1
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Li S, Kasciukovic T, Tanaka TU. Kinetochore-microtubule error correction for biorientation: lessons from yeast. Biochem Soc Trans 2024; 52:29-39. [PMID: 38305688 PMCID: PMC10903472 DOI: 10.1042/bst20221261] [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: 11/23/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
Accurate chromosome segregation in mitosis relies on sister kinetochores forming stable attachments to microtubules (MTs) extending from opposite spindle poles and establishing biorientation. To achieve this, erroneous kinetochore-MT interactions must be resolved through a process called error correction, which dissolves improper kinetochore-MT attachment and allows new interactions until biorientation is achieved. The Aurora B kinase plays key roles in driving error correction by phosphorylating Dam1 and Ndc80 complexes, while Mps1 kinase, Stu2 MT polymerase and phosphatases also regulate this process. Once biorientation is formed, tension is applied to kinetochore-MT interaction, stabilizing it. In this review article, we discuss the mechanisms of kinetochore-MT interaction, error correction and biorientation. We focus mainly on recent insights from budding yeast, where the attachment of a single MT to a single kinetochore during biorientation simplifies the analysis of error correction mechanisms.
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Affiliation(s)
- Shuyu Li
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Taciana Kasciukovic
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Tomoyuki U. Tanaka
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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2
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Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D. Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Science 2023; 382:1184-1190. [PMID: 38060647 PMCID: PMC7615550 DOI: 10.1126/science.adj8736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
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Affiliation(s)
- Kyle W. Muir
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher Batters
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Tom Dendooven
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alister Burt
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
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3
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Sankaranarayanan SR, Polisetty SD, Das K, Dumbrepatil A, Medina-Pritchard B, Singleton M, Jeyaprakash AA, Sanyal K. Functional plasticity in chromosome-microtubule coupling on the evolutionary time scale. Life Sci Alliance 2023; 6:e202201720. [PMID: 37793775 PMCID: PMC10551642 DOI: 10.26508/lsa.202201720] [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: 09/12/2022] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
The Dam1 complex is essential for mitotic progression across evolutionarily divergent fungi. Upon analyzing amino acid (aa) sequences of Dad2, a Dam1 complex subunit, we identified a conserved 10-aa-long Dad2 signature sequence (DSS). An arginine residue (R126) in the DSS is essential for viability in Saccharomyces cerevisiae that possesses point centromeres. The corresponding arginine residues are functionally important but not essential for viability in Candida albicans and Cryptococcus neoformans; both carry several kilobases long regional centromeres. The purified recombinant Dam1 complex containing either Dad2ΔDSS or Dad2R126A failed to bind microtubules (MTs) or form any visible rings like the WT complex. Intriguingly, functional analysis revealed that the requirement of the conserved arginine residue for chromosome biorientation and mitotic progression reduced with increasing centromere length. We propose that plasticity of the invariant arginine of Dad2 in organisms with regional centromeres is achieved by conditional elevation of the kinetochore protein(s) to enable multiple kinetochore MTs to bind to each chromosome. The capacity of a chromosome to bind multiple kinetochore MTs may mask the deleterious effects of such lethal mutations.
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Affiliation(s)
- Sundar Ram Sankaranarayanan
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Satya Dev Polisetty
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Kuladeep Das
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Arti Dumbrepatil
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Bethan Medina-Pritchard
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Martin Singleton
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - A Arockia Jeyaprakash
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Gene Center and Department of Biochemistry, Ludwig-Maximilian-Universität, Munich, Germany
| | - Kaustuv Sanyal
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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4
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Witus SR, Tuttle LM, Li W, Zelter A, Wang M, Kermoade KE, Wilburn DB, Davis TN, Brzovic PS, Zhao W, Klevit RE. BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation. EMBO J 2023; 42:e113565. [PMID: 37305927 PMCID: PMC10390874 DOI: 10.15252/embj.2023113565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
BRCA1/BARD1 is a tumor suppressor E3 ubiquitin (Ub) ligase with roles in DNA damage repair and in transcriptional regulation. BRCA1/BARD1 RING domains interact with nucleosomes to facilitate mono-ubiquitylation of distinct residues on the C-terminal tail of histone H2A. These enzymatic domains constitute a small fraction of the heterodimer, raising the possibility of functional chromatin interactions involving other regions such as the BARD1 C-terminal domains that bind nucleosomes containing the DNA damage signal H2A K15-Ub and H4 K20me0, or portions of the expansive intrinsically disordered regions found in both subunits. Herein, we reveal novel interactions that support robust H2A ubiquitylation activity mediated through a high-affinity, intrinsically disordered DNA-binding region of BARD1. These interactions support BRCA1/BARD1 recruitment to chromatin and sites of DNA damage in cells and contribute to their survival. We also reveal distinct BRCA1/BARD1 complexes that depend on the presence of H2A K15-Ub, including a complex where a single BARD1 subunit spans adjacent nucleosome units. Our findings identify an extensive network of multivalent BARD1-nucleosome interactions that serve as a platform for BRCA1/BARD1-associated functions on chromatin.
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Affiliation(s)
- Samuel R Witus
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Lisa M Tuttle
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Wenjing Li
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
| | - Alex Zelter
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Meiling Wang
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
| | | | - Damien B Wilburn
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOHUSA
| | - Trisha N Davis
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Peter S Brzovic
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Weixing Zhao
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
| | - Rachel E Klevit
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
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5
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Hoopmann MR, Shteynberg DD, Zelter A, Riffle M, Lyon AS, Agard DA, Luan Q, Nolen BJ, MacCoss MJ, Davis TN, Moritz RL. Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline. J Proteome Res 2023; 22:647-655. [PMID: 36629399 PMCID: PMC10234491 DOI: 10.1021/acs.jproteome.2c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between 15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of cross-links improve the sensitivity and accuracy of correct cross-link identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multiplatform.
