1
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Kenner LR, Anand AA, Nguyen HC, Myasnikov AG, Klose CJ, McGeever LA, Tsai JC, Miller-Vedam LE, Walter P, Frost A. eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response. Science 2019; 364:491-495. [PMID: 31048491 DOI: 10.1126/science.aaw2922] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/08/2019] [Indexed: 12/20/2022]
Abstract
The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a guanosine triphosphatase that becomes activated by eIF2B, a two-fold symmetric and heterodecameric complex that functions as eIF2's dedicated nucleotide exchange factor. Phosphorylation converts eIF2 from a substrate into an inhibitor of eIF2B. We report cryo-electron microscopy structures of eIF2 bound to eIF2B in the dephosphorylated state. The structures reveal that the eIF2B decamer is a static platform upon which one or two flexible eIF2 trimers bind and align with eIF2B's bipartite catalytic centers to catalyze nucleotide exchange. Phosphorylation refolds eIF2α, allowing it to contact eIF2B at a different interface and, we surmise, thereby sequestering it into a nonproductive complex.
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Affiliation(s)
- Lillian R Kenner
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Aditya A Anand
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Henry C Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Alexander G Myasnikov
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Centre for Integrative Biology, Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 67404 Illkirch, France
| | - Carolin J Klose
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Lea A McGeever
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Jordan C Tsai
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Lakshmi E Miller-Vedam
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA
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2
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Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open 2018; 7:7/7/bio036103. [PMID: 30037883 PMCID: PMC6078352 DOI: 10.1242/bio.036103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.
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Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kyle A Barlow
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Daniel Asarnow
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Yuliya Birman
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Derek Britain
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Charlotte A Nelson
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Pooja Suresh
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ruilin Tian
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taylor Arhar
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Beatrice E Ary
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - David P Bauer
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ian D Bergman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Rachel M Brunetti
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Cynthia M Chio
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Shizhong A Dai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Miles S Dickinson
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Susanna K Elledge
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Cole V M Helsell
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nathan L Hendel
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Emily Kang
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Nadja Kern
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Matvei S Khoroshkin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Lisa L Kirkemo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Greyson R Lewis
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kevin Lou
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Wesley M Marin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Alison M Maxwell
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter F McTigue
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | | | - Tamas L Nagy
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Andrew M Natale
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sergei Pourmal
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Gabriel K Reder
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nicholas J Rettko
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter J Rohweder
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Daniel M C Schwarz
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sophia K Tan
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Paul V Thomas
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ryan W Tibble
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Jason P Town
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Mary K Tsai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Douglas R Wassarman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Alexander M Wolff
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taia S Wu
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Derek Bogdanoff
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Jennifer Li
- Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Shane O'Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA .,Institute for Neurodegenerative Diseases, University of California, San Francisco 94158, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
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3
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Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Conformational variation of proteins at room temperature is not dominated by radiation damage. J Synchrotron Radiat 2017; 24:73-82. [PMID: 28009548 PMCID: PMC5182021 DOI: 10.1107/s1600577516017343] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/28/2016] [Indexed: 05/09/2023]
Abstract
Protein crystallography data collection at synchrotrons is routinely carried out at cryogenic temperatures to mitigate radiation damage. Although damage still takes place at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by approximately 100-fold. Recent studies have shown that flash-cooling decreases the heterogeneity of the conformational ensemble and can hide important functional mechanisms from observation. These discoveries have motivated increasing numbers of experiments to be carried out at room temperature. However, the trade-offs between increased risk of radiation damage and increased observation of alternative conformations at room temperature relative to cryogenic temperature have not been examined. A considerable amount of effort has previously been spent studying radiation damage at cryo-temperatures, but the relevance of these studies to room temperature diffraction is not well understood. Here, the effects of radiation damage on the conformational landscapes of three different proteins (T. danielli thaumatin, hen egg-white lysozyme and human cyclophilin A) at room (278 K) and cryogenic (100 K) temperatures are investigated. Increasingly damaged datasets were collected at each temperature, up to a maximum dose of the order of 107 Gy at 100 K and 105 Gy at 278 K. Although it was not possible to discern a clear trend between damage and multiple conformations at either temperature, it was observed that disorder, monitored by B-factor-dependent crystallographic order parameters, increased with higher absorbed dose for the three proteins at 100 K. At 278 K, however, the total increase in this disorder was only statistically significant for thaumatin. A correlation between specific radiation damage affecting side chains and the amount of disorder was not observed. This analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.
