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Ziegelhoffer T, Verma AK, Delewski W, Schilke BA, Hill PM, Pitek M, Marszalek J, Craig EA. NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo. Nucleic Acids Res 2024; 52:3346-3357. [PMID: 38224454 PMCID: PMC11014269 DOI: 10.1093/nar/gkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
The area surrounding the tunnel exit of the 60S ribosomal subunit is a hub for proteins involved in maturation and folding of emerging nascent polypeptide chains. How different factors vie for positioning at the tunnel exit in the complex cellular environment is not well understood. We used in vivo site-specific cross-linking to approach this question, focusing on two abundant factors-the nascent chain-associated complex (NAC) and the Hsp70 chaperone system that includes the J-domain protein co-chaperone Zuotin. We found that NAC and Zuotin can cross-link to each other at the ribosome, even when translation initiation is inhibited. Positions yielding NAC-Zuotin cross-links indicate that when both are present the central globular domain of NAC is modestly shifted from the mutually exclusive position observed in cryogenic electron microscopy analysis. Cross-linking results also suggest that, even in NAC's presence, Hsp70 can situate in a manner conducive for productive nascent chain interaction-with the peptide binding site at the tunnel exit and the J-domain of Zuotin appropriately positioned to drive stabilization of nascent chain binding. Overall, our results are consistent with the idea that, in vivo, the NAC and Hsp70 systems can productively position on the ribosome simultaneously.
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Affiliation(s)
- Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Amit K Verma
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Brenda A Schilke
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Paige M Hill
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80-307, Poland
| | - Jaroslaw Marszalek
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80-307, Poland
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
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2
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Jagtap PKA, Müller M, Kiss AE, Thomae AW, Lapouge K, Beck M, Becker PB, Hennig J. Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless. Mol Cell 2023; 83:4318-4333.e10. [PMID: 37989319 DOI: 10.1016/j.molcel.2023.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 07/27/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023]
Abstract
RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We explored the interplay between the RecA and auxiliary domains of the RNA helicase maleless (MLE) from Drosophila using structural and functional studies. We discovered that MLE exists in a dsRNA-bound open conformation and that the auxiliary dsRBD2 domain aligns the substrate RNA with the accessible helicase tunnel. In an ATP-dependent manner, dsRBD2 associates with the helicase module, leading to tunnel closure around ssRNA. Furthermore, our structures provide a rationale for blunt-ended dsRNA unwinding and 3'-5' translocation by MLE. Structure-based MLE mutations confirm the functional relevance of our model for RNA unwinding. Our findings contribute to our understanding of the fundamental mechanics of auxiliary domains in DExH helicase MLE, which serves as a model for its human ortholog and potential therapeutic target, DHX9/RHA.
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Affiliation(s)
- Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany.
| | - Marisa Müller
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Anna E Kiss
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany; Core Facility Bioimaging at the Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69117 Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany.
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3
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Karl LA, Galanti L, Bantele SC, Metzner F, Šafarić B, Rajappa L, Foster B, Pires VB, Bansal P, Chacin E, Basquin J, Duderstadt KE, Kurat CF, Bartke T, Hopfner KP, Pfander B. A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler. Life Sci Alliance 2023; 6:e202201790. [PMID: 37468166 PMCID: PMC10355287 DOI: 10.26508/lsa.202201790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Fun30 is the prototype of the Fun30-SMARCAD1-ETL subfamily of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single-subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30Δ mutant. In vitro, Fun30 protein lacking the SAM-key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity and nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome-remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.
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Affiliation(s)
- Leonhard A Karl
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Susanne Cs Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Barbara Šafarić
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Benjamin Foster
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Vanessa Borges Pires
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Jerôme Basquin
- Crystallization Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
- Physik Department, Technische Universität München, Munich, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
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4
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A case of convergent evolution: Several viral and bacterial pathogens hijack RSK kinases through a common linear motif. Proc Natl Acad Sci U S A 2022; 119:2114647119. [PMID: 35091472 PMCID: PMC8812568 DOI: 10.1073/pnas.2114647119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
Microbes have been coevolving with their host for millions of years, exploiting host resources to their own benefit. We show that viral and bacterial pathogens convergently evolved to hijack cellular mitogen-activated protein kinase (MAPK) p90-ribosomal S6-kinases (RSKs). Theiler's virus leader (L) protein binds RSKs and prevents their dephosphorylation, thus maintaining the kinases active. Recruitment of RSKs enables L-protein-mediated inhibition of eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2 or PKR) and stress granule formation. Strikingly, ORF45 protein of Kaposi's sarcoma-associated herpesvirus (KSHV) and YopM protein of Yersinia use the same peptide motif as L to recruit and activate RSKs. All three proteins interact with a conserved surface-located loop of RSKs, likely acting as an allosteric regulation site. Some unrelated viruses and bacteria thus evolved to harness RSKs in a common fashion, yet to target distinct aspects of innate immunity. As documented for Varicella zoster virus ORF11, additional pathogens likely evolved to hijack RSKs, using a similar short linear motif.
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5
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Windgassen TA, Leroux M, Sandler SJ, Keck JL. Function of a strand-separation pin element in the PriA DNA replication restart helicase. J Biol Chem 2018; 294:2801-2814. [PMID: 30593500 DOI: 10.1074/jbc.ra118.006870] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/26/2018] [Indexed: 11/06/2022] Open
Abstract
DNA helicases are motor proteins that couple the chemical energy of nucleoside triphosphate hydrolysis to the mechanical functions required for DNA unwinding. Studies of several helicases have identified strand-separating "pin" structures that are positioned to intercept incoming dsDNA and promote strand separation during helicase translocation. However, pin structures vary among helicases and it remains unclear whether they confer a conserved unwinding mechanism. Here, we tested the biochemical and cellular roles of a putative pin element within the Escherichia coli PriA DNA helicase. PriA orchestrates replication restart in bacteria by unwinding the lagging-strand arm of abandoned DNA replication forks and reloading the replicative helicase with the help of protein partners that combine with PriA to form what is referred to as a primosome complex. Using in vitro protein-DNA cross-linking, we localized the putative pin (a β-hairpin within a zinc-binding domain in PriA) near the ssDNA-dsDNA junction of the lagging strand in a PriA-DNA replication fork complex. Removal of residues at the tip of the β-hairpin eliminated PriA DNA unwinding, interaction with the primosome protein PriB, and cellular function. We isolated a spontaneous intragenic suppressor mutant of the priA β-hairpin deletion mutant in which 22 codons around the deletion site were duplicated. This suppressor variant and an Ala-substituted β-hairpin PriA variant displayed wildtype levels of DNA unwinding and PriB binding in vitro These results suggest essential but sequence nonspecific roles for the PriA pin element and coupling of PriA DNA unwinding to its interaction with PriB.