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Affiliation(s)
| | | | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA, USA 98195
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA 98195
| | - Andrew S. Lyon
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA 94143
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA 94143
| | - Qing Luan
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA 97403
| | - Brad J. Nolen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA 97403
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA 98195
| | - Trisha N. Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA 98195
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6
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Reiter KH, Zelter A, Janowska MK, Riffle M, Shulman N, MacLean BX, Tamura K, Chambers MC, MacCoss MJ, Davis TN, Guttman M, Brzovic PS, Klevit RE. Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain. Structure 2022; 30:1269-1284.e6. [PMID: 35716664 PMCID: PMC9444911 DOI: 10.1016/j.str.2022.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/15/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022]
Abstract
RING-between-RING (RBR) E3 ligases mediate ubiquitin transfer through an obligate E3-ubiquitin thioester intermediate prior to substrate ubiquitination. Although RBRs share a conserved catalytic module, substrate recruitment mechanisms remain enigmatic, and the relevant domains have yet to be identified for any member of the class. Here we characterize the interaction between the auto-inhibited RBR, HHARI (AriH1), and its target protein, 4EHP, using a combination of XL-MS, HDX-MS, NMR, and biochemical studies. The results show that (1) a di-aromatic surface on the catalytic HHARI Rcat domain forms a binding platform for substrates and (2) a phosphomimetic mutation on the auto-inhibitory Ariadne domain of HHARI promotes release and reorientation of Rcat for transthiolation and substrate modification. The findings identify a direct binding interaction between a RING-between-RING ligase and its substrate and suggest a general model for RBR substrate recognition.
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Affiliation(s)
- Katherine H Reiter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maria K Janowska
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Shulman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kaipo Tamura
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew C Chambers
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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7
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Flores RL, Peterson ZE, Zelter A, Riffle M, Asbury CL, Davis TN. Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load. J Cell Biol 2022; 221:213102. [PMID: 35353161 DOI: 10.1083/jcb.202107016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 01/15/2023] Open
Abstract
Accurate mitosis requires kinetochores to make persistent, load-bearing attachments to dynamic microtubule tips, thereby coupling chromosome movements to tip growth and shortening. This tip-coupling behavior depends on the conserved Ndc80 complex and, in budding yeast, on the Dam1 complex, which bind each other directly via three distinct interacting regions. The functional relevance of these multiple interactions was mysterious. Here we show that interactions between two of these regions support the high rupture strengths that occur when applied force is rapidly increased and also support the stability of tip-coupling when force is held constant over longer durations. The contribution of either of these two regions to tip-coupling is reduced by phosphorylation by Aurora B kinase. The third interaction region makes no apparent contribution to rupture strength, but its phosphorylation by Aurora B kinase specifically decreases the long-term stability of tip-coupling. The specific reduction of long-term stability relative to short-term strength might have important implications for mitotic error correction.
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Affiliation(s)
- Rachel L Flores
- Department of Biochemistry, University of Washington, Seattle, WA
| | | | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA
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8
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Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 2022; 11:66975. [PMID: 35485925 PMCID: PMC9122500 DOI: 10.7554/elife.66975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Doublecortin (DCX) is a microtubule (MT)-associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX that explain these disorders are incompletely determined. Here, we describe the molecular architecture of the DCX–MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-electron microscopy, and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving the C-terminal structured domain and its disordered tail, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-terminal tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in its tail, our study shows that lattice-driven self-assembly is an important property of DCX.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, Canada
| | | | | | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Gary Brouhard
- Department of Biology, McGill University, Montreal, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
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9
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Rafiei A, Schriemer DC. A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins. Methods Mol Biol 2022; 2456:211-222. [PMID: 35612744 DOI: 10.1007/978-1-0716-2124-0_14] [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] [Indexed: 11/25/2022]
Abstract
Microtubule-associated proteins (MAPs) engage microtubules (MTs) to regulate both the MT state and wide variety of cytoskeletal functions. A comprehensive understanding of MAPs function requires the structural characterization of physical contacts MAPs make with other proteins, particularly when engaged with the microtubule (MT) lattice. Most of the interaction between MAPs and MTs evade classical structural determination techniques, as the interactions can be both heterogenous and sub-stoichiometric. Crosslinking mass spectrometry (XL-MS) can aid in MAP-MT structure analysis by providing a wealth of residue-based distance restraints. This protocol provides an XL-MS workflow for accurate and unbiased sampling of an equilibrated MAP-MT interaction, involving modifications to the preparation and validation of a MAP-MT construct suitable for crosslinking with fast-sampling heterobifunctional crosslinkers. The distance restrains obtained by this protocol can be used to generate accurate models assembled with an integrative structural modeling approach.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
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10
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Dudziak A, Engelhard L, Bourque C, Klink BU, Rombaut P, Kornakov N, Jänen K, Herzog F, Gatsogiannis C, Westermann S. Phospho-regulated Bim1/EB1 interactions trigger Dam1c ring assembly at the budding yeast outer kinetochore. EMBO J 2021; 40:e108004. [PMID: 34313341 PMCID: PMC8441410 DOI: 10.15252/embj.2021108004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Kinetochores form the link between chromosomes and microtubules of the mitotic spindle. The heterodecameric Dam1 complex (Dam1c) is a major component of the Saccharomyces cerevisiae outer kinetochore, assembling into 3 MDa‐sized microtubule‐embracing rings, but how ring assembly is specifically initiated in vivo remains to be understood. Here, we describe a molecular pathway that provides local control of ring assembly during the establishment of sister kinetochore bi‐orientation. We show that Dam1c and the general microtubule plus end‐associated protein (+TIP) Bim1/EB1 form a stable complex depending on a conserved motif in the Duo1 subunit of Dam1c. EM analyses reveal that Bim1 crosslinks protrusion domains of adjacent Dam1c heterodecamers and promotes the formation of oligomers with defined curvature. Disruption of the Dam1c‐Bim1 interaction impairs kinetochore localization of Dam1c in metaphase and delays mitosis. Phosphorylation promotes Dam1c‐Bim1 binding by relieving an intramolecular inhibition of the Dam1 C‐terminus. In addition, Bim1 recruits Bik1/CLIP‐170 to Dam1c and induces formation of full rings even in the absence of microtubules. Our data help to explain how new kinetochore end‐on attachments are formed during the process of attachment error correction.
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Affiliation(s)
- Alexander Dudziak
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Lena Engelhard
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Cole Bourque
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Björn Udo Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Pascaline Rombaut
- Gene Center Munich, Ludwig Maximilian University Munich, Munich, Germany
| | - Nikolay Kornakov
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karolin Jänen
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Franz Herzog
- Gene Center Munich, Ludwig Maximilian University Munich, Munich, Germany
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Stefan Westermann
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
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11
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Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA. CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. eLife 2021; 10:e65168. [PMID: 33949948 PMCID: PMC8099430 DOI: 10.7554/elife.65168] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/12/2021] [Indexed: 01/08/2023] Open
Abstract
Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In Saccharomyces cerevisiae, γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub-assemblies, which associate helically to template MT growth. γTuRC assembly provides a key point of regulation for the MT cytoskeleton. Here, we combine crosslinking mass spectrometry, X-ray crystallography, and cryo-EM structures of both monomeric and dimeric γTuSCs, and open and closed helical γTuRC assemblies in complex with Spc110p to elucidate the mechanisms of γTuRC assembly. γTuRC assembly is substantially aided by the evolutionarily conserved CM1 motif in Spc110p spanning a pair of adjacent γTuSCs. By providing the highest resolution and most complete views of any γTuSC assembly, our structures allow phosphorylation sites to be mapped, surprisingly suggesting that they are mostly inhibitory. A comparison of our structures with the CM1 binding site in the human γTuRC structure at the interface between GCP2 and GCP6 allows for the interpretation of significant structural changes arising from CM1 helix binding to metazoan γTuRC.
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Affiliation(s)
- Axel F Brilot
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Andrew S Lyon
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Alex Zelter
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Shruthi Viswanath
- Department of Bioengineering and Therapeutic Sciences, University of California at San FranciscoSan FranciscoUnited States
| | - Alison Maxwell
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
| | - Michael J MacCoss
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Eric G Muller
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California at San FranciscoSan FranciscoUnited States
| | - Trisha N Davis
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California at San FranciscoSan FranciscoUnited States
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12
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Doodhi H, Kasciukovic T, Clayton L, Tanaka TU. Aurora B switches relative strength of kinetochore-microtubule attachment modes for error correction. J Cell Biol 2021; 220:211981. [PMID: 33851957 PMCID: PMC8050843 DOI: 10.1083/jcb.202011117] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 11/24/2022] Open
Abstract
To establish chromosome biorientation, aberrant kinetochore–microtubule interaction must be resolved (error correction) by Aurora B kinase. Aurora B differentially regulates kinetochore attachment to the microtubule plus end and its lateral side (end-on and lateral attachment, respectively). However, it is still unclear how kinetochore–microtubule interactions are exchanged during error correction. Here, we reconstituted the budding yeast kinetochore–microtubule interface in vitro by attaching the Ndc80 complexes to nanobeads. These Ndc80C nanobeads recapitulated in vitro the lateral and end-on attachments of authentic kinetochores on dynamic microtubules loaded with the Dam1 complex. This in vitro assay enabled the direct comparison of lateral and end-on attachment strength and showed that Dam1 phosphorylation by Aurora B makes the end-on attachment weaker than the lateral attachment. Similar reconstitutions with purified kinetochore particles were used for comparison. We suggest the Dam1 phosphorylation weakens interaction with the Ndc80 complex, disrupts the end-on attachment, and promotes the exchange to a new lateral attachment, leading to error correction.
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Affiliation(s)
- Harinath Doodhi
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Taciana Kasciukovic
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lesley Clayton
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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13
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Gutierrez A, Kim JO, Umbreit NT, Asbury CL, Davis TN, Miller MP, Biggins S. Cdk1 Phosphorylation of the Dam1 Complex Strengthens Kinetochore-Microtubule Attachments. Curr Biol 2020; 30:4491-4499.e5. [PMID: 32946748 PMCID: PMC7497780 DOI: 10.1016/j.cub.2020.08.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/20/2020] [Accepted: 08/14/2020] [Indexed: 12/01/2022]
Abstract
To ensure the faithful inheritance of DNA, a macromolecular protein complex called the kinetochore sustains the connection between chromosomes and force-generating dynamic microtubules during cell division. Defects in this process lead to aneuploidy, a common feature of cancer cells and the cause of many developmental diseases [1, 2, 3, 4]. One of the major microtubule-binding activities in the kinetochore is mediated by the conserved Ndc80 complex (Ndc80c) [5, 6, 7]. In budding yeast, the retention of kinetochores on dynamic microtubule tips also depends on the essential heterodecameric Dam1 complex (Dam1c) [8, 9, 10, 11, 12, 13, 14, 15], which binds to the Ndc80c and is proposed to be a functional ortholog of the metazoan Ska complex [16, 17]. The load-bearing activity of the Dam1c depends on its ability to oligomerize, and the purified complex spontaneously self-assembles into microtubule-encircling oligomeric rings, which are proposed to function as collars that allow kinetochores to processively track the plus-end tips of microtubules and harness the forces generated by disassembling microtubules [10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22]. However, it is unknown whether there are specific regulatory events that promote Dam1c oligomerization to ensure accurate segregation. Here, we used a reconstitution system to discover that Cdk1, the major mitotic kinase that drives the cell cycle, phosphorylates the Ask1 component of the Dam1c to increase its residence time on microtubules and enhance kinetochore-microtubule attachment strength. We propose that Cdk1 activity promotes Dam1c oligomerization to ensure that kinetochore-microtubule attachments are stabilized as kinetochores come under tension in mitosis. Cdk1 phosphorylation of Dam1c strengthens kinetochore-microtubule attachments Ask1 is the key Cdk1 target in Dam1c that enhances for kinetochore-microtubule attachments Dynamic phosphorylation of Dam1c by Cdk1 is important in vivo Cdk1 phosphorylation of Ask1 appears to promote Dam1c oligomerization
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Affiliation(s)
- Abraham Gutierrez
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Jae Ook Kim
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Matthew P Miller
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA.
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14
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Structural view of the yeast Dam1 complex, a ring-shaped molecular coupler for the dynamic microtubule end. Essays Biochem 2020; 64:359-370. [PMID: 32579171 DOI: 10.1042/ebc20190079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
In a dividing eukaryotic cell, proper chromosome segregation requires the dynamic yet persistent attachment of kinetochores to spindle microtubules. In the budding yeast Saccharomyces cerevisiae, this function is especially crucial because each kinetochore is attached to a single microtubule; consequently, loss of attachment could lead to unrecoverable chromosome loss. The highly specialized heterodecameric Dam1 protein complex achieves this coupling by assembling into a microtubule-encircling ring that glides near the end of the dynamic microtubule to mediate chromosome motion. In recent years, we have learned a great deal about the structural properties of the Dam1 heterodecamer, its mechanism of self-assembly into rings, and its tethering to the kinetochore by the elongated Ndc80 complex. The most remarkable progress has resulted from defining the fine structures of helical bundles within Dam1 heterodecamer. In this review, we critically analyze structural observations collected by diverse approaches with the goal of obtaining a unified view of Dam1 ring architecture. A considerable consistency between different studies supports a coherent model of the circular core of the Dam1 ring. However, there are persistent uncertainties about the composition of ring protrusions and flexible extensions, as well as their roles in mediating ring core assembly and interactions with the Ndc80 complex and microtubule.
