰ Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
¹¹ Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
¹² Department of Microbiology and Immunology and Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
¹³ NYU Langone Health, New York, NY 10016, USA. [email protected] [email protected] [email protected].
¹⁴ High Throughput Biology Center and Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
¹⁵ Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
¹⁶ Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
¹⁷ Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA. [email protected] [email protected] [email protected].
¹⁸ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. [email protected] [email protected] [email protected].
¹⁹ Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

^# Contributed equally.

Abstract

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Histones / chemistry
Histones / genetics
Multiprotein Complexes / chemistry*
Multiprotein Complexes / genetics*
Mutation
Protein Conformation
Protein Interaction Mapping
Protein Interaction Maps / genetics*
Saccharomyces cerevisiae / genetics
Saccharomyces cerevisiae / metabolism*
Saccharomyces cerevisiae Proteins / chemistry*
Saccharomyces cerevisiae Proteins / genetics*

Substances

Histones
Multiprotein Complexes
Saccharomyces cerevisiae Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding