151
|
Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
Collapse
Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
| |
Collapse
|
152
|
Xue Y, Van C, Pradhan SK, Su T, Gehrke J, Kuryan BG, Kitada T, Vashisht A, Tran N, Wohlschlegel J, Peterson CL, Kurdistani SK, Carey MF. The Ino80 complex prevents invasion of euchromatin into silent chromatin. Genes Dev 2015; 29:350-5. [PMID: 25691465 PMCID: PMC4335291 DOI: 10.1101/gad.256255.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here we show that the Ino80 chromatin remodeling complex (Ino80C) directly prevents euchromatin from invading transcriptionally silent chromatin within intergenic regions and at the border of euchromatin and heterochromatin. Deletion of Ino80C subunits leads to increased H3K79 methylation and noncoding RNA polymerase II (Pol II) transcription centered at the Ino80C-binding sites. The effect of Ino80C is direct, as it blocks H3K79 methylation by Dot1 in vitro. Heterochromatin stimulates the binding of Ino80C in vitro and in vivo. Our data reveal that Ino80C serves as a general silencing complex that restricts transcription to gene units in euchromatin.
Collapse
Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Jason Gehrke
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Benjamin G Kuryan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Tasuku Kitada
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA;
| |
Collapse
|
153
|
Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M. Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures. J Struct Biol 2015; 189:177-83. [PMID: 25661704 PMCID: PMC4359615 DOI: 10.1016/j.jsb.2015.01.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 12/25/2022]
Abstract
Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html.
Collapse
Affiliation(s)
- Jan Kosinski
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alexander von Appen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Kai Karius
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| |
Collapse
|
154
|
Lakomek K, Stoehr G, Tosi A, Schmailzl M, Hopfner KP. Structural basis for dodecameric assembly states and conformational plasticity of the full-length AAA+ ATPases Rvb1 · Rvb2. Structure 2015; 23:483-495. [PMID: 25661652 DOI: 10.1016/j.str.2014.12.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/14/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
As building blocks of diverse macromolecular complexes, the AAA+ ATPases Rvb1 and Rvb2 are crucial for many cellular activities including cancer-related processes. Their oligomeric structure and function remain unclear. We report the crystal structures of full-length heteromeric Rvb1·Rvb2 complexes in distinct nucleotide binding states. Chaetomium thermophilum Rvb1·Rvb2 assemble into hexameric rings of alternating molecules and into stable dodecamers. Intriguingly, the characteristic oligonucleotide-binding (OB) fold domains (DIIs) of Rvb1 and Rvb2 occupy unequal places relative to the compact AAA+ core ring. While Rvb1's DII forms contacts between hexamers, Rvb2's DII is rotated 100° outward, occupying lateral positions. ATP was retained bound to Rvb1 but not Rvb2 throughout purification, suggesting nonconcerted ATPase activities and nucleotide binding. Significant conformational differences between nucleotide-free and ATP-/ADP-bound states in the crystal structures and in solution suggest that the functional role of Rvb1·Rvb2 is mediated by highly interconnected structural switches. Our structures provide an atomic framework for dodecameric states and Rvb1·Rvb2's conformational plasticity.
Collapse
Affiliation(s)
- Kristina Lakomek
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Gabriele Stoehr
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Alessandro Tosi
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Monika Schmailzl
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University Munich, 81377 Munich, Germany; Center for Integrated Protein Sciences, Ludwig-Maximilians University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
| |
Collapse
|
155
|
Gerhold CB, Hauer MH, Gasser SM. INO80-C and SWR-C: Guardians of the Genome. J Mol Biol 2015; 427:637-51. [DOI: 10.1016/j.jmb.2014.10.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 01/01/2023]
|
156
|
Jeganathan A, Leong V, Zhao L, Huen J, Nano N, Houry WA, Ortega J. Yeast rvb1 and rvb2 proteins oligomerize as a conformationally variable dodecamer with low frequency. J Mol Biol 2015; 427:1875-86. [PMID: 25636407 DOI: 10.1016/j.jmb.2015.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/16/2014] [Accepted: 01/16/2015] [Indexed: 01/10/2023]
Abstract
Rvb1 and Rvb2 are conserved AAA+ (ATPases associated with diverse cellular activities) proteins found at the core of large multicomponent complexes that play key roles in chromatin remodeling, integrity of the telomeres, ribonucleoprotein complex biogenesis and other essential cellular processes. These proteins contain an AAA+ domain for ATP binding and hydrolysis and an insertion domain proposed to bind DNA/RNA. Yeast Rvb1 and Rvb2 proteins oligomerize primarily as heterohexameric rings. The six AAA+ core domains form the body of the ring and the insertion domains protrude from one face of the ring. Conversely, human Rvbs form a mixture of hexamers and dodecamers made of two stacked hexamers interacting through the insertion domains. Human dodecamers adopt either a contracted or a stretched conformation. Here, we found that yeast Rvb1/Rvb2 complexes when assembled in vivo mainly form hexamers but they also assemble as dodecamers with a frequency lower than 10%. Yeast dodecamers adopt not only the stretched and contracted structures that have been described for human Rvb1/Rvb2 dodecamers but also intermediate conformations in between these two extreme states. The orientation of the insertion domains of Rvb1 and Rvb2 proteins in these conformers changes as the dodecamer transitions from the stretched structure to a more contracted structure. Finally, we observed that for the yeast proteins, oligomerization as a dodecamer inhibits the ATPase activity of the Rvb1/Rvb2 complex. These results indicate that although human and yeast Rvb1 and Rvb2 proteins share high degree of homology, there are significant differences in their oligomeric behavior and dynamics.
Collapse
Affiliation(s)
- Ajitha Jeganathan
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Vivian Leong
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Liang Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Nardin Nano
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1.
| |
Collapse
|
157
|
Rivera-Calzada A, López-Perrote A, Melero R, Boskovic J, Muñoz-Hernández H, Martino F, Llorca O. Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.2.36] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
158
|
Affiliation(s)
- Robert K McGinty
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
159
|
Bizarro J, Charron C, Boulon S, Westman B, Pradet-Balade B, Vandermoere F, Chagot ME, Hallais M, Ahmad Y, Leonhardt H, Lamond A, Manival X, Branlant C, Charpentier B, Verheggen C, Bertrand E. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. ACTA ACUST UNITED AC 2014; 207:463-80. [PMID: 25404746 PMCID: PMC4242836 DOI: 10.1083/jcb.201404160] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
During small nucleolar ribonucleoprotein complex assembly, a pre-snoRNP complex consisting only of protein components forms first, followed by displacement of the ZNHIT3 subunit when C/D snoRNAs bind and dynamic loading and unloading of RuvBL AAA+ ATPases. In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90–R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA+ adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs.
Collapse
Affiliation(s)
- Jonathan Bizarro
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Christophe Charron
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Séverine Boulon
- Centre de Recherches de Biochimie Macromoléculaire, Unité Mixte de Recherche 5237, 34293 Montpellier, Cedex 5, France
| | - Belinda Westman
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Bérengère Pradet-Balade
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Franck Vandermoere
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 5203, Institut de Génomique Fonctionnelle, F-34000 Montpellier, France Institut National de la Santé et de la Recherche Médicale, U661, F-34000 Montpellier, France Unité Mixte de Recherche 5203, Université de Montpellier 1 and Université de Montpellier 2, F-34000 Montpellier, France
| | - Marie-Eve Chagot
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Marie Hallais
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Yasmeen Ahmad
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Heinrich Leonhardt
- Munich Center for Integrated Protein Science (CiPS) and Department of Biology, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany Munich Center for Integrated Protein Science (CiPS) and Department of Biology, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Angus Lamond
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Céline Verheggen
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| | - Edouard Bertrand
- Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France
| |
Collapse
|
160
|
Magalska A, Schellhaus A, Moreno-Andrés D, Zanini F, Schooley A, Sachdev R, Schwarz H, Madlung J, Antonin W. RuvB-like ATPases Function in Chromatin Decondensation at the End of Mitosis. Dev Cell 2014; 31:305-318. [DOI: 10.1016/j.devcel.2014.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/22/2014] [Accepted: 09/03/2014] [Indexed: 10/24/2022]
|
161
|
|
162
|
Queval R, Papin C, Dalvai M, Bystricky K, Humbert O. Reptin and Pontin oligomerization and activity are modulated through histone H3 N-terminal tail interaction. J Biol Chem 2014; 289:33999-4012. [PMID: 25336637 DOI: 10.1074/jbc.m114.576785] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pontin/RUVBL1 and Reptin/RUVBL2 are DNA-dependent ATPases involved in numerous cellular processes and are essential components of chromatin remodeling complexes and transcription factor assemblies. However, their existence as monomeric and oligomeric forms with differential activity in vivo reflects their versatility. Using a biochemical approach, we have studied the role of the nucleosome core particle and histone N-terminal tail modifications in the assembly and enzymatic activities of Reptin/Pontin. We demonstrate that purified Reptin and Pontin form stable complexes with nucleosomes. The ATPase activity of Reptin/Pontin is modulated by acetylation and methylation of the histone H3 N terminus. In vivo, association of Reptin with the progesterone receptor gene promoter is concomitant with changes in H3 marks of the surrounding nucleosomes. Furthermore, the presence of H3 tail peptides regulates the monomer-oligomer transition of Reptin/Pontin. Proteins that are pulled down by monomeric Reptin/Pontin differ from those that can bind to hexamers. We propose that changes in the oligomeric status of Reptin/Pontin create a platform that brings specific cofactors close to gene promoters and loads regulatory factors to establish an active state of chromatin.
Collapse
Affiliation(s)
- Richard Queval
- From the Laboratoire de Biologie Moléculaire Eucaryote, CNRS/UMR 5099, F-31062 Toulouse Cedex, the Université de Toulouse, UPS, 31062 Toulouse Cedex, and
| | - Christophe Papin
- the Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Mathieu Dalvai
- From the Laboratoire de Biologie Moléculaire Eucaryote, CNRS/UMR 5099, F-31062 Toulouse Cedex, the Université de Toulouse, UPS, 31062 Toulouse Cedex, and
| | - Kerstin Bystricky
- From the Laboratoire de Biologie Moléculaire Eucaryote, CNRS/UMR 5099, F-31062 Toulouse Cedex, the Université de Toulouse, UPS, 31062 Toulouse Cedex, and
| | - Odile Humbert
- From the Laboratoire de Biologie Moléculaire Eucaryote, CNRS/UMR 5099, F-31062 Toulouse Cedex, the Université de Toulouse, UPS, 31062 Toulouse Cedex, and
| |
Collapse
|
163
|
Osakabe A, Takahashi Y, Murakami H, Otawa K, Tachiwana H, Oma Y, Nishijima H, Shibahara KI, Kurumizaka H, Harata M. DNA binding properties of the actin-related protein Arp8 and its role in DNA repair. PLoS One 2014; 9:e108354. [PMID: 25299602 PMCID: PMC4191963 DOI: 10.1371/journal.pone.0108354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/26/2014] [Indexed: 12/05/2022] Open
Abstract
Actin and actin-related proteins (Arps), which are members of the actin family, are essential components of many of these remodeling complexes. Actin, Arp4, Arp5, and Arp8 are found to be evolutionarily conserved components of the INO80 chromatin remodeling complex, which is involved in transcriptional regulation, DNA replication, and DNA repair. A recent report showed that Arp8 forms a module in the INO80 complex and this module can directly capture a nucleosome. In the present study, we showed that recombinant human Arp8 binds to DNAs, and preferentially binds to single-stranded DNA. Analysis of the binding of adenine nucleotides to Arp8 mutants suggested that the ATP-binding pocket, located in the evolutionarily conserved actin fold, plays a regulatory role in the binding of Arp8 to DNA. To determine the cellular function of Arp8, we derived tetracycline-inducible Arp8 knockout cells from a cultured human cell line. Analysis of results obtained after treating these cells with aphidicolin and camptothecin revealed that Arp8 is involved in DNA repair. Together with the previous observation that Arp8, but not γ-H2AX, is indispensable for recruiting INO80 complex to DSB in human, results of our study suggest an individual role for Arp8 in DNA repair.
Collapse
Affiliation(s)
- Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yuichiro Takahashi
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hirokazu Murakami
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Kenji Otawa
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yukako Oma
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hitoshi Nishijima
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Kei-ich Shibahara
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- * E-mail: (HK); (MH)
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- * E-mail: (HK); (MH)
| |
Collapse
|
164
|
Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in integrative structural modeling. Curr Opin Struct Biol 2014; 28:96-104. [PMID: 25173450 PMCID: PMC4252396 DOI: 10.1016/j.sbi.2014.08.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/24/2014] [Accepted: 08/05/2014] [Indexed: 01/08/2023]
Abstract
Integrative structural modeling uses multiple types of input information and proceeds in four stages: (i) gathering information, (ii) designing model representation and converting information into a scoring function, (iii) sampling good-scoring models, and (iv) analyzing models and information. In the first stage, uncertainty originates from data that are sparse, noisy, ambiguous, or derived from heterogeneous samples. In the second stage, uncertainty can originate from a representation that is too coarse for the available information or a scoring function that does not accurately capture the information. In the third stage, the major source of uncertainty is insufficient sampling. In the fourth stage, clustering, cross-validation, and other methods are used to estimate the precision and accuracy of the models and information.
Collapse
Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA.
| |
Collapse
|
165
|
A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
Collapse
|
166
|
Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics 2014; 13:2927-43. [PMID: 25161197 DOI: 10.1074/mcp.m114.041673] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope.
Collapse
Affiliation(s)
- Yi Shi
- From the ‡Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Javier Fernandez-Martinez
- ¶Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
| | - Elina Tjioe
- ‖Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
| | - Riccardo Pellarin
- ‖Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
| | - Seung Joong Kim
- ‖Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
| | - Rosemary Williams
- ¶Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
| | - Dina Schneidman-Duhovny
- ‖Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
| | - Andrej Sali
- ‖Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158
| | - Michael P Rout
- ¶Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065;
| | - Brian T Chait
- From the ‡Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065;
| |
Collapse
|
167
|
Klinker H, Haas C, Harrer N, Becker PB, Mueller-Planitz F. Rapid purification of recombinant histones. PLoS One 2014; 9:e104029. [PMID: 25090252 PMCID: PMC4121265 DOI: 10.1371/journal.pone.0104029] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/07/2014] [Indexed: 11/25/2022] Open
Abstract
The development of methods to assemble nucleosomes from recombinant histones decades ago has transformed chromatin research. Nevertheless, nucleosome reconstitution remains time consuming to this day, not least because the four individual histones must be purified first. Here, we present a streamlined purification protocol of recombinant histones from bacteria. We termed this method “rapid histone purification” (RHP) as it circumvents isolation of inclusion bodies and thereby cuts out the most time-consuming step of traditional purification protocols. Instead of inclusion body isolation, whole cell extracts are prepared under strongly denaturing conditions that directly solubilize inclusion bodies. By ion exchange chromatography, the histones are purified from the extracts. The protocol has been successfully applied to all four canonical Drosophila and human histones. RHP histones and histones that were purified from isolated inclusion bodies had similar purities. The different purification strategies also did not impact the quality of octamers reconstituted from these histones. We expect that the RHP protocol can be readily applied to the purification of canonical histones from other species as well as the numerous histone variants.
Collapse
Affiliation(s)
- Henrike Klinker
- Molecular Biology Unit, Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Germany
| | - Caroline Haas
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nadine Harrer
- Molecular Biology Unit, Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Peter B. Becker
- Molecular Biology Unit, Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Germany
| | - Felix Mueller-Planitz
- Molecular Biology Unit, Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
| |
Collapse
|
168
|
A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database. J Proteomics 2014; 108:65-77. [DOI: 10.1016/j.jprot.2014.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/23/2014] [Accepted: 05/08/2014] [Indexed: 11/23/2022]
|
169
|
Gerhold CB, Gasser SM. INO80 and SWR complexes: relating structure to function in chromatin remodeling. Trends Cell Biol 2014; 24:619-31. [PMID: 25088669 DOI: 10.1016/j.tcb.2014.06.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 02/04/2023]
Abstract
Virtually all DNA-dependent processes require selective and controlled access to the DNA sequence. Governing this access are sophisticated molecular machines, nucleosome remodelers, which regulate the composition and structure of chromatin, allowing conversion from open to closed states. In most cases these multisubunit remodelers operate in concert to organize chromatin structure by depositing, moving, evicting, or selectively altering nucleosomes in an ATP-dependent manner. Despite sharing a conserved domain architecture, chromatin remodelers differ significantly in how they bind to their nucleosomal substrates. Recent structural studies link specific interactions between nucleosomes and remodelers to the diverse tasks they carry out. We review here insights into the modular organization of the INO80 family of nucleosome remodelers. Understanding their structural diversity will help to shed light on how these related ATPases modify their nucleosomal substrates.
Collapse
Affiliation(s)
- Christian B Gerhold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
170
|
Vassileva I, Yanakieva I, Peycheva M, Gospodinov A, Anachkova B. The mammalian INO80 chromatin remodeling complex is required for replication stress recovery. Nucleic Acids Res 2014; 42:9074-86. [PMID: 25016522 PMCID: PMC4132725 DOI: 10.1093/nar/gku605] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A number of studies have implicated the yeast INO80 chromatin remodeling complex in DNA replication, but the function of the human INO80 complex during S phase remains poorly understood. Here, we have systematically investigated the involvement of the catalytic subunit of the human INO80 complex during unchallenged replication and under replication stress by following the effects of its depletion on cell survival, S-phase checkpoint activation, the fate of individual replication forks, and the consequences of fork collapse. We report that INO80 was specifically needed for efficient replication elongation, while it was not required for initiation of replication. In the absence of the Ino80 protein, cells became hypersensitive to hydroxyurea and displayed hyperactive ATR-Chk1 signaling. Using bulk and fiber labeling of DNA, we found that cells deficient for Ino80 and Arp8 had impaired replication restart after treatment with replication inhibitors and accumulated double-strand breaks as evidenced by the formation of γ-H2AX and Rad51 foci. These data indicate that under conditions of replication stress mammalian INO80 protects stalled forks from collapsing and allows their subsequent restart.
Collapse
Affiliation(s)
- Ivelina Vassileva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Iskra Yanakieva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Michaela Peycheva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Anastas Gospodinov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Boyka Anachkova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| |
Collapse
|
171
|
Villa E, Lasker K. Finding the right fit: chiseling structures out of cryo-electron microscopy maps. Curr Opin Struct Biol 2014; 25:118-25. [PMID: 24814094 DOI: 10.1016/j.sbi.2014.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 11/19/2022]
Abstract
Cryo-electron microscopy is a central tool for studying the architecture of macromolecular complexes at subnanometer resolution. Interpretation of an electron microscopy map requires its computational integration with data about the structure's components from all available sources, notably atomic models. Selecting a protocol for EM density-guided integrative structural modeling depends on the resolution and quality of the EM map as well as the available complimentary datasets. Here, we review rigid, flexible, and de novo integrative fitting into EM maps and provide guidelines and considerations for the design of modeling experiments. Finally, we discuss efforts towards establishing unified criteria for map and model assessment and validation.
Collapse
Affiliation(s)
- Elizabeth Villa
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States.
| | - Keren Lasker
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, United States.
| |
Collapse
|
172
|
Flemming D, Stelter P, Hurt E. Utilizing the Dyn2 dimerization-zipper as a tool to probe NPC structure and function. Methods Cell Biol 2014; 122:99-115. [PMID: 24857727 DOI: 10.1016/b978-0-12-417160-2.00005-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The discovery of dynein light chain 2 (Dyn2) as a member of the nucleoporins in yeast led to a series of applications to study NPC structure and function. Its intriguing ability to act as a hub for the parallel dimerization of two short amino acid sequence motifs (DID) prompted us to utilize it as a tool for probing nucleocytoplasmic transport in vivo. Further, the distinct structure of the Dyn2-DID rod, which is easily visible in the electron microscope, allowed us to develop a precise structural label on proteins or protein complexes. This label was used to identify the position of subunits in NPC subcomplexes or to derive at pseudo-atomic models of single large Nups. The versatility for various applications of the DID-Dyn2 system makes it an attractive molecular tool beyond the nuclear pore and transport field.