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15
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Löhr T, Camilloni C, Bonomi M, Vendruscolo M. A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference. Methods Mol Biol 2020; 2022:313-340. [PMID: 31396909 DOI: 10.1007/978-1-4939-9608-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformational sampling. In this chapter, we provide a step-by-step guide to perform and analyse metadynamic metainference simulations using the ISDB module of the open-source PLUMED library, as well as a series of practical tips to avoid common mistakes. Specifically, we will guide the reader in the process of learning how to model the structural ensemble of a small disordered peptide by combining state-of-the-art molecular mechanics force fields with nuclear magnetic resonance data, including chemical shifts, scalar couplings and residual dipolar couplings.
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Affiliation(s)
- Thomas Löhr
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
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16
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Mintseris J, Gygi SP. High-density chemical cross-linking for modeling protein interactions. Proc Natl Acad Sci U S A 2020; 117:93-102. [PMID: 31848235 PMCID: PMC6955236 DOI: 10.1073/pnas.1902931116] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Detailed mechanistic understanding of protein complex function is greatly enhanced by insights from its 3-dimensional structure. Traditional methods of protein structure elucidation remain expensive and labor-intensive and require highly purified starting material. Chemical cross-linking coupled with mass spectrometry offers an alternative that has seen increased use, especially in combination with other experimental approaches like cryo-electron microscopy. Here we report advances in method development, combining several orthogonal cross-linking chemistries as well as improvements in search algorithms, statistical analysis, and computational cost to achieve coverage of 1 unique cross-linked position pair for every 7 amino acids at a 1% false discovery rate. This is accomplished without any peptide-level fractionation or enrichment. We apply our methods to model the complex between a carbonic anhydrase (CA) and its protein inhibitor, showing that the cross-links are self-consistent and define the interaction interface at high resolution. The resulting model suggests a scaffold for development of a class of protein-based inhibitors of the CA family of enzymes. We next cross-link the yeast proteasome, identifying 3,893 unique cross-linked peptides in 3 mass spectrometry runs. The dataset includes 1,704 unique cross-linked position pairs for the proteasome subunits, more than half of them intersubunit. Using multiple recently solved cryo-EM structures, we show that observed cross-links reflect the conformational dynamics and disorder of some proteasome subunits. We further demonstrate that this level of cross-linking density is sufficient to model the architecture of the 19-subunit regulatory particle de novo.
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Affiliation(s)
- Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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17
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Miller MP, Evans RK, Zelter A, Geyer EA, MacCoss MJ, Rice LM, Davis TN, Asbury CL, Biggins S. Kinetochore-associated Stu2 promotes chromosome biorientation in vivo. PLoS Genet 2019; 15:e1008423. [PMID: 31584935 PMCID: PMC6795502 DOI: 10.1371/journal.pgen.1008423] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/16/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022] Open
Abstract
Accurate segregation of chromosomes to daughter cells is a critical aspect of cell division. It requires the kinetochores on duplicated chromosomes to biorient, attaching to microtubules from opposite poles of the cell. Bioriented attachments come under tension, while incorrect attachments lack tension and must be released to allow proper attachments to form. A well-studied error correction pathway is mediated by the Aurora B kinase, which destabilizes low tension-bearing attachments. We recently discovered that in vitro, kinetochores display an additional intrinsic tension-sensing pathway that utilizes Stu2. The contribution of kinetochore-associated Stu2 to error correction in cells, however, was unknown. Here, we identify a Stu2 mutant that abolishes its kinetochore function and show that it causes biorientation defects in vivo. We also show that this Stu2-mediated pathway functions together with the Aurora B-mediated pathway. Altogether, our work indicates that cells employ multiple pathways to ensure biorientation and the accuracy of chromosome segregation. The precise regulation of cell division is critical to processes such as self-renewal, proliferation and development. A key event in the cell cycle is the partitioning of every pair of duplicated chromosomes to daughter cells. Defects in chromosome partitioning lead to aneuploidy, a condition that is a common hallmark of cancer cells and the cause of some birth defects. Chromosomes segregate using their kinetochores, the specialized protein structures that are assembled on centromeric DNA sequences and attach to spindle microtubules. Here, we report that a protein that associates with kinetochores called Stu2 ensures that each kinetochore attaches to the proper microtubules. We identified a Stu2 mutant that does not associate with kinetochores and found that it generates aneuploidy. Together, our work identifies a previously unknown mechanism where cells ensure that chromosomes are accurately inherited during cell division.
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Affiliation(s)
- Matthew P. Miller
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rena K. Evans
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States of America
| | - Elisabeth A. Geyer
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Luke M. Rice
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Trisha N. Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States of America
| | - Charles L. Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington, United States of America
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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18
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Rafiei A, Schriemer DC. A microtubule crosslinking protocol for integrative structural modeling activities. Anal Biochem 2019; 586:113416. [PMID: 31499019 DOI: 10.1016/j.ab.2019.113416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 11/15/2022]
Abstract
Microtubules (MTs) are key components in the cytoskeleton of the eukaryotic cell, and play roles in processes such as intracellular transport and cell division. An improved understanding MT regulation requires structural analysis of the extensive interactions between the MT lattice and its regulatory proteins, but MT interactions are challenging for even the most advanced structural methods to characterize. Integrative methods involving crosslinking mass spectrometry (XL-MS) can extend structural analysis to many interaction classes, but the representation of MTs in crosslinking data-sets has been surprisingly low. Here, we explore the basis for the underrepresentation of the MT lattice and present an enhanced method for mapping MT structural features using an optimized set of reagents, together with fluorescence detection to ensure MT structural integrity. Through the application of stringent identification criteria, 91 unique crosslinks were identified, 78 of which were uniquely matched to 7 distinct structural features of the MT lattice. Of note, 4 crosslinks were detected for the lattice-A protofilament organization. The lattice-A structure defines a "seam" or discontinuity in MTs and is an emerging site of interest for MT regulation. Our methodology should be broadly applicable to integrative structural studies involving any MT-protein interaction.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada.