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Affiliation(s)
- Tricia A Windgassen
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
| | - Maxime Leroux
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Steven J Sandler
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - James L Keck
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706 and
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6
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Epigenetic chromatin modification by amber suppression technology. Curr Opin Chem Biol 2018; 45:1-9. [DOI: 10.1016/j.cbpa.2018.01.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/28/2018] [Indexed: 01/10/2023]
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7
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Abstract
ATP-dependent nucleosome remodeling factors sculpt the nucleosomal landscape of eukaryotic chromatin. They deposit or evict nucleosomes or reposition them along DNA in a process termed nucleosome sliding. Remodeling has traditionally been analyzed using mononucleosomes as a model substrate. In vivo, however, nucleosomes form extended arrays with regular spacing. Here, we describe how regularly spaced nucleosome arrays can be reconstituted in vitro and how these arrays can be used to dissect remodeling in the test tube. We outline two assays. The first assay senses various structural changes to a specific nucleosome within the nucleosomal array whereas the second assay is specific toward detecting repositioning of nucleosomes within the array. Both assays exploit changes to the accessibility of DNA to restriction enzymes during the remodeling reaction.
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8
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Dempsey DR, Cole PA. Protein Chemical Approaches to Understanding PTEN Lipid Phosphatase Regulation. Methods Enzymol 2018; 607:405-422. [PMID: 30149868 DOI: 10.1016/bs.mie.2018.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Since the discovery of C-tail phosphorylation of PTEN almost 20 years ago, much progress has been made in understanding its regulatory influences on the cellular function of PTEN. Phosphorylation of Ser380, Thr382, Thr383, and Ser385 drives a PTEN conformational change from an open to closed state where catalytic function is impaired, plasma membrane binding is reduced, and cellular stability is enhanced. Despite these advances, a detailed structural and mechanistic model of how these phosphorylations impact PTEN function is lacking. We discuss here several recent approaches to analyzing PTEN phosphorylation and highlight several insights that have come from this work. We also discuss remaining challenges for the PTEN regulation field and potential directions for future research.
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Affiliation(s)
- Daniel R Dempsey
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, United States; Department of Medicine, Harvard Medical School, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Philip A Cole
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, United States; Department of Medicine, Harvard Medical School, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States.
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9
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Blank ML, Parker ML, Ramaswamy R, Powell CJ, English ED, Adomako-Ankomah Y, Pernas LF, Workman SD, Boothroyd JC, Boulanger MJ, Boyle JP. A Toxoplasma gondii locus required for the direct manipulation of host mitochondria has maintained multiple ancestral functions. Mol Microbiol 2018; 108:519-535. [PMID: 29505111 PMCID: PMC6245547 DOI: 10.1111/mmi.13947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 01/16/2023]
Abstract
The Toxoplasma gondii locus mitochondrial association factor 1 (MAF1) encodes multiple paralogs, some of which mediate host mitochondrial association (HMA). Previous work showed that HMA was a trait that arose in T. gondii through neofunctionalization of an ancestral MAF1 ortholog. Structural analysis of HMA-competent and incompetent MAF1 paralogs (MAF1b and MAF1a, respectively) revealed that both paralogs harbor an ADP ribose binding macro-domain, with comparatively low (micromolar) affinity for ADP ribose. Replacing the 16 C-terminal residues of MAF1b with those of MAF1a abrogated HMA, and we also show that only three residues in the C-terminal helix are required for MAF1-mediated HMA. Importantly these same three residues are also required for the in vivo growth advantage conferred by MAF1b, providing a definitive link between in vivo proliferation and manipulation of host mitochondria. Co-immunoprecipitation assays reveal that the ability to interact with the mitochondrial MICOS complex is shared by HMA-competent and incompetent MAF1 paralogs and mutants. The weak ADPr coordination and ability to interact with the MICOS complex shared between divergent paralogs may represent modular ancestral functions for this tandemly expanded and diversified T. gondii locus.
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Affiliation(s)
- Matthew L. Blank
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michelle L. Parker
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Raghavendran Ramaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Cameron J. Powell
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Elizabeth D. English
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yaw Adomako-Ankomah
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lena F. Pernas
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sean D. Workman
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - John C. Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Martin J. Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Jon P. Boyle
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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10
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Harrer N, Schindler CEM, Bruetzel LK, Forné I, Ludwigsen J, Imhof A, Zacharias M, Lipfert J, Mueller-Planitz F. Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling. Structure 2018; 26:282-294.e6. [PMID: 29395785 DOI: 10.1016/j.str.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 10/25/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022]
Abstract
Chromatin remodeling factors assume critical roles by regulating access to nucleosomal DNA. To determine the architecture of the Drosophila ISWI remodeling enzyme, we developed an integrative structural approach that combines protein cross-linking, mass spectrometry, small-angle X-ray scattering, and computational modeling. The resulting structural model shows the ATPase module in a resting state with both ATPase lobes twisted against each other, providing support for a conformation that was recently trapped by crystallography. The autoinhibiting NegC region does not protrude from the ATPase module as suggested previously. The regulatory NTR domain is located near both ATPase lobes. The full-length enzyme is flexible and can adopt a compact structure in solution with the C-terminal HSS domain packing against the ATPase module. Our data imply a series of conformational changes upon activation of the enzyme and illustrate how the NTR, NegC, and HSS domains contribute to regulation of the ATPase module.
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Affiliation(s)
- Nadine Harrer
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Christina E M Schindler
- Physics Department (T38), Technical University of Munich, 85748 Garching, Germany; Center for Integrated Protein Science Munich, 81377 Munich, Germany
| | - Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany
| | - Ignasi Forné
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Johanna Ludwigsen
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Axel Imhof
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Martin Zacharias
- Physics Department (T38), Technical University of Munich, 85748 Garching, Germany; Center for Integrated Protein Science Munich, 81377 Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany.
| | - Felix Mueller-Planitz
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany.
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Belsom A, Mudd G, Giese S, Auer M, Rappsilber J. Complementary Benzophenone Cross-Linking/Mass Spectrometry Photochemistry. Anal Chem 2017; 89:5319-5324. [PMID: 28430416 PMCID: PMC5441754 DOI: 10.1021/acs.analchem.6b04938] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Use
of a heterobifunctional photoactivatable cross-linker, sulfo-SDA
(diazirine), has yielded high-density data that facilitated structure
modeling of individual proteins. We expand the photoactivatable chemistry
toolbox here with a second reagent, sulfo-SBP (benzophenone). This
further increases the density of photo-cross-linking to a factor of
20× over conventional cross-linking. Importantly, the two different
photoactivatable groups display orthogonal directionality, enabling
access to different protein regions, unreachable with a single cross-linker.
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Affiliation(s)
- Adam Belsom
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Gemma Mudd
- School of Biological Sciences and Medical School, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Sven Giese
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany
| | - Manfred Auer
- School of Biological Sciences and Medical School, University of Edinburgh , Edinburgh EH9 3BF, U.K
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, U.K.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin , 13355 Berlin, Germany
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12
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Ludwigsen J, Pfennig S, Singh AK, Schindler C, Harrer N, Forné I, Zacharias M, Mueller-Planitz F. Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail. eLife 2017; 6. [PMID: 28109157 PMCID: PMC5305211 DOI: 10.7554/elife.21477] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/20/2017] [Indexed: 01/08/2023] Open
Abstract
ISWI-family nucleosome remodeling enzymes need the histone H4 N-terminal tail to mobilize nucleosomes. Here we mapped the H4-tail binding pocket of ISWI. Surprisingly the binding site was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the N-terminal region (NTR) of ISWI, indicating that AutoN does not act as a simple pseudosubstrate as suggested previously. Rather, AutoN cooperated with a hitherto uncharacterized motif, termed AcidicN, to confer H4-tail sensitivity and discriminate between DNA and nucleosomes. A third motif in the NTR, ppHSA, was functionally required in vivo and provided structural stability by clamping the NTR to Lobe 2 of the ATPase domain. This configuration is reminiscent of Chd1 even though Chd1 contains an unrelated NTR. Our results shed light on the intricate structural and functional regulation of ISWI by the NTR and uncover surprising parallels with Chd1. DOI:http://dx.doi.org/10.7554/eLife.21477.001 In the cells of animals, plants and other eukaryotes, DNA wraps tightly around proteins called histones to form structures known as nucleosomes that resemble beads on a string. When nucleosomes are sufficiently close to each other they interact and clump together, which compacts the DNA and prevents the genes in that stretch of DNA being activated. But how do cells mobilize their nucleosomes? A nucleosome remodeling enzyme called ISWI can slide nucleosomes along DNA. ISWI becomes active when it interacts with a ‘tail’ region of a histone protein called H4. However, the H4 tail prefers to interact with neighboring nucleosomes instead of with ISWI. Therefore when ISWI slides a nucleosome close to another one, the H4 tail of the nucleosome binds instead to its new neighbor so that ISWI cannot continue to slide. By this mechanism, ISWI is proposed to pile up nucleosomes, which subsequently compact, leading to the inactivation of this part of the genome. To investigate how ISWI recognizes the H4 tail, Ludwigsen et al. mapped where the H4 tail binds to ISWI by combining the biochemical methods of cross-linking and mass spectrometry. In addition, mutagenesis experiments identified a new motif in the enzyme that is essential for recognizing the H4 tail. In the absence of the nucleosome, this motif – called AcidicN – works with a neighboring motif called AutoN to keep ISWI in an inactive state. The two motifs also work together to enable ISWI to distinguish between nucleosomes and DNA. Further evidence suggests that other remodeling enzymes have similar regulation mechanisms; therefore this method of controlling nucleosome remodeling may have been conserved throughout evolution. Further studies are now needed to detect the shape changes that occur in ISWI as it recognizes the histone tail and work out how this leads to nucleosome remodeling. Inside cells, ISWI is usually found within large complexes that consist of many proteins. It therefore also remains to be discovered whether the proteins in these complexes impose additional layers of regulation and complexity on the activity of ISWI. DOI:http://dx.doi.org/10.7554/eLife.21477.002
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Affiliation(s)
- Johanna Ludwigsen
- Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sabrina Pfennig
- Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ashish K Singh
- Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christina Schindler
- Physics Department (T38), Technische Universität München, Munich, Germany.,Center for Integrated Protein Science Munich, Munich, Germany
| | - Nadine Harrer
- Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ignasi Forné
- Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Zacharias
- Physics Department (T38), Technische Universität München, Munich, Germany.,Center for Integrated Protein Science Munich, Munich, Germany
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13
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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14
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An evolutionary conserved Hexim1 peptide binds to the Cdk9 catalytic site to inhibit P-TEFb. Proc Natl Acad Sci U S A 2016; 113:12721-12726. [PMID: 27791144 DOI: 10.1073/pnas.1612331113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The positive transcription elongation factor (P-TEFb) is required for the transcription of most genes by RNA polymerase II. Hexim proteins associated with 7SK RNA bind to P-TEFb and reversibly inhibit its activity. P-TEFb comprises the Cdk9 cyclin-dependent kinase and a cyclin T. Hexim proteins have been shown to bind the cyclin T subunit of P-TEFb. How this binding leads to inhibition of the kinase activity of Cdk9 has remained elusive, however. Using a photoreactive amino acid incorporated into proteins, we show that in live cells, cell extracts, and in vitro reconstituted complexes, Hexim1 cross-links and thus contacts Cdk9. Notably, replacement of a phenylalanine, F208, belonging to an evolutionary conserved Hexim1 peptide (202PYNTTQFLM210) known as the "PYNT" sequence, cross-links a peptide within the activation segment that controls access to the Cdk9 catalytic cleft. Reciprocally, Hexim1 is cross-linked by a photoreactive amino acid replacing Cdk9 W193, a tryptophan within this activation segment. These findings provide evidence of a direct interaction between Cdk9 and its inhibitor, Hexim1. Based on similarities with Cdk2 3D structure, the Cdk9 peptide cross-linked by Hexim1 corresponds to the substrate binding-site. Accordingly, the Hexim1 PYNT sequence is proposed to interfere with substrate binding to Cdk9 and thereby to inhibit its kinase activity.
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15
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Windgassen TA, Keck JL. An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase. Nucleic Acids Res 2016; 44:9745-9757. [PMID: 27484483 PMCID: PMC5175346 DOI: 10.1093/nar/gkw690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
Abstract
Helicases couple ATP hydrolysis to nucleic acid binding and unwinding via molecular mechanisms that remain poorly defined for most enzyme subfamilies within the superfamily 2 (SF2) helicase group. A crystal structure of the PriA SF2 DNA helicase, which governs restart of prematurely terminated replication processes in bacteria, revealed the presence of an aromatic-rich loop (ARL) on the presumptive DNA-binding surface of the enzyme. The position and sequence of the ARL was similar to loops known to couple ATP hydrolysis with DNA binding in a subset of other SF2 enzymes, however, the roles of the ARL in PriA had not been investigated. Here, we show that changes within the ARL sequence uncouple PriA ATPase activity from DNA binding. In vitro protein-DNA crosslinking experiments define a residue- and nucleotide-specific interaction map for PriA, showing that the ARL binds replication fork junctions whereas other sites bind the leading or lagging strands. We propose that DNA binding to the ARL allosterically triggers ATP hydrolysis in PriA. Additional SF2 helicases with similarly positioned loops may also couple DNA binding to ATP hydrolysis using related mechanisms.