Collapse
Affiliation(s)
- Dirk Flemming
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Philipp Stelter
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld, Heidelberg, Germany
| |
Collapse
|
173
|
Abstract
Currently, there is no method to distinguish between the roles of a subunit in one multisubunit protein complex from its roles in other complexes in vivo. This is because a mutation in a common subunit will affect all complexes containing that subunit. Here, we describe a unique method to discriminate between the functions of a common subunit in different multisubunit protein complexes. In this method, a common subunit in a multisubunit protein complex is genetically fused to a subunit that is specific to that complex and point mutated. The resulting phenotype(s) identify the specific function(s) of the subunit in that complex only. Histone H2B is a common subunit in nucleosomes containing H2A/H2B or Htz1/H2B dimers. The H2B was fused to H2A or Htz1 and point mutated. This strategy revealed that H2B has common and distinct functions in different nucleosomes. This method could be used to study common subunits in other multisubunit protein complexes.
Collapse
|
174
|
Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat Protoc 2013; 9:120-37. [DOI: 10.1038/nprot.2013.168] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
175
|
Trnka MJ, Baker PR, Robinson PJJ, Burlingame AL, Chalkley RJ. Matching cross-linked peptide spectra: only as good as the worse identification. Mol Cell Proteomics 2013; 13:420-34. [PMID: 24335475 DOI: 10.1074/mcp.m113.034009] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chemical cross-linking mass spectrometry identifies interacting surfaces within a protein assembly through labeling with bifunctional reagents and identifying the covalently modified peptides. These yield distance constraints that provide a powerful means to model the three-dimensional structure of the assembly. Bioinformatic analysis of cross-linked data resulting from large protein assemblies is challenging because each cross-linked product contains two covalently linked peptides, each of which must be correctly identified from a complex matrix of potential confounders. Protein Prospector addresses these issues through a complementary mass modification strategy in which each peptide is searched and identified separately. We demonstrate this strategy with an analysis of RNA polymerase II. False discovery rates (FDRs) are assessed via comparison of cross-linking data to crystal structure, as well as by using a decoy database strategy. Parameters that are most useful for positive identification of cross-linked spectra are explored. We find that fragmentation spectra generally contain more product ions from one of the two peptides constituting the cross-link. Hence, metrics reflecting the quality of the spectral match to the less confident peptide provide the most discriminatory power between correct and incorrect matches. A support vector machine model was built to further improve classification of cross-linked peptide hits. Furthermore, the frequency with which peptides cross-linked via common acylating reagents fragment to produce diagnostic, cross-linker-specific ions is assessed. The threshold for successful identification of the cross-linked peptide product depends upon the complexity of the sample under investigation. Protein Prospector, by focusing the reliability assessment on the least confident peptide, is better able to control the FDR for results as larger complexes and databases are analyzed. In addition, when FDR thresholds are calculated separately for intraprotein and interprotein results, a further improvement in the number of unique cross-links confidently identified is achieved. These improvements are demonstrated on two previously published cross-linking datasets.
Collapse
Affiliation(s)
- Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158
| | | | | | | | | |
Collapse
|
176
|
Kapoor P, Shen X. Mechanisms of nuclear actin in chromatin-remodeling complexes. Trends Cell Biol 2013; 24:238-46. [PMID: 24246764 DOI: 10.1016/j.tcb.2013.10.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 10/04/2013] [Accepted: 10/22/2013] [Indexed: 10/26/2022]
Abstract
The mystery of nuclear actin has puzzled biologists for decades largely due to the lack of defined experimental systems. However, the development of actin-containing chromatin-modifying complexes as a defined genetic and biochemical system in the past decade has provided an unprecedented opportunity to dissect the mechanism of actin in the nucleus. Although the established functions of actin mostly rely on its dynamic polymerization, the novel finding of the mechanism of action of actin in the INO80 chromatin-remodeling complex suggests a conceptually distinct mode of actin that functions as a monomer. In this review we highlight the new paradigm and discuss how actin interaction with chromatin suggests a fundamental divergence between conventional cytoplasmic actin and nuclear actin. Furthermore, we provide how this framework could be applied to investigations of nuclear actin in other actin-containing chromatin-modifying complexes.
Collapse
Affiliation(s)
- Prabodh Kapoor
- Department of Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Xuetong Shen
- Department of Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA.
| |
Collapse
|