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19
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Hamilton G, Dimitrova Y, Davis TN. Seeing is believing: our evolving view of kinetochore structure, composition, and assembly. Curr Opin Cell Biol 2019; 60:44-52. [PMID: 31078123 DOI: 10.1016/j.ceb.2019.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/20/2019] [Accepted: 03/28/2019] [Indexed: 11/26/2022]
Abstract
This review highlights three recent trends in the field of kinetochore biology: the proliferation of structural data for kinetochore protein complexes (including CBF3, Dam1c, Mis12cMIND, and CENP-NLChl4/Iml3); the growing consensus that the kinetochore is a dynamic structure whose composition changes as the cell cycle progresses; and the mounting evidence of multiple pathways whereby the microtubule-binding elements of the outer kinetochore may be recruited by inner kinetochore proteins. Our focus is on the two best-studied systems in the field: human and budding yeast kinetochores. This review will demonstrate the remarkable similarity of these two systems, as well as their intriguing differences.
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Affiliation(s)
- Grace Hamilton
- Department of Biochemistry, University of Washington Box 357350, 1705 NE Pacific St., Seattle, WA 98195-7350, USA
| | - Yoana Dimitrova
- Genentech, Inc., 1 DNA Way, MS: 27, South San Francisco, CA 94080, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington Box 357350, 1705 NE Pacific St., Seattle, WA 98195-7350, USA.
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20
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Zhang X, Hooykaas PJJ. The Agrobacterium VirD5 protein hyperactivates the mitotic Aurora kinase in host cells. THE NEW PHYTOLOGIST 2019; 222:1551-1560. [PMID: 30667529 PMCID: PMC6667905 DOI: 10.1111/nph.15700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/13/2019] [Indexed: 06/08/2023]
Abstract
Aided by translocated virulence proteins, Agrobacterium tumefaciens transforms plant cells with oncogenic T-DNA. In the host cells the virulence protein VirD5 moves to the nucleus, where it becomes localized at the kinetochores, and disturbs faithful chromosome segregation, but the molecular mechanism underlying this remains unknown. To gain more insight, we screened amongst the kinetochore proteins for VirD5 interactors using bimolecular fluorescence complementation assays, and tested chromosome segregation in yeast cells. We found that VirD5 interacts with the conserved mitotic Aurora kinase Ipl1 in yeast and likewise with plant Aurora kinases. In vitro VirD5 was found to stimulate the activity of Ipl1. Phosphorylation of substrates by Ipl1 in vivo is known to result in the detachment between kinetochore and spindle microtubule. This is necessary for error correction, but increased Ipl1/Aurora kinase activity is known to cause spindle instability, explaining enhanced chromosome mis-segregation seen in the presence of VirD5. That activation of the Ipl1/Aurora kinase at least partially underlies the toxicity of VirD5 became apparent by artificial boosting the activity of the specific counteracting phosphatase Glc7 in vivo, which relieved the toxicity. These findings reveal a novel mechanism by which a pathogenic bacterium manipulates host cells.
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Affiliation(s)
- Xiaorong Zhang
- Department of Molecular and Developmental GeneticsInstitute of BiologyLeiden UniversitySylviusweg 72Leiden2333BEthe Netherlands
| | - Paul J. J. Hooykaas
- Department of Molecular and Developmental GeneticsInstitute of BiologyLeiden UniversitySylviusweg 72Leiden2333BEthe Netherlands
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21
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Ziemianowicz DS, Ng D, Schryvers AB, Schriemer DC. Photo-Cross-Linking Mass Spectrometry and Integrative Modeling Enables Rapid Screening of Antigen Interactions Involving Bacterial Transferrin Receptors. J Proteome Res 2018; 18:934-946. [DOI: 10.1021/acs.jproteome.8b00629] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomyces cerevisiae. Genetics 2018; 211:531-547. [PMID: 30546002 DOI: 10.1534/genetics.118.301727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
The Dam1 complex is an essential component of the outer kinetochore that mediates attachments between spindle microtubules and chromosomes. Dam1p, a subunit of the Dam1 complex, binds to microtubules and is regulated by Aurora B/Ipl1p phosphorylation. We find that overexpression of cAMP-dependent protein kinase (PKA) catalytic subunits (i.e., TPK1, TPK2, TPK3) is lethal in DAM1 mutants and increases the rate of chromosome loss in wild-type cells. Replacing an evolutionarily conserved PKA site (S31) in Dam1p with a nonphosphorylatable alanine suppressed the high-copy PKA dosage lethality in dam1-1 Consistent with Dam1p as a target of PKA, we find that in vitro PKA can directly phosphorylate S31 in Dam1p and we observed phosphorylation of S31 in Dam1p purified from asynchronously growing yeast cells. Cells carrying high-copy TPK2 or a Dam1p phospho-mimetic S31D mutant displayed a reduction in Dam1p localization at the kinetochore, suggesting that PKA phosphorylation plays a role in assembly and/or stability of the Dam1 complex. Furthermore, we observed spindle defects associated with S31 phosphorylation. Finally, we find that phosphorylation of Dam1p on S31 is reduced when glucose is limiting as well as during α-factor arrest, conditions that inhibit PKA activity. These observations suggest that the PKA site of Dam1p participates in regulating kinetochore activity. While PKA is a well-established effector of glucose signaling, our work shows for the first time that glucose-dependent PKA activity has an important function in chromosome segregation.
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23
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Ng CT, Deng L, Chen C, Lim HH, Shi J, Surana U, Gan L. Electron cryotomography analysis of Dam1C/DASH at the kinetochore-spindle interface in situ. J Cell Biol 2018; 218:455-473. [PMID: 30504246 PMCID: PMC6363454 DOI: 10.1083/jcb.201809088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
In dividing cells, depolymerizing spindle microtubules move chromosomes by pulling at their kinetochores. While kinetochore subcomplexes have been studied extensively in vitro, little is known about their in vivo structure and interactions with microtubules or their response to spindle damage. Here we combine electron cryotomography of serial cryosections with genetic and pharmacological perturbation to study the yeast chromosome segregation machinery in vivo. Each kinetochore microtubule has one (rarely, two) Dam1C/DASH outer kinetochore assemblies. Dam1C/DASH contacts the microtubule walls and does so with its flexible "bridges"; there are no contacts with the protofilaments' curved tips. In metaphase, ∼40% of the Dam1C/DASH assemblies are complete rings; the rest are partial rings. Ring completeness and binding position along the microtubule are sensitive to kinetochore attachment and tension, respectively. Our study and those of others support a model in which each kinetochore must undergo cycles of conformational change to couple microtubule depolymerization to chromosome movement.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Li Deng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology Agency for Science Technology and Research, Singapore.,Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology Agency for Science Technology and Research, Singapore.,Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore.,Department of Pharmacology, National University of Singapore, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
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24
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DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, Kuhlman B, Klevit RE. A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation. Mol Cell 2018; 72:753-765.e6. [PMID: 30392931 DOI: 10.1016/j.molcel.2018.09.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 12/27/2022]
Abstract
DNA methylation patterns regulate gene expression programs and are maintained through a highly coordinated process orchestrated by the RING E3 ubiquitin ligase UHRF1. UHRF1 controls DNA methylation inheritance by reading epigenetic modifications to histones and DNA to activate histone H3 ubiquitylation. Here, we find that all five domains of UHRF1, including the previously uncharacterized ubiquitin-like domain (UBL), cooperate for hemi-methylated DNA-dependent H3 ubiquitin ligation. Our structural and biochemical studies, including mutations found in cancer genomes, reveal a bifunctional requirement for the UBL in histone modification: (1) the UBL makes an essential interaction with the backside of the E2 and (2) the UBL coordinates with other UHRF1 domains that recognize epigenetic marks on DNA and histone H3 to direct ubiquitin to H3. Finally, we show UBLs from other E3s also have a conserved interaction with the E2, Ube2D, highlighting a potential prevalence of interactions between UBLs and E2s.