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Affiliation(s)
- Tricia A Windgassen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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16
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Chen Z, Dempsey DR, Thomas SN, Hayward D, Bolduc DM, Cole PA. Molecular Features of Phosphatase and Tensin Homolog (PTEN) Regulation by C-terminal Phosphorylation. J Biol Chem 2016; 291:14160-14169. [PMID: 27226612 DOI: 10.1074/jbc.m116.728980] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 12/27/2022] Open
Abstract
PTEN is a tumor suppressor that functions to negatively regulate the PI3K/AKT pathway as the lipid phosphatase for phosphatidylinositol 3,4,5-triphosphate. Phosphorylation of a cluster of Ser/Thr residues (amino acids 380-385) on the C-terminal tail serves to alter the conformational state of PTEN from an open active state to a closed inhibited state, resulting in a reduction of plasma membrane localization and inhibition of enzyme activity. The relative contribution of each phosphorylation site to PTEN autoinhibition and the structural basis for the conformational closure is still unclear. To further the structural understanding of PTEN regulation by C-terminal tail phosphorylation, we used protein semisynthesis to insert stoichiometric and site-specific phospho-Ser/Thr(s) in the C-terminal tail of PTEN. Additionally, we employed photo-cross-linking to map the intramolecular PTEN interactions of the phospho-tail. Systematic evaluation of the PTEN C-tail phospho-cluster showed autoinhibition, and conformational closure was influenced by the aggregate effect of multiple phospho-sites rather than dominated by a single phosphorylation site. Moreover, photo-cross-linking suggested a direct interaction between the PTEN C-tail and a segment in the N-terminal region of the catalytic domain. Mutagenesis experiments provided additional insights into how the PTEN phospho-tail interacts with both the C2 and catalytic domains.
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Affiliation(s)
- Zan Chen
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Daniel R Dempsey
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Stefani N Thomas
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Dawn Hayward
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - David M Bolduc
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205.
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17
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Automated structure modeling of large protein assemblies using crosslinks as distance restraints. Nat Methods 2016; 13:515-20. [PMID: 27111507 DOI: 10.1038/nmeth.3838] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/19/2016] [Indexed: 11/08/2022]
Abstract
Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure.
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18
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Berlin S, Szobota S, Reiner A, Carroll EC, Kienzler MA, Guyon A, Xiao T, Trauner D, Isacoff EY. A family of photoswitchable NMDA receptors. eLife 2016; 5. [PMID: 26929991 PMCID: PMC4786437 DOI: 10.7554/elife.12040] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/31/2016] [Indexed: 02/07/2023] Open
Abstract
NMDA receptors, which regulate synaptic strength and are implicated in learning and memory, consist of several subtypes with distinct subunit compositions and functional properties. To enable spatiotemporally defined, rapid and reproducible manipulation of function of specific subtypes, we engineered a set of photoswitchable GluN subunits ('LiGluNs'). Photo-agonism of GluN2A or GluN2B elicits an excitatory drive to hippocampal neurons that can be shaped in time to mimic synaptic activation. Photo-agonism of GluN2A at single dendritic spines evokes spine-specific calcium elevation and expansion, the morphological correlate of LTP. Photo-antagonism of GluN2A alone, or in combination with photo-antagonism of GluN1a, reversibly blocks excitatory synaptic currents, prevents the induction of long-term potentiation and prevents spine expansion. In addition, photo-antagonism in vivo disrupts synaptic pruning of developing retino-tectal projections in larval zebrafish. By providing precise and rapidly reversible optical control of NMDA receptor subtypes, LiGluNs should help unravel the contribution of specific NMDA receptors to synaptic transmission, integration and plasticity.
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Affiliation(s)
- Shai Berlin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Stephanie Szobota
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Andreas Reiner
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Elizabeth C Carroll
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Michael A Kienzler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Alice Guyon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia Antipolis, Nice, France
| | - Tong Xiao
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Dirk Trauner
- Department of Chemistry, Center of Integrated Protein Science, University of Munich, Munich, Germany
| | - Ehud Y Isacoff
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States.,Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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19
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Peleg S, Feller C, Forne I, Schiller E, Sévin DC, Schauer T, Regnard C, Straub T, Prestel M, Klima C, Schmitt Nogueira M, Becker L, Klopstock T, Sauer U, Becker PB, Imhof A, Ladurner AG. Life span extension by targeting a link between metabolism and histone acetylation in Drosophila. EMBO Rep 2016; 17:455-69. [PMID: 26781291 PMCID: PMC4772992 DOI: 10.15252/embr.201541132] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/09/2015] [Indexed: 12/16/2022] Open
Abstract
Old age is associated with a progressive decline of mitochondrial function and changes in nuclear chromatin. However, little is known about how metabolic activity and epigenetic modifications change as organisms reach their midlife. Here, we assessed how cellular metabolism and protein acetylation change during early aging in Drosophila melanogaster. Contrary to common assumptions, we find that flies increase oxygen consumption and become less sensitive to histone deacetylase inhibitors as they reach midlife. Further, midlife flies show changes in the metabolome, elevated acetyl-CoA levels, alterations in protein-notably histone-acetylation, as well as associated transcriptome changes. Based on these observations, we decreased the activity of the acetyl-CoA-synthesizing enzyme ATP citrate lyase (ATPCL) or the levels of the histone H4 K12-specific acetyltransferase Chameau. We find that these targeted interventions both alleviate the observed aging-associated changes and promote longevity. Our findings reveal a pathway that couples changes of intermediate metabolism during aging with the chromatin-mediated regulation of transcription and changes in the activity of associated enzymes that modulate organismal life span.
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Affiliation(s)
- Shahaf Peleg
- Department of Physiological Chemistry, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Christian Feller
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Ignasi Forne
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Protein Analysis Unit, Biomedical Center, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Evelyn Schiller
- Institute of Experimental Genetics, Helmholtz Zentrum Munich, German Research Center for Environment and Health (GmbH), Neuherberg, Germany
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland PhD Program on Systems Biology, Life Science Zürich, Zürich, Switzerland
| | - Tamas Schauer
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Catherine Regnard
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Tobias Straub
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Matthias Prestel
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Caroline Klima
- Department of Physiological Chemistry, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Melanie Schmitt Nogueira
- Department of Physiological Chemistry, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Lore Becker
- Institute of Experimental Genetics, Helmholtz Zentrum Munich, German Research Center for Environment and Health (GmbH), Neuherberg, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institut, Department of Neurology, Ludwig-Maximilians University, Munich, Germany DZNE - German Center for Neurodegenerative Diseases, Munich, Germany Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Protein Analysis Unit, Biomedical Center, Ludwig-Maximilians University, Planegg-Martinsried, Germany Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Andreas G Ladurner
- Department of Physiological Chemistry, Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Planegg-Martinsried, Germany Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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20
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DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1. Proc Natl Acad Sci U S A 2015; 112:E6862-71. [PMID: 26604313 DOI: 10.1073/pnas.1521365112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Sensing and responding to nutritional status is a major challenge for microbial life. In Escherichia coli, the global response to amino acid starvation is orchestrated by guanosine-3',5'-bisdiphosphate and the transcription factor DksA. DksA alters transcription by binding to RNA polymerase and allosterically modulating its activity. Using genetic analysis, photo-cross-linking, and structural modeling, we show that DksA binds and acts upon RNA polymerase through prominent features of both the nucleotide-access secondary channel and the active-site region. This work is, to our knowledge, the first demonstration of a molecular function for Sequence Insertion 1 in the β subunit of RNA polymerase and significantly advances our understanding of how DksA binds to RNA polymerase and alters transcription.
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21
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Grimm M, Zimniak T, Kahraman A, Herzog F. xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints. Nucleic Acids Res 2015; 43:W362-9. [PMID: 25956653 PMCID: PMC4489277 DOI: 10.1093/nar/gkv463] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/27/2015] [Indexed: 01/31/2023] Open
Abstract
The identification of crosslinks by mass spectrometry has recently been established as an integral part of the hybrid structural analysis of protein complexes and networks. The crosslinking analysis determines distance restraints between two covalently linked amino acids which are typically summarized in a table format that precludes the immediate and comprehensive interpretation of the topological data. xVis displays crosslinks in clear schematic representations in form of a circular, bar or network diagram. The interactive graphs indicate the linkage sites and identification scores, depict the spatial proximity of structurally and functionally annotated protein regions and the evolutionary conservation of amino acids and facilitate clustering of proteins into subcomplexes according to the crosslink density. Furthermore, xVis offers two options for the qualitative assessment of the crosslink identifications by filtering crosslinks according to identification scores or false discovery rates and by displaying the corresponding fragment ion spectrum of each crosslink for the manual validation of the mass spectrometric data. Our web server provides an easy-to-use tool for the fast topological and functional interpretation of distance information on protein complex architectures and for the evaluation of crosslink fragment ion spectra. xVis is available under a Creative Commons Attribution-ShareAlike 4.0 International license at http://xvis.genzentrum.lmu.de/.
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Affiliation(s)
- Maximilian Grimm
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Tomasz Zimniak
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Abdullah Kahraman
- Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
| | - Franz Herzog
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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22
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A presequence-binding groove in Tom70 supports import of Mdl1 into mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1850-9. [PMID: 25958336 DOI: 10.1016/j.bbamcr.2015.04.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/23/2015] [Accepted: 04/30/2015] [Indexed: 11/21/2022]
Abstract
The translocase of the outer mitochondrial membrane (TOM complex) is the general entry gate into mitochondria for almost all imported proteins. A variety of specific receptors allow the TOM complex to recognize targeting signals of various precursor proteins that are transported along different import pathways. Aside from the well-characterized presequence receptors Tom20 and Tom22 a third TOM receptor, Tom70, binds proteins of the carrier family containing multiple transmembrane segments. Here we demonstrate that Tom70 directly binds to presequence peptides using a dedicated groove. A single point mutation in the cavity of this pocket (M551R) reduces the presequence binding affinity of Tom70 ten-fold and selectively impairs import of the presequence-containing precursor Mdl1 but not the ADP/ATP carrier (AAC). Hence Tom70 contributes to the presequence import pathway by recognition of the targeting signal of the Mdl1 precursor.
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23
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Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density. Mol Cell Biol 2015; 35:1588-605. [PMID: 25733687 DOI: 10.1128/mcb.01070-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 02/14/2015] [Indexed: 12/14/2022] Open
Abstract
Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI- and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the Hand-Sant-Slide (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.
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24
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Schiller SM. Protein Tectons in Synthetic Biology. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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25
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Sinz A. The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks. Expert Rev Proteomics 2014; 11:733-43. [DOI: 10.1586/14789450.2014.960852] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Taylor AF, Amundsen SK, Guttman M, Lee KK, Luo J, Ranish J, Smith GR. Control of RecBCD enzyme activity by DNA binding- and Chi hotspot-dependent conformational changes. J Mol Biol 2014; 426:3479-99. [PMID: 25073102 DOI: 10.1016/j.jmb.2014.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/02/2014] [Accepted: 07/20/2014] [Indexed: 11/28/2022]
Abstract
Faithful repair of DNA double-strand breaks by homologous recombination is crucial to maintain functional genomes. The major Escherichia coli pathway of DNA break repair requires RecBCD enzyme, a complex protein machine with multiple activities. Upon encountering a Chi recombination hotspot (5' GCTGGTGG 3') during DNA unwinding, RecBCD's unwinding, nuclease, and RecA-loading activities change dramatically, but the physical basis for these changes is unknown. Here, we identify, during RecBCD's DNA unwinding, two Chi-stimulated conformational changes involving RecC. One produced a marked, long-lasting, Chi-dependent increase in protease sensitivity of a small patch, near the Chi recognition domain, on the solvent-exposed RecC surface. The other change was identified by crosslinking of an artificial amino acid inserted in this RecC patch to RecB. Small-angle X-ray scattering analysis confirmed a major conformational change upon binding of DNA to the enzyme and is consistent with these two changes. We propose that, upon DNA binding, the RecB nuclease domain swings from one side of RecC to the other; when RecBCD encounters Chi, the nuclease domain returns to its initial position determined by crystallography, where it nicks DNA exiting from RecC and loads RecA onto the newly generated 3'-ended single-stranded DNA during continued unwinding; a crevice between RecB and RecC increasingly narrows during these steps. This model provides a physical basis for the intramolecular "signal transduction" from Chi to RecC to RecD to RecB inferred previously from genetic and enzymatic analyses, and it accounts for the enzymatic changes that accompany Chi's stimulation of recombination.
