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Zamel J, Chen J, Zaer S, Harris PD, Drori P, Lebendiker M, Kalisman N, Dokholyan NV, Lerner E. Structural and dynamic insights into α-synuclein dimer conformations. Structure 2023; 31:411-423.e6. [PMID: 36809765 PMCID: PMC10081966 DOI: 10.1016/j.str.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
Abstract
Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed β-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.
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Affiliation(s)
- Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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Claus C, Slavin M, Ansseau E, Lancelot C, Bah K, Lassche S, Fiévet M, Greco A, Tomaiuolo S, Tassin A, Dudome V, Kusters B, Declèves AE, Laoudj-Chenivesse D, van Engelen BGM, Nonclercq D, Belayew A, Kalisman N, Coppée F. The double homeodomain protein DUX4c is associated with regenerating muscle fibers and RNA-binding proteins. Skelet Muscle 2023; 13:5. [PMID: 36882853 PMCID: PMC9990282 DOI: 10.1186/s13395-022-00310-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/30/2022] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND We have previously demonstrated that double homeobox 4 centromeric (DUX4C) encoded for a functional DUX4c protein upregulated in dystrophic skeletal muscles. Based on gain- and loss-of-function studies we have proposed DUX4c involvement in muscle regeneration. Here, we provide further evidence for such a role in skeletal muscles from patients affected with facioscapulohumeral muscular dystrophy (FSHD). METHODS DUX4c was studied at RNA and protein levels in FSHD muscle cell cultures and biopsies. Its protein partners were co-purified and identified by mass spectrometry. Endogenous DUX4c was detected in FSHD muscle sections with either its partners or regeneration markers using co-immunofluorescence or in situ proximity ligation assay. RESULTS We identified new alternatively spliced DUX4C transcripts and confirmed DUX4c immunodetection in rare FSHD muscle cells in primary culture. DUX4c was detected in nuclei, cytoplasm or at cell-cell contacts between myocytes and interacted sporadically with specific RNA-binding proteins involved, a.o., in muscle differentiation, repair, and mass maintenance. In FSHD muscle sections, DUX4c was found in fibers with unusual shape or central/delocalized nuclei (a regeneration feature) staining for developmental myosin heavy chain, MYOD or presenting intense desmin labeling. Some couples of myocytes/fibers locally exhibited peripheral DUX4c-positive areas that were very close to each other, but in distinct cells. MYOD or intense desmin staining at these locations suggested an imminent muscle cell fusion. We further demonstrated DUX4c interaction with its major protein partner, C1qBP, inside myocytes/myofibers that presented features of regeneration. On adjacent muscle sections, we could unexpectedly detect DUX4 (the FSHD causal protein) and its interaction with C1qBP in fusing myocytes/fibers. CONCLUSIONS DUX4c upregulation in FSHD muscles suggests it contributes not only to the pathology but also, based on its protein partners and specific markers, to attempts at muscle regeneration. The presence of both DUX4 and DUX4c in regenerating FSHD muscle cells suggests DUX4 could compete with normal DUX4c functions, thus explaining why skeletal muscle is particularly sensitive to DUX4 toxicity. Caution should be exerted with therapeutic agents aiming for DUX4 suppression because they might also repress the highly similar DUX4c and interfere with its physiological role.
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Affiliation(s)
- Clothilde Claus
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Moriya Slavin
- Department of Biological Chemistry, the Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eugénie Ansseau
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Céline Lancelot
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Karimatou Bah
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Saskia Lassche
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands.,Department of Neurology, Zuyderland Medical Center, Heerlen, the Netherlands
| | - Manon Fiévet
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Sara Tomaiuolo
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium.,Laboratory of Respiratory Physiology and Rehabilitation, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Virginie Dudome
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Benno Kusters
- Department of Pathology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Anne-Emilie Declèves
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | | | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Denis Nonclercq
- Laboratory of Histology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Alexandra Belayew
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium
| | - Nir Kalisman
- Department of Biological Chemistry, the Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Frédérique Coppée
- Laboratory of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000, Mons, Belgium.
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Chen J, Zaer S, Drori P, Zamel J, Joron K, Kalisman N, Lerner E, Dokholyan NV. Multifunctions of α‐Synuclein Explained by Its Dynamic Heterogeneous Conformations with a Hierarchy of Transition Times. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l8019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Sofia Zaer
- The Hebrew University of JerusalemJerusalem
| | - Paz Drori
- The Hebrew University of JerusalemJerusalem
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Chen J, Zaer S, Drori P, Zamel J, Joron K, Kalisman N, Lerner E, Dokholyan NV. The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds. Structure 2021; 29:1048-1064.e6. [PMID: 34015255 PMCID: PMC8419013 DOI: 10.1016/j.str.2021.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 11/22/2022]
Abstract
α-Synuclein plays an important role in synaptic functions by interacting with synaptic vesicle membrane, while its oligomers and fibrils are associated with several neurodegenerative diseases. The specific monomer structures that promote its membrane binding and self-association remain elusive due to its transient nature as an intrinsically disordered protein. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of α-synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.
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Affiliation(s)
- Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Khalil Joron
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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5
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Slavin M, Zamel J, Zohar K, Eliyahu T, Braitbard M, Brielle E, Baraz L, Stolovich-Rain M, Friedman A, Wolf DG, Rouvinski A, Linial M, Schneidman-Duhovny D, Kalisman N. Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2103554118. [PMID: 34373319 PMCID: PMC8403911 DOI: 10.1073/pnas.2103554118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Atomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches. In situ cross-linking and mass spectrometry (in situ CLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targeted in situ CLMS to structurally probe Nsp1, Nsp2, and nucleocapsid (N) proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and obtained cross-link sets with an average density of one cross-link per 20 residues. We then employed integrative modeling that computationally combined the cross-linking data with domain structures to determine full-length atomic models. For the Nsp2, the cross-links report on a complex topology with long-range interactions. Integrative modeling with structural prediction of individual domains by the AlphaFold2 system allowed us to generate a single consistent all-atom model of the full-length Nsp2. The model reveals three putative metal binding sites and suggests a role for Nsp2 in zinc regulation within the replication-transcription complex. For the N protein, we identified multiple intra- and interdomain cross-links. Our integrative model of the N dimer demonstrates that it can accommodate three single RNA strands simultaneously, both stereochemically and electrostatically. For the Nsp1, cross-links with the 40S ribosome were highly consistent with recent cryogenic electron microscopy structures. These results highlight the importance of cellular context for the structural probing of recalcitrant proteins and demonstrate the effectiveness of targeted in situ CLMS and integrative modeling.
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Affiliation(s)
- Moriya Slavin
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Keren Zohar
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tsiona Eliyahu
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Esther Brielle
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Leah Baraz
- Hadassah Academic College Jerusalem, Jerusalem 9101001, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Miri Stolovich-Rain
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ahuva Friedman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, 9190401 Jerusalem, Israel
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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Zamel J, Cohen S, Zohar K, Kalisman N. Facilitating In Situ Cross-Linking and Mass Spectrometry by Antibody-Based Protein Enrichment. J Proteome Res 2021; 20:3701-3708. [PMID: 34151562 DOI: 10.1021/acs.jproteome.1c00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cross-linking of living cells followed by mass spectrometry identification of cross-linked peptides (in situ CLMS) is an emerging technology to study protein structures in their native environment. One of the inherent difficulties of this technology is the high complexity of the samples following cell lysis. Currently, this difficulty largely limits the identification of cross-links to the more abundant proteins in the cell. Here, we describe a targeted approach in which an antibody is used to purify a specific protein-of-interest out of the cell lysate. Mass spectrometry analysis of the protein material that binds to the antibody can then identify considerably more cross-links on the target protein. By using an antibody against the CCT chaperonin, we identified over 200 cross-links that provide in situ evidence for the subunit arrangement of the CCT particle and its interactions with prefoldin. Similar targeting with an antibody against tubulin provided in situ evidence for the structure of the microtubule. Finally, the approach was also successful in identifying cross-links within a protein that expresses at a low level. These results demonstrate the general utility of antibody-based sample simplification for in situ CLMS and greatly expand the scope of protein systems that are amenable to in situ structural studies.
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Affiliation(s)
- Joanna Zamel
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shon Cohen
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Keren Zohar
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nir Kalisman
- Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Abstract
![]()
Development
of new reagents for protein cross-linking is constantly
ongoing. The chemical formulas for the linker adducts formed by these
reagents are usually deduced from expert knowledge and then validated
by mass spectrometry. Clearly, it would be more rigorous to infer
the chemical compositions of the adducts directly from the data without
any prior assumptions on their chemistries. Unfortunately, the analysis
tools that are currently available to detect chemical modifications
on linear peptides are not applicable to the case of two cross-linked
peptides. Here, we show that an adaptation of the open search strategy
that works on linear peptides can be used to characterize cross-link
modifications in pairs of peptides. We benchmark our approach by correctly
inferring the linker masses of two well-known reagents, DSS and formaldehyde,
to accuracies of a few parts per million. We then investigate the
cross-linking chemistries of two poorly characterized reagents: EMCS
and glutaraldehyde. In the case of EMCS, we find that the expected
cross-linking chemistry is accompanied by a competing chemistry that
targets other amino acid types. In the case of glutaraldehyde, we
find that the chemical formula of the dominant linker is C5H4, which indicates a ringed aromatic structure. These
results demonstrate how, with very little effort, our approach can
yield nontrivial insights to better characterize new cross-linkers.
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Affiliation(s)
- Moriya Slavin
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tamar Tayri-Wilk
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Hala Milhem
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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8
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Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE. Structure of the Human Core Centromeric Nucleosome Complex. Curr Biol 2019; 29:2625-2639.e5. [PMID: 31353180 PMCID: PMC6702948 DOI: 10.1016/j.cub.2019.06.062] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/14/2019] [Accepted: 06/21/2019] [Indexed: 10/26/2022]
Abstract
Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the histone H3 variant, CENP-A, and its binding proteins, CENP-C (through its central domain; CD) and CENP-N (through its N-terminal domain; NT). CENP-C can engage nucleosomes through two domains: the CD and the CENP-C motif (CM). CENP-CCD is part of the CCNC by virtue of its high specificity for CENP-A nucleosomes and ability to stabilize CENP-A at the centromere. CENP-CCM is thought to engage a neighboring nucleosome, either one containing conventional H3 or CENP-A, and a crystal structure of a nucleosome complex containing two copies of CENP-CCM was reported. Recent structures containing a single copy of CENP-NNT bound to the CENP-A nucleosome in the absence of CENP-C were reported. Here, we find that one copy of CENP-N is lost for every two copies of CENP-C on centromeric chromatin just prior to kinetochore formation. We present the structures of symmetric and asymmetric forms of the CCNC that vary in CENP-N stoichiometry. Our structures explain how the central domain of CENP-C achieves its high specificity for CENP-A nucleosomes and how CENP-C and CENP-N sandwich the histone H4 tail. The natural centromeric DNA path in our structures corresponds to symmetric surfaces for CCNC assembly, deviating from what is observed in prior structures using artificial sequences. At mitosis, we propose that CCNC asymmetry accommodates its asymmetric connections at the chromosome/kinetochore interface. VIDEO ABSTRACT.
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Affiliation(s)
- Praveen Kumar Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Trevor Van Eeuwen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moriya Slavin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chen Xu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem 2019; 91:6953-6961. [PMID: 31045356 PMCID: PMC6625963 DOI: 10.1021/acs.analchem.9b00658] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,Faculty of Science , University of Zurich , 8006 Zurich , Switzerland
| | - Bruno C Amaral
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Philip Andrews
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Christoph Borchers
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada
| | - Nicolas I Brodie
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Yong Cao
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Stéphane Chaignepain
- CBMN, UMR 5248, CNRS , Université de Bordeaux, INP Bordeaux , Pessac 33607 , France
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Stéphane Claverol
- Centre de Génomique Fonctionnelle, Plateforme Protéome , Université de Bordeaux , Bordeaux 33000 , France
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Trisha Davis
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Gianluca Degliesposti
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Nufar Edinger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Michael Götze
- Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Francisco Gomes-Neto
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Fabio C Gozzo
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Craig Gutierrez
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Caroline Haupt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Lan Huang
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Michael R Hoopmann
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Oleg Klykov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Zdeněk Kukačka
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Fan Liu
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Michael J MacCoss
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Karl Mechtler
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Ravit Mesika
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Robert L Moritz
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nagarjuna Nagaraj
- Biochemistry Core Facility , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Victor Nesati
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Ana G C Neves-Ferreira
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Robert Ninnis
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Petr Novák
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Francis J O'Reilly
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany
| | - Matthias Pelzing
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Evgeniy Petrotchenko
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Lolita Piersimoni
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Manolo Plasencia
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Tara Pukala
- Discipline of Chemistry, Faculty of Sciences , University of Adelaide , North Terrace, Adelaide , South Australia 5005 , Australia
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , EH9 3BF Edinburgh , U.K
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Carolin Sailer
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,PhD Program in Systems Biology , University of Zurich and ETH Zurich , 8092 Zurich , Switzerland
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Yi Shi
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Moriya Slavin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Frank Sobott
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , 2020 Antwerp , Belgium.,The Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology , University of Leeds , LS2 9JT Leeds , U.K
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Heike Stephanowitz
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Florian Stengel
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Christian E Stieger
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Esben Trabjerg
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Michael Trnka
- UCSF Mass Spectrometry Facility , Genentech Hall, 600 16th Street , San Francisco , California 94158 , United States
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Yufei Xiang
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - Sule Yilmaz
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Alex Zelter
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Daniel Ziemianowicz
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
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10
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Abstract
Integrative structure modeling computationally combines data from multiple sources of information with the aim of obtaining structural insights that are not revealed by any single approach alone. In the first part of this review, we survey the commonly used sources of structural information and the computational aspects of model building. Throughout the past decade, integrative modeling was applied to various biological systems, with a focus on large protein complexes. Recent progress in the field of cryo-electron microscopy (cryo-EM) has resolved many of these complexes to near-atomic resolution. In the second part of this review, we compare a range of published integrative models with their higher-resolution counterparts with the aim of critically assessing their accuracy. This comparison gives a favorable view of integrative modeling and demonstrates its ability to yield accurate and informative results. We discuss possible roles of integrative modeling in the new era of cryo-EM and highlight future challenges and directions.
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Affiliation(s)
- Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; .,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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11
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Ben-Aharon Z, Levitt M, Kalisman N. Automatic Inference of Sequence from Low-Resolution Crystallographic Data. Structure 2018; 26:1546-1554.e2. [PMID: 30293812 DOI: 10.1016/j.str.2018.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 04/18/2018] [Accepted: 08/23/2018] [Indexed: 11/17/2022]
Abstract
At resolutions worse than 3.5 Å, the electron density is weak or nonexistent at the locations of the side chains. Consequently, the assignment of the protein sequences to their correct positions along the backbone is a difficult problem. In this work, we propose a fully automated computational approach to assign sequence at low resolution. It is based on our surprising observation that standard reciprocal-space indicators, such as the initial unrefined R value, are sensitive enough to detect an erroneous sequence assignment of even a single backbone position. Our approach correctly determines the amino acid type for 15%, 13%, and 9% of the backbone positions in crystallographic datasets with resolutions of 4.0 Å, 4.5 Å, and 5.0 Å, respectively. We implement these findings in an application for threading a sequence onto a backbone structure. For the three resolution ranges, the application threads 83%, 81%, and 64% of the sequences exactly as in the deposited PDB structures.
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Affiliation(s)
- Ziv Ben-Aharon
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nir Kalisman
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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12
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Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Levitt M, Kornberg RD, Gibbons BJ. Architecture of an RNA polymerase II transcription pre-initiation complex. Science 2013; 342:1238724. [PMID: 24072820 PMCID: PMC4039082 DOI: 10.1126/science.1238724] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The protein density and arrangement of subunits of a complete, 32-protein, RNA polymerase II (pol II) transcription pre-initiation complex (PIC) were determined by means of cryogenic electron microscopy and a combination of chemical cross-linking and mass spectrometry. The PIC showed a marked division in two parts, one containing all the general transcription factors (GTFs) and the other pol II. Promoter DNA was associated only with the GTFs, suspended above the pol II cleft and not in contact with pol II. This structural principle of the PIC underlies its conversion to a transcriptionally active state; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol II cleft.