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Affiliation(s)
- Paul A DaRosa
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27499, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Peter Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27499, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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25
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Jenni S, Harrison SC. Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface. Science 2018; 360:552-558. [PMID: 29724956 DOI: 10.1126/science.aar6436] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Kinetochores connect mitotic-spindle microtubules with chromosomes, allowing microtubule depolymerization to pull chromosomes apart during anaphase while resisting detachment as the microtubule shortens. The heterodecameric DASH/Dam1 complex (DASH/Dam1c), an essential component of yeast kinetochores, assembles into a microtubule-encircling ring. The ring associates with rodlike Ndc80 complexes to organize the kinetochore-microtubule interface. We report the cryo-electron microscopy structure (at ~4.5-angstrom resolution) of a DASH/Dam1c ring and a molecular model of its ordered components, validated by evolutionary direct-coupling analysis. Integrating this structure with that of the Ndc80 complex and with published interaction data yields a molecular picture of kinetochore-microtubule attachment, including how flexible, C-terminal extensions of DASH/Dam1c subunits project and contact widely separated sites on the Ndc80 complex rod and how phosphorylation at previously identified sites might regulate kinetochore assembly.
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Affiliation(s)
- Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard University, 250 Longwood Avenue, Boston, MA 02115, USA
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26
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Gaalswyk K, Muniyat MI, MacCallum JL. The emerging role of physical modeling in the future of structure determination. Curr Opin Struct Biol 2018; 49:145-153. [DOI: 10.1016/j.sbi.2018.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022]
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27
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Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex. Proc Natl Acad Sci U S A 2018; 115:E1409-E1418. [PMID: 29386393 DOI: 10.1073/pnas.1716622115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Arp2/3 complex nucleates branched actin filaments important for cellular motility and endocytosis. WASP family proteins are Arp2/3 complex activators that play multiple roles in branching nucleation, but little is known about the structural bases of these WASP functions, owing to an incomplete understanding of how WASP binds Arp2/3 complex. Recent data show WASP binds two sites, and biochemical and structural studies led to models in which the WASP C segment engages the barbed ends of the Arp3 and Arp2 subunits while the WASP A segment binds the back side of the complex on Arp3. However, electron microscopy reconstructions showed density for WASP inconsistent with these models on the opposite (front) side of Arp2/3 complex. Here we use chemical cross-linking and mass spectrometry (XL-MS) along with computational docking and structure-based mutational analysis to map the two WASP binding sites on the complex. Our data corroborate the barbed end and back side binding models and show one WASP binding site on Arp3, on the back side of the complex, and a second site on the bottom of the complex, spanning Arp2 and ARPC1. The XL-MS-identified cross-links rule out the front side binding model and show that the A segment of WASP binds along the bottom side of the ARPC1 subunit, instead of at the Arp2/ARPC1 interface, as suggested by FRET experiments. The identified binding sites support the Arp3 tail release model to explain WASP-mediated activating conformational changes in Arp2/3 complex and provide insight into the roles of WASP in branching nucleation.
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28
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Meyer RE, Brown J, Beck L, Dawson DS. Mps1 promotes chromosome meiotic chromosome biorientation through Dam1. Mol Biol Cell 2017; 29:479-489. [PMID: 29237818 PMCID: PMC6014172 DOI: 10.1091/mbc.e17-08-0503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/01/2017] [Accepted: 12/07/2017] [Indexed: 11/11/2022] Open
Abstract
During meiosis, chromosomes attach to microtubules at their kinetochores and are moved by microtubule depolymerization. The Mps1 kinase is essential for this process. Phosphorylation of Dam1 by Mps1 allows kinetochores to move processively poleward along microtubules during the biorientation process. In budding yeast meiosis, homologous chromosomes become linked by chiasmata and then move back and forth on the spindle until they are bioriented, with the kinetochores of the partners attached to microtubules from opposite spindle poles. Certain mutations in the conserved kinase, Mps1, result in catastrophic meiotic segregation errors but mild mitotic defects. We tested whether Dam1, a known substrate of Mps1, was necessary for its critical meiotic role. We found that kinetochore–microtubule attachments are established even when Dam1 is not phosphorylated by Mps1, but that Mps1 phosphorylation of Dam1 sustains those connections. But the meiotic defects when Dam1 is not phosphorylated are not nearly as catastrophic as when Mps1 is inactivated. The results demonstrate that one meiotic role of Mps1 is to stabilize connections that have been established between kinetochores and microtubles by phosphorylating Dam1.
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Affiliation(s)
- Régis E Meyer
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Jamin Brown
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Lindsay Beck
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
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29
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Jin F, Bokros M, Wang Y. The phosphorylation of a kinetochore protein Dam1 by Aurora B/Ipl1 kinase promotes chromosome bipolar attachment in yeast. Sci Rep 2017; 7:11880. [PMID: 28928489 PMCID: PMC5605499 DOI: 10.1038/s41598-017-12329-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/07/2017] [Indexed: 01/08/2023] Open
Abstract
The interaction between chromosomes and spindle microtubules is essential for chromosome segregation. The kinetochore complex mediates this interaction. Previous studies indicate that the stability of kinetochore attachment is regulated by Aurora B/Ipl1 kinase and this regulation is conserved from yeast to mammalian cells. In budding yeast Saccharomyces cerevisiae, the ten-subunit Dam1/DASH complex bridges the interaction between kinetochores and microtubules, and some in vitro evidence indicates that the phosphorylation of Dam1 protein by Ipl1 kinase destabilizes this interaction. However, it is not clear if Dam1 phosphorylation is sufficient to regulate the stability of kinetochore attachment in vivo. Also, the significance of this regulation in response to chromosome detachment has not been fully investigated. Here we report that phospho-deficient dam1-3A mutants show stabilized kinetochore-microtubule attachment in vivo. This significantly delays the establishment of chromosome bipolar attachment after the disruption of kinetochore-microtubule interaction by a microtubule depolymerizing drug nocodazole. Moreover, dam1-3A cells show dramatic chromosome mis-segregation after treatment with nocodazole, presumably due to the combination of compromised bipolar attachment and premature spindle assembly checkpoint silencing in the mutant cells. Therefore, the regulation of Dam1 phosphorylation imposed by Ipl1 kinase is critical for faithful chromosome segregation.