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Affiliation(s)
- Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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27
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Liu Z, Szarecka A, Yonkunas M, Speranskiy K, Kurnikova M, Cascio M. Crosslinking constraints and computational models as complementary tools in modeling the extracellular domain of the glycine receptor. PLoS One 2014; 9:e102571. [PMID: 25025226 PMCID: PMC4099341 DOI: 10.1371/journal.pone.0102571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/20/2014] [Indexed: 01/03/2023] Open
Abstract
The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel superfamily, is the major inhibitory neurotransmitter-gated receptor in the spinal cord and brainstem. In these receptors, the extracellular domain binds agonists, antagonists and various other modulatory ligands that act allosterically to modulate receptor function. The structures of homologous receptors and binding proteins provide templates for modeling of the ligand-binding domain of GlyR, but limitations in sequence homology and structure resolution impact on modeling studies. The determination of distance constraints via chemical crosslinking studies coupled with mass spectrometry can provide additional structural information to aid in model refinement, however it is critical to be able to distinguish between intra- and inter-subunit constraints. In this report we model the structure of GlyBP, a structural and functional homolog of the extracellular domain of human homomeric α1 GlyR. We then show that intra- and intersubunit Lys-Lys crosslinks in trypsinized samples of purified monomeric and oligomeric protein bands from SDS-polyacrylamide gels may be identified and differentiated by MALDI-TOF MS studies of limited resolution. Thus, broadly available MS platforms are capable of providing distance constraints that may be utilized in characterizing large complexes that may be less amenable to NMR and crystallographic studies. Systematic studies of state-dependent chemical crosslinking and mass spectrometric identification of crosslinked sites has the potential to complement computational modeling efforts by providing constraints that can validate and refine allosteric models.
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Affiliation(s)
- Zhenyu Liu
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Agnieszka Szarecka
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, Michigan, United States of America
| | - Michael Yonkunas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kirill Speranskiy
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Maria Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Michael Cascio
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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An in vivo photo-cross-linking approach reveals a homodimerization domain of Aha1 in S. cerevisiae. PLoS One 2014; 9:e89436. [PMID: 24614167 PMCID: PMC3948627 DOI: 10.1371/journal.pone.0089436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 01/23/2014] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions play an essential role in almost any biological processes. Therefore, there is a particular need for methods which describe the interactions of a defined target protein in its physiological context. Here we report a method to photo-cross-link interacting proteins in S. cerevisiae by using the non-canonical amino acid p-azido-L-phenylalanine (pAzpa). Based on the expanded genetic code the photoreactive non-canonical amino acid pAzpa was site-specifically incorporated at eight positions into a domain of Aha1 that was previously described to bind Hsp90 in vitro to function as a cochaperone of Hsp90 and activates its ATPase activity. In vivo photo-cross-linking to the cognate binding partner of Aha1 was carried out by irradiation of mutant strains with UV light (365 nm) to induce covalent intermolecular bonds. Surprisingly, an interaction between Aha1 and Hsp90 was not detected, although, we could confirm binding of suppressed pAzpa containing Aha1 to Hsp90 by native co-immunoprecipitation. However, a homodimer consisting of two covalently crosslinked Aha1 monomers was identified by mass spectrometry. This homodimer could also be confirmed using p-benzoyl-L-phenylalanine, another photoreactive non-canonical amino acid. Crosslinking was highly specific as it was dependent on irradiation using UV light, the exact position of the non-canonical amino acid in the protein sequence as well as on the addition of the non-canonical amino acid to the growth medium. Therefore it seems possible that an interaction of Aha1 with Hsp90 takes place at different positions than previously described in vitro highlighting the importance of in vivo techniques to study protein-protein interactions. Accordingly, the expanded genetic code can easily be applied to other S. cerevisiae proteins to study their interaction under physiological relevant conditions in vivo.
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29
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Klinker H, Mueller-Planitz F, Yang R, Forné I, Liu CF, Nordenskiöld L, Becker PB. ISWI remodelling of physiological chromatin fibres acetylated at lysine 16 of histone H4. PLoS One 2014; 9:e88411. [PMID: 24516652 PMCID: PMC3916430 DOI: 10.1371/journal.pone.0088411] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/04/2014] [Indexed: 01/04/2023] Open
Abstract
ISWI is the catalytic subunit of several ATP-dependent chromatin remodelling factors that catalyse the sliding of nucleosomes along DNA and thereby endow chromatin with structural flexibility. Full activity of ISWI requires residues of a basic patch of amino acids in the N-terminal 'tail' of histone H4. Previous studies employing oligopeptides and mononucleosomes suggested that acetylation of the H4 tail at lysine 16 (H4K16) within the basic patch may inhibit the activity of ISWI. On the other hand, the acetylation of H4K16 is known to decompact chromatin fibres. Conceivably, decompaction may enhance the accessibility of nucleosomal DNA and the H4 tail for ISWI interactions. Such an effect can only be evaluated at the level of nucleosome arrays. We probed the influence of H4K16 acetylation on the ATPase and nucleosome sliding activity of Drosophila ISWI in the context of defined, in vitro reconstituted chromatin fibres with physiological nucleosome spacing and linker histone content. Contrary to widespread expectations, the acetylation did not inhibit ISWI activity, but rather stimulated ISWI remodelling under certain conditions. Therefore, the effect of H4K16 acetylation on ISWI remodelling depends on the precise nature of the substrate.
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Affiliation(s)
- Henrike Klinker
- Department of Molecular Biology, Adolf Butenandt Institut, Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Felix Mueller-Planitz
- Department of Molecular Biology, Adolf Butenandt Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ignasi Forné
- Center for Integrated Protein Science Munich, Munich, Germany
- Protein Analysis Unit, Adolf Butenandt Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peter B. Becker
- Department of Molecular Biology, Adolf Butenandt Institut, Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
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Mueller-Planitz F, Klinker H, Becker PB. Nucleosome sliding mechanisms: new twists in a looped history. Nat Struct Mol Biol 2013; 20:1026-32. [PMID: 24008565 DOI: 10.1038/nsmb.2648] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/12/2013] [Indexed: 01/11/2023]
Abstract
Nucleosomes, the basic organizational units of chromatin, package and regulate eukaryotic genomes. ATP-dependent nucleosome-remodeling factors endow chromatin with structural flexibility by promoting assembly or disruption of nucleosomes and the exchange of histone variants. Furthermore, most remodeling factors induce nucleosome movements through sliding of histone octamers on DNA. We summarize recent progress toward unraveling the basic nucleosome sliding mechanism and the interplay of the remodelers' DNA translocases with accessory domains. Such domains optimize and regulate the basic sliding reaction and exploit sliding to achieve diverse structural effects, such as nucleosome positioning or eviction, or the regular spacing of nucleosomes in chromatin.