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Affiliation(s)
- Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ana González
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Lillian R. Kenner
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - Daniel A. Keedy
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
| | - Henry van den Bedem
- Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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4
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Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. eLife 2016; 5. [PMID: 27111525 PMCID: PMC4862753 DOI: 10.7554/elife.15802] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022] Open
Abstract
Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum. DOI:http://dx.doi.org/10.7554/eLife.15802.001 The ability of an organism to grow and reproduce, that is, it’s “fitness”, is determined by how its genes interact with the environment. Yeast is a model organism in which researchers can control the exact mutations present in the yeast’s genes (its genotype) and the conditions in which the yeast cells live (their environment). This allows researchers to measure how a yeast cell’s genotype and environment affect its fitness. Ubiquitin is a protein that many organisms depend on to manage cell stress by acting as a tag that targets other proteins for degradation. Essential proteins such as ubiquitin often remain unchanged by mutation over long periods of time. As a result, these proteins evolve very slowly. Like all proteins, ubiquitin is built from a chain of amino acid molecules linked together, and the ubiquitin proteins of yeast and humans are made of almost identical sequences of amino acids. Although ubiquitin has barely changed its sequence over evolution, previous studies have shown that – under normal growth conditions in the laboratory – most amino acids in ubiquitin can be mutated without any loss of cell fitness. This led Mavor et al. to hypothesize that treating the yeast cells with chemicals that cause cell stress might lead to amino acids in ubiquitin becoming more sensitive to mutation. To test this idea, a class of graduate students at the University of California, San Francisco grew yeast cells with different ubiquitin mutations together, and with different chemicals that induce cell stress, and measured their growth rates. Sequencing the ubiquitin gene in the thousands of tested yeast cells revealed that three of the chemicals cause a shared set of amino acids in ubiquitin to become more sensitive to mutation. This result suggests that these amino acids are important for the stress response, possibly by altering the ability of yeast cells to target certain proteins for degradation. Conversely, another chemical causes yeast to become more tolerant to changes in the ubiquitin sequence. The experiments also link changes in particular amino acids in ubiquitin to specific stress responses. Mavor et al. show that many of ubquitin’s amino acids are sensitive to mutation under different stress conditions, while others can be mutated to form different amino acids without effecting fitness. By testing the effects of other chemicals, future experiments could further characterize how the yeast’s genotype and environment interact. DOI:http://dx.doi.org/10.7554/eLife.15802.002
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Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Kyle Barlow
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Samuel Thompson
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Benjamin A Barad
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Alain R Bonny
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Clinton L Cario
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Garrett Gaskins
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Zairan Liu
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Laura Deming
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Seth D Axen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Elena Caceres
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Adolfo Cuesta
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Rachel E Gate
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Kaitlin R Hulce
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Weiyue Ji
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Steven M Moss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Marco Mravic
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Ryan K Muir
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stefan Niekamp
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Chimno I Nnadi
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Eugene Palovcak
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Tyler D Ross
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Eugenia C Salcedo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stephanie K See
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Meena Subramaniam
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Allison W Wong
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Jennifer Li
- UCSF Science and Health Education Partnership, University of California, San Francisco, San Francisco, United States
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
| | - Benjamin P Roscoe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Center for Advanced Technology, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
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5
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Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 2015; 4. [PMID: 26422513 PMCID: PMC4721965 DOI: 10.7554/elife.07574] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/29/2015] [Indexed: 12/14/2022] Open
Abstract
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. DOI:http://dx.doi.org/10.7554/eLife.07574.001 Proteins are the workhorses of the cell. The shape that a protein molecule adopts enables it to carry out its role. However, a protein’s shape, or 'conformation', is not static. Instead, a protein can shift between different conformations. This is particularly true for enzymes – the proteins that catalyze chemical reactions. The region of an enzyme where the chemical reaction happens, known as the active site, often has to change its conformation to allow catalysis to proceed. Changes in temperature can also make a protein shift between alternative conformations. Understanding how a protein shifts between conformations gives insight into how it works. A common method for studying protein conformation is X-ray crystallography. This technique uses a beam of X-rays to figure out where the atoms of the protein are inside a crystal made of millions of copies of that protein. At room temperature or biological temperature, X-rays can rapidly damage the protein. Because of this, most crystal structures are determined at very low temperatures to minimize damage. But cooling to low temperatures changes the conformations that the protein adopts, and usually causes fewer conformations to be present. Keedy, Kenner, Warkentin, Woldeyes et al. have used X-ray crystallography from a very low temperature (-173°C or 100 K) to above room temperature (up to 27°C or 300 K) to explore the alternative conformations of an enzyme called cyclophilin A. These alternative conformations include those that have previously been linked to this enzyme’s activity. Starting at a low temperature, parts of the enzyme were seen to shift from having a single conformation to many conformations above a threshold temperature. Unexpectedly, different parts of the enzyme have different threshold temperatures, suggesting that there isn’t a single transition across the whole protein. Instead, it appears the way a protein’s conformation changes in response to temperature is more complex than was previously realized. This result suggests that conformations in different parts of a protein are coupled to each other in complex ways. Keedy, Kenner, Warkentin, Woldeyes et al. then performed X-ray crystallography at room temperature using an X-ray free-electron laser (XFEL). This technique can capture the protein’s structure before radiation damage occurs, and confirmed that the alternative conformations observed were not affected by radiation damage. The combination of X-ray crystallography at multiple temperatures, new analysis methods for identifying and measuring alternative conformations, and XFEL crystallography should help future studies to characterize conformational changes in other proteins. DOI:http://dx.doi.org/10.7554/eLife.07574.002
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | | | - Rahel A Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Jesse B Hopkins
- Department of Physics, Cornell University, Ithaca, United States
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Andrew H Van Benschoten
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henrik Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Robert E Thorne
- Department of Physics, Cornell University, Ithaca, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell 2012; 150:413-25. [PMID: 22817900 DOI: 10.1016/j.cell.2012.05.036] [Citation(s) in RCA: 315] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 03/21/2012] [Accepted: 05/18/2012] [Indexed: 11/24/2022]
Abstract
Protein function is often regulated by posttranslational modifications (PTMs), and recent advances in mass spectrometry have resulted in an exponential increase in PTM identification. However, the functional significance of the vast majority of these modifications remains unknown. To address this problem, we compiled nearly 200,000 phosphorylation, acetylation, and ubiquitination sites from 11 eukaryotic species, including 2,500 newly identified ubiquitylation sites for Saccharomyces cerevisiae. We developed methods to prioritize the functional relevance of these PTMs by predicting those that likely participate in cross-regulatory events, regulate domain activity, or mediate protein-protein interactions. PTM conservation within domain families identifies regulatory "hot spots" that overlap with functionally important regions, a concept that we experimentally validated on the HSP70 domain family. Finally, our analysis of the evolution of PTM regulation highlights potential routes for neutral drift in regulatory interactions and suggests that only a fraction of modification sites are likely to have a significant biological role.
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Affiliation(s)
- Pedro Beltrao
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94107, USA.
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