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Affiliation(s)
- Fengzhi Jin
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.,Yerkes National Primate Research Center, Emory Vaccine Center, 954 Gatewood Rd NE, Atlanta, GA, 30329, USA
| | - Michael Bokros
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA.
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30
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Mps1 Regulates Kinetochore-Microtubule Attachment Stability via the Ska Complex to Ensure Error-Free Chromosome Segregation. Dev Cell 2017; 41:143-156.e6. [PMID: 28441529 DOI: 10.1016/j.devcel.2017.03.025] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 02/16/2017] [Accepted: 03/30/2017] [Indexed: 12/18/2022]
Abstract
The spindle assembly checkpoint kinase Mps1 not only inhibits anaphase but also corrects erroneous attachments that could lead to missegregation and aneuploidy. However, Mps1's error correction-relevant substrates are unknown. Using a chemically tuned kinetochore-targeting assay, we show that Mps1 destabilizes microtubule attachments (K fibers) epistatically to Aurora B, the other major error-correcting kinase. Through quantitative proteomics, we identify multiple sites of Mps1-regulated phosphorylation at the outer kinetochore. Substrate modification was microtubule sensitive and opposed by PP2A-B56 phosphatases that stabilize chromosome-spindle attachment. Consistently, Mps1 inhibition rescued K-fiber stability after depleting PP2A-B56. We also identify the Ska complex as a key effector of Mps1 at the kinetochore-microtubule interface, as mutations that mimic constitutive phosphorylation destabilized K fibers in vivo and reduced the efficiency of the Ska complex's conversion from lattice diffusion to end-coupled microtubule binding in vitro. Our results reveal how Mps1 dynamically modifies kinetochores to correct improper attachments and ensure faithful chromosome segregation.
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31
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Üretmen Kagıalı ZC, Şentürk A, Özkan Küçük NE, Qureshi MH, Özlü N. Proteomics in Cell Division. Proteomics 2017; 17. [PMID: 28548456 DOI: 10.1002/pmic.201600100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes, and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, the authors first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone, and centrosomes. The authors also highlight MS-based large-scale analyses of the cellular components that are largely understudied during cell division such as the cell surface and lipids. Then, the authors focus on posttranslational modification analyses, especially phosphorylation and the resulting crosstalk with other modifications as a cell undergoes cell division. Combining proteomic approaches that probe the biochemistry of cell division components with functional genomic assays will lead to breakthroughs toward a systems-level understanding of cell division.
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Affiliation(s)
| | - Aydanur Şentürk
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Mohammad Haroon Qureshi
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.,Biomedical Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
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32
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Computational modeling of protein assemblies. Curr Opin Struct Biol 2017; 44:179-189. [DOI: 10.1016/j.sbi.2017.04.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 01/18/2023]
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33
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van Hooff JJE, Snel B, Kops GJPL. Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1. Genome Biol Evol 2017; 9:1295-1303. [PMID: 28472331 PMCID: PMC5439489 DOI: 10.1093/gbe/evx088] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 12/27/2022] Open
Abstract
Faithful chromosome segregation relies on kinetochores, the large protein complexes that connect chromatin to spindle microtubules. Although human and yeast kinetochores are largely homologous, they track microtubules with the unrelated protein complexes Ska (Ska-C, human) and Dam1 (Dam1-C, yeast). We here uncovered that Ska-C and Dam1-C are both widespread among eukaryotes, but in an exceptionally inverse manner, supporting their functional analogy. Within the complexes, all Ska-C and various Dam1-C subunits are ancient paralogs, showing that gene duplication shaped these complexes. We examined various evolutionary scenarios to explain the nearly mutually exclusive patterns of Ska-C and Dam1-C in present-day species. We propose that Ska-C was present in the last eukaryotic common ancestor, that subsequently Dam1-C displaced Ska-C in an early fungus and was horizontally transferred to diverse non-fungal lineages, displacing Ska-C in these lineages too.
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Affiliation(s)
- Jolien J. E. van Hooff
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, The Netherlands
- Molecular Cancer Research, University Medical Center Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, The Netherlands
| | - Geert J. P. L. Kops
- Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- Molecular Cancer Research, University Medical Center Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, The Netherlands
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34
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Weisz DA, Liu H, Zhang H, Thangapandian S, Tajkhorshid E, Gross ML, Pakrasi HB. Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II. Proc Natl Acad Sci U S A 2017; 114:2224-2229. [PMID: 28193857 PMCID: PMC5338524 DOI: 10.1073/pnas.1620360114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b559, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b559, in close proximity to the QB site. Protein-protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the "mass tags" selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein-protein interactions in membrane protein complexes.
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Affiliation(s)
- Daniel A Weisz
- Department of Biology, Washington University, St. Louis, MO 63130
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Haijun Liu
- Department of Biology, Washington University, St. Louis, MO 63130
| | - Hao Zhang
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Sundarapandian Thangapandian
- Department of Biochemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Department of Biochemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130;
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35
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Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN. The Ndc80 complex bridges two Dam1 complex rings. eLife 2017; 6. [PMID: 28191870 PMCID: PMC5354518 DOI: 10.7554/elife.21069] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/11/2017] [Indexed: 12/18/2022] Open
Abstract
Strong kinetochore-microtubule attachments are essential for faithful segregation of sister chromatids during mitosis. The Dam1 and Ndc80 complexes are the main microtubule binding components of the Saccharomyces cerevisiae kinetochore. Cooperation between these two complexes enhances kinetochore-microtubule coupling and is regulated by Aurora B kinase. We show that the Ndc80 complex can simultaneously bind and bridge across two Dam1 complex rings through a tripartite interaction, each component of which is regulated by Aurora B kinase. Mutations in any one of the Ndc80p interaction regions abrogates the Ndc80 complex's ability to bind two Dam1 rings in vitro, and results in kinetochore biorientation and microtubule attachment defects in vivo. We also show that an extra-long Ndc80 complex, engineered to space the two Dam1 rings further apart, does not support growth. Taken together, our work suggests that each kinetochore in vivo contains two Dam1 rings and that proper spacing between the rings is vital.