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Affiliation(s)
- Felix Mueller-Planitz
- 1] Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität, Munich, Germany. [2] Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität, Munich, Germany
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31
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Nucleosome sliding by Chd1 does not require rigid coupling between DNA-binding and ATPase domains. EMBO Rep 2013; 14:1098-103. [PMID: 24126763 DOI: 10.1038/embor.2013.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 11/08/2022] Open
Abstract
Chromatin remodellers are ATP-dependent motor proteins that physically reposition and reorganize nucleosomes. Chd1 and Iswi-type remodellers possess a DNA-binding domain (DBD) needed for efficient nucleosome mobilization; however, it has not been clear how this domain physically contributes to remodelling. Here we show that the Chd1 DBD promotes nucleosome sliding simply by tethering the remodeller to nucleosome substrates. Nucleosome sliding activity was largely resistant to increasing length and flexibility of the linker connecting the DBD and ATPase motor, arguing that the ATPase motor does not shift DNA onto the nucleosome by pulling on the DBD.
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32
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No need for a power stroke in ISWI-mediated nucleosome sliding. EMBO Rep 2013; 14:1092-7. [PMID: 24113208 DOI: 10.1038/embor.2013.160] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/04/2013] [Accepted: 09/16/2013] [Indexed: 11/08/2022] Open
Abstract
Nucleosome remodelling enzymes of the ISWI family reposition nucleosomes in eukaryotes. ISWI contains an ATPase and a HAND-SANT-SLIDE (HSS) domain. Conformational changes between these domains have been proposed to be critical for nucleosome repositioning by pulling flanking DNA into the nucleosome. We inserted flexible linkers at strategic sites in ISWI to disrupt this putative power stroke and assess its functional importance by quantitative biochemical assays. Notably, the flexible linkers did not disrupt catalysis. Instead of engaging in a power stroke, the HSS module might therefore assist DNA to ratchet into the nucleosome. Our results clarify the roles had by the domains and suggest that the HSS domain evolved to optimize a rudimentary remodelling engine.
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33
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Leo G, Altucci C, Bourgoin-Voillard S, Gravagnuolo AM, Esposito R, Marino G, Costello CE, Velotta R, Birolo L. Ultraviolet laser-induced cross-linking in peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1660-8. [PMID: 23754800 PMCID: PMC3882510 DOI: 10.1002/rcm.6610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 05/29/2023]
Abstract
RATIONALE The aim of this study was to demonstrate, and to characterize by high-resolution mass spectrometry that it is possible to preferentially induce covalent cross-links in peptides by using high-energy femtosecond ultraviolet (UV) laser pulses. The cross-link is readily formed only when aromatic amino acids are present in the peptide sequence. METHODS Three peptides, xenopsin, angiotensin I, and interleukin, individually or in combination, were exposed to high-energy femtosecond UV laser pulses, either alone or in the presence of spin trapping molecules, the reaction products being characterized by high resolution mass spectrometry. RESULTS High-resolution mass spectrometry and spin trapping strategies showed that cross-linking occurs readily, proceeds via a radical mechanism, and is the highly dominant reaction, proceeding without causing significant photo-damage in the investigated range of experimental parameters. CONCLUSIONS High-energy femtosecond UV laser pulses can be used to induce covalent cross-links between aromatic amino acids in peptides, overcoming photo-oxidation processes, that predominate as the mean laser pulse intensity approaches illumination conditions achievable with conventional UV light sources.
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Affiliation(s)
- Gabriella Leo
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Sandrine Bourgoin-Voillard
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Alfredo M. Gravagnuolo
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Rosario Esposito
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Gennaro Marino
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Raffaele Velotta
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Leila Birolo
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
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34
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Schwarz R, Tänzler D, Ihling CH, Müller MQ, Kölbel K, Sinz A. Monitoring conformational changes in peroxisome proliferator-activated receptor α by a genetically encoded photoamino acid, cross-linking, and mass spectrometry. J Med Chem 2013; 56:4252-63. [PMID: 23639233 DOI: 10.1021/jm400446b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical cross-linking combined with an enzymatic digestion and mass spectrometric analysis of the reaction products has evolved into an alternative strategy to structurally resolve protein complexes. We investigated conformational changes in peroxisome proliferator-activated receptor α (PPARα) upon ligand binding. Using E. coli cells with a special tRNA/aminoacyl-tRNA synthetase pair, two PPARα variants were prepared in which Leu-258 or Phe-273 were site-specifically replaced by the genetically encoded photoreactive amino acid p-benzoylphenylalanine (Bpa). PPARα variants were subjected to UV-induced cross-linking, both in the absence and in the presence of ligands. After the photo-cross-linking reaction, reaction mixtures were enzymatically digested and peptides were analyzed by mass spectrometry. The inter-residue distances disclosed by the photochemical cross-links served to monitor conformational changes in PPARα upon agonist and antagonist binding. The data obtained with our strategy emphasize the potential of genetically encoded internal photo-cross-linkers in combination with mass spectrometry as an alternative method to monitor in-solution 3D-protein structures.
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Affiliation(s)
- Rico Schwarz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
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35
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Xu J, Tack D, Hughes RA, Ellington AD, Gray JJ. Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex. J Struct Biol 2013; 185:215-22. [PMID: 23680795 DOI: 10.1016/j.jsb.2013.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/04/2013] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
Abstract
Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody-antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes.
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Affiliation(s)
- Jianqing Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Drew Tack
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Randall A Hughes
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78758, USA
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78758, USA.
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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The myosin chaperone UNC-45 is organized in tandem modules to support myofilament formation in C. elegans. Cell 2013; 152:183-95. [PMID: 23332754 PMCID: PMC3549490 DOI: 10.1016/j.cell.2012.12.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/01/2012] [Accepted: 12/11/2012] [Indexed: 01/16/2023]
Abstract
The UCS (UNC-45/CRO1/She4) chaperones play an evolutionarily conserved role in promoting myosin-dependent processes, including cytokinesis, endocytosis, RNA transport, and muscle development. To investigate the protein machinery orchestrating myosin folding and assembly, we performed a comprehensive analysis of Caenorhabditis elegans UNC-45. Our structural and biochemical data demonstrate that UNC-45 forms linear protein chains that offer multiple binding sites for cooperating chaperones and client proteins. Accordingly, Hsp70 and Hsp90, which bind to the TPR domain of UNC-45, could act in concert and with defined periodicity on captured myosin molecules. In vivo analyses reveal the elongated canyon of the UCS domain as a myosin-binding site and show that multimeric UNC-45 chains support organization of sarcomeric repeats. In fact, expression of transgenes blocking UNC-45 chain formation induces dominant-negative defects in the sarcomere structure and function of wild-type worms. Together, these findings uncover a filament assembly factor that directly couples myosin folding with myofilament formation.
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37
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Paramelle D, Miralles G, Subra G, Martinez J. Chemical cross-linkers for protein structure studies by mass spectrometry. Proteomics 2013; 13:438-56. [PMID: 23255214 DOI: 10.1002/pmic.201200305] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 12/24/2022]
Abstract
The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies.
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Affiliation(s)
- David Paramelle
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, Singapore
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38
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Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A 2013; 110:3339-44. [PMID: 23341599 DOI: 10.1073/pnas.1217632110] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is constituted by a complex molecular network that integrates a number of regulatory cues needed to maintain organismal homeostasis. To this effect, posttranslational modifications of clock proteins modulate circadian rhythms and are thought to convert physiological signals into changes in protein regulatory function. To explore reversible lysine acetylation that is dependent on the clock, we have characterized the circadian acetylome in WT and Clock-deficient (Clock(-/-)) mouse liver by quantitative mass spectrometry. Our analysis revealed that a number of mitochondrial proteins involved in metabolic pathways are heavily influenced by clock-driven acetylation. Pathways such as glycolysis/gluconeogenesis, citric acid cycle, amino acid metabolism, and fatty acid metabolism were found to be highly enriched hits. The significant number of metabolic pathways whose protein acetylation profile is altered in Clock(-/-) mice prompted us to link the acetylome to the circadian metabolome previously characterized in our laboratory. Changes in enzyme acetylation over the circadian cycle and the link to metabolite levels are discussed, revealing biological implications connecting the circadian clock to cellular metabolic state.
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39
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Mueller-Planitz F, Klinker H, Ludwigsen J, Becker PB. The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nat Struct Mol Biol 2012. [PMID: 23202585 DOI: 10.1038/nsmb.2457] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
ISWI slides nucleosomes along DNA, enabling the structural changes of chromatin required for the regulated use of eukaryotic genomes. Prominent mechanistic models imply cooperation of the ISWI ATPase domain with a C-terminal DNA-binding function residing in the HAND-SANT-SLIDE (HSS) domain. Contrary to these models, we show by quantitative biochemical means that all fundamental aspects of nucleosome remodeling are contained within the compact ATPase module of Drosophila ISWI. This domain can independently associate with DNA and nucleosomes, which in turn activate ATP turnover by inducing a conformational change in the enzyme, and it can autonomously reposition nucleosomes. The role of the HSS domain is to increase the affinity and specificity for nucleosomes. Nucleosome-remodeling enzymes may thus have evolved directly from ancestral helicase-type motors, and peripheral domains have furnished regulatory capabilities that bias the remodeling reaction toward different structural outcomes.
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40
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Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 2012; 492:280-4. [PMID: 23143334 PMCID: PMC3631562 DOI: 10.1038/nature11625] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 09/27/2012] [Indexed: 12/25/2022]
Abstract
Chromatin remodeling complexes (CRCs) mobilize nucleosomes to mediate the access of DNA-binding factors to their sites in vivo. These CRCs contain a catalytic subunit that bears an ATPase/DNA translocase domain, and flanking regions that bind nucleosomal epitopes1. A central question is whether and how these flanking regions regulate ATP hydrolysis or the coupling of hydrolysis to DNA translocation, to affect nucleosome sliding efficiency. ISWIfamily CRCs contain ISWI2, which utilizes its ATPase/DNA translocase domain to pump DNA around the histone octamer to enable sliding3-7_ENREF_13. ISWI is positively regulated by two ‘activating’ nucleosomal epitopes: the ‘basic patch’ on the H4 tail, and extranucleosomal (linker) DNA8-13. Previous work defined the HSS domain in the ISWI C-terminus that binds linker DNA, needed for ISWI activity14,15. Here, we define two new, conserved, and separate regulatory regions on Drosophila ISWI, AutoN and NegC, that negatively regulate ATP hydrolysis (AutoN) or the coupling of ATP hydrolysis to productive DNA translocation (NegC). Rather than ‘activating’, the two aforementioned nucleosomal epitopes actually inhibit the negative regulation of AutoN and NegC. Remarkably, mutation/removal of AutoN and NegC enables significant nucleosome sliding without the H4 ‘basic patch’ or extranucleosomal DNA, or the HSS domain – converting ISWI to biochemical attributes of SWI/SNF-family ATPases. Thus, the ISWI ATPase catalytic core is an intrinsically-active DNA translocase which conducts nucleosome sliding, onto which selective ‘inhibition-of-inhibition’ modules are placed, to help ensure that remodeling occurs only in the presence of proper nucleosomal epitopes. This supports a general concept for the specialization of chromatin remodeling ATPases, where specific regulatory modules adapt an ancient active DNA translocase to conduct particular tasks only on the appropriate chromatin landscape.
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Schreiner B, Westerburg H, Forné I, Imhof A, Neupert W, Mokranjac D. Role of the AAA protease Yme1 in folding of proteins in the intermembrane space of mitochondria. Mol Biol Cell 2012; 23:4335-46. [PMID: 22993211 PMCID: PMC3496608 DOI: 10.1091/mbc.e12-05-0420] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We show here that the i-AAA protease Yme1 has a role in folding of proteins in the intermembrane space of mitochondria and identify a number of endogenous proteins that aggregate in its absence. Thus the function of Yme1 in mitochondrial proteostasis extends beyond its role in proteolytic removal of misfolded and nonassembled inner membrane proteins. The vast majority of mitochondrial proteins are synthesized in the cytosol and transported into the organelle in a largely, if not completely, unfolded state. The proper function of mitochondria thus depends on folding of several hundreds of proteins in the various subcompartments of the organelle. Whereas folding of proteins in the mitochondrial matrix is supported by members of several chaperone families, very little is known about folding of proteins in the intermembrane space (IMS). We targeted dihydrofolate reductase (DHFR) as a model substrate to the IMS of yeast mitochondria and analyzed its folding. DHFR can fold in this compartment, and its aggregation upon heat shock can be prevented in an ATP-dependent manner. Yme1, an AAA (ATPases associated with diverse cellular activities) protease of the IMS, prevented aggregation of DHFR. Analysis of protein aggregates in mitochondria lacking Yme1 revealed the presence of a number of proteins involved in the establishment of mitochondrial ultrastructure, lipid metabolism, protein import, and respiratory growth. These findings explain the pleiotropic effects of deletion of YME1 and suggest an important role for Yme1 as a folding assistant, in addition to its proteolytic function, in the protein homeostasis of mitochondria
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Affiliation(s)
- Bernadette Schreiner
- Adolf Butenandt Institute, Physiological Chemistry, University of Munich, 81377 Munich, Germany
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