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Affiliation(s)
- Jae Ook Kim
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Athena Bollozos
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
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36
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Bonomi M, Heller GT, Camilloni C, Vendruscolo M. Principles of protein structural ensemble determination. Curr Opin Struct Biol 2017; 42:106-116. [PMID: 28063280 DOI: 10.1016/j.sbi.2016.12.004] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/18/2016] [Accepted: 12/06/2016] [Indexed: 01/19/2023]
Abstract
The biological functions of protein molecules are intimately dependent on their conformational dynamics. This aspect is particularly evident for disordered proteins, which constitute perhaps one-third of the human proteome. Therefore, structural ensembles often offer more useful representations of proteins than individual conformations. Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. These principles concern primarily how to deal with conformationally heterogeneous states, and with experimental measurements that are averaged over such states and affected by a variety of errors. We first review the growing literature of recent methods that combine experimental and computational information to model structural ensembles, highlighting their similarities and differences. We then address some conceptual problems in the determination of structural ensembles and define future goals towards the establishment of objective criteria for the comparison, validation, visualization and dissemination of such ensembles.
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Affiliation(s)
| | | | - Carlo Camilloni
- Department of Chemistry and Institute for Advanced Study, Technische Universität München, D-85747 Garching, Germany
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37
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Legal T, Zou J, Sochaj A, Rappsilber J, Welburn JPI. Molecular architecture of the Dam1 complex-microtubule interaction. Open Biol 2016; 6:rsob.150237. [PMID: 26962051 PMCID: PMC4821239 DOI: 10.1098/rsob.150237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mitosis is a highly regulated process that allows the equal distribution of the genetic material to the daughter cells. Chromosome segregation requires the formation of a bipolar mitotic spindle and assembly of a multi-protein structure termed the kinetochore to mediate attachments between condensed chromosomes and spindle microtubules. In budding yeast, a single microtubule attaches to each kinetochore, necessitating robustness and processivity of this kinetochore-microtubule attachment. The yeast kinetochore-localized Dam1 complex forms a direct interaction with the spindle microtubule. In vitro, the Dam1 complex assembles as a ring around microtubules and couples microtubule depolymerization with cargo movement. However, the subunit organization within the Dam1 complex, its higher-order oligomerization and how it interacts with microtubules remain under debate. Here, we used chemical cross-linking and mass spectrometry to define the architecture and subunit organization of the Dam1 complex. This work reveals that both the C termini of Duo1 and Dam1 subunits interact with the microtubule and are critical for microtubule binding of the Dam1 complex, placing Duo1 and Dam1 on the inside of the ring structure. Integrating this information with available structural data, we provide a coherent model for how the Dam1 complex self-assembles around microtubules.
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Affiliation(s)
- Thibault Legal
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Juan Zou
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alicja Sochaj
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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38
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Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, Stoddard BL, Fairlie WD, Hockenbery DM, Baker D. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. eLife 2016; 5. [PMID: 27805565 PMCID: PMC5127641 DOI: 10.7554/elife.20352] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/01/2016] [Indexed: 01/07/2023] Open
Abstract
Many cancers overexpress one or more of the six human pro-survival BCL2 family proteins to evade apoptosis. To determine which BCL2 protein or proteins block apoptosis in different cancers, we computationally designed three-helix bundle protein inhibitors specific for each BCL2 pro-survival protein. Following in vitro optimization, each inhibitor binds its target with high picomolar to low nanomolar affinity and at least 300-fold specificity. Expression of the designed inhibitors in human cancer cell lines revealed unique dependencies on BCL2 proteins for survival which could not be inferred from other BCL2 profiling methods. Our results show that designed inhibitors can be generated for each member of a closely-knit protein family to probe the importance of specific protein-protein interactions in complex biological processes.
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Affiliation(s)
- Stephanie Berger
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Erik Procko
- Department of Biochemistry, University of Washington, Seattle, United States.,Department of Biochemistry, University of Illinois, Urbana, United States
| | - Daciana Margineantu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Erinna F Lee
- Department of Chemistry and Physics, LaTrobe Institute for Molecular Science, Melbourne, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Australia.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Betty W Shen
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, United States.,Institute for Protein Design, University of Washington, Seattle, United States
| | - Kusum Chawla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Jean-Marc Garnier
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia.,Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Patrick S Stayton
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Barry L Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - W Douglas Fairlie
- Department of Chemistry and Physics, LaTrobe Institute for Molecular Science, Melbourne, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, Australia.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - David M Hockenbery
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, United States.,Institute for Protein Design, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
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39
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Bonomi M, Camilloni C, Vendruscolo M. Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics. Sci Rep 2016; 6:31232. [PMID: 27561930 PMCID: PMC4999896 DOI: 10.1038/srep31232] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023] Open
Abstract
Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide.
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Affiliation(s)
- Massimiliano Bonomi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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40
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Riffle M, Jaschob D, Zelter A, Davis TN. ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. J Proteome Res 2016; 15:2863-70. [PMID: 27302480 PMCID: PMC4977572 DOI: 10.1021/acs.jproteome.6b00274] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
ProXL
is a Web application and accompanying database designed for
sharing, visualizing, and analyzing bottom-up protein cross-linking
mass spectrometry data with an emphasis on structural analysis and
quality control. ProXL is designed to be independent of any particular
software pipeline. The import process is simplified by the use of
the ProXL XML data format, which shields developers of data importers
from the relative complexity of the relational database schema. The
database and Web interfaces function equally well for any software
pipeline and allow data from disparate pipelines to be merged and
contrasted. ProXL includes robust public and private data sharing
capabilities, including a project-based interface designed to ensure
security and facilitate collaboration among multiple researchers.
ProXL provides multiple interactive and highly dynamic data visualizations
that facilitate structural-based analysis of the observed cross-links
as well as quality control. ProXL is open-source, well-documented,
and freely available at https://github.com/yeastrc/proxl-web-app.
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Affiliation(s)
- Michael Riffle
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.,Department of Genome Sciences, University of Washington , Seattle, Washington 98195, United States
| | - Daniel Jaschob
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Alex Zelter
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
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