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Affiliation(s)
- Kenji Murakami
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Hans Elmlund
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Nir Kalisman
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - David A. Bushnell
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Christopher M. Adams
- Stanford University Mass Spectrometry, Stanford University, Stanford, CA 94305, U.S.A
| | - Maia Azubel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Dominika Elmlund
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Yael Levi-Kalisman
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Xin Liu
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Michael Levitt
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Brian J. Gibbons
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
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13
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Kalisman N, Schröder GF, Levitt M. The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning. Structure 2013; 21:540-9. [PMID: 23478063 DOI: 10.1016/j.str.2013.01.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/20/2013] [Accepted: 01/28/2013] [Indexed: 12/22/2022]
Abstract
In eukaryotes, CCT is essential for the correct and efficient folding of many cytosolic proteins, most notably actin and tubulin. Structural studies of CCT have been hindered by the failure of standard crystallographic analysis to resolve its eight different subunit types at low resolutions. Here, we exhaustively assess the R value fit of all possible CCT models to available crystallographic data of the closed and open forms with resolutions of 3.8 Å and 5.5 Å, respectively. This unbiased analysis finds the native subunit arrangements with overwhelming significance. The resulting structures provide independent crystallographic proof of the subunit arrangement of CCT and map major asymmetrical features of the particle onto specific subunits. The actin and tubulin substrates both bind around subunit CCT6, which shows other structural anomalies. CCT is thus clearly partitioned, both functionally and evolutionary, into a substrate-binding side that is opposite to the ATP-hydrolyzing side.
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Affiliation(s)
- Nir Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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14
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Yahalom R, Reshef D, Wiener A, Frankel S, Kalisman N, Lerner B, Keasar C. Structure-based identification of catalytic residues. Proteins 2011; 79:1952-63. [PMID: 21491495 DOI: 10.1002/prot.23020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 01/14/2011] [Accepted: 01/28/2011] [Indexed: 11/10/2022]
Abstract
The identification of catalytic residues is an essential step in functional characterization of enzymes. We present a purely structural approach to this problem, which is motivated by the difficulty of evolution-based methods to annotate structural genomics targets that have few or no homologs in the databases. Our approach combines a state-of-the-art support vector machine (SVM) classifier with novel structural features that augment structural clues by spatial averaging and Z scoring. Special attention is paid to the class imbalance problem that stems from the overwhelming number of non-catalytic residues in enzymes compared to catalytic residues. This problem is tackled by: (1) optimizing the classifier to maximize a performance criterion that considers both Type I and Type II errors in the classification of catalytic and non-catalytic residues; (2) under-sampling non-catalytic residues before SVM training; and (3) during SVM training, penalizing errors in learning catalytic residues more than errors in learning non-catalytic residues. Tested on four enzyme datasets, one specifically designed by us to mimic the structural genomics scenario and three previously evaluated datasets, our structure-based classifier is never inferior to similar structure-based classifiers and comparable to classifiers that use both structural and evolutionary features. In addition to the evaluation of the performance of catalytic residue identification, we also present detailed case studies on three proteins. This analysis suggests that many false positive predictions may correspond to binding sites and other functional residues. A web server that implements the method, our own-designed database, and the source code of the programs are publicly available at http://www.cs.bgu.ac.il/∼meshi/functionPrediction.
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Affiliation(s)
- Ran Yahalom
- Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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15
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Levi-Kalisman Y, Jadzinsky PD, Kalisman N, Tsunoyama H, Tsukuda T, Bushnell DA, Kornberg RD. Synthesis and Characterization of Au102(p-MBA)44 Nanoparticles. J Am Chem Soc 2011; 133:2976-82. [DOI: 10.1021/ja109131w] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yael Levi-Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Pablo D. Jadzinsky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Nir Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Hironori Tsunoyama
- Section of Catalytic Assemblies, Catalysis Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - Tatsuya Tsukuda
- Section of Catalytic Assemblies, Catalysis Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - David A. Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
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16
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Abstract
Protein structure refinement is an important but unsolved problem; it must be solved if we are to predict biological function that is very sensitive to structural details. Specifically, critical assessment of techniques for protein structure prediction (CASP) shows that the accuracy of predictions in the comparative modeling category is often worse than that of the template on which the homology model is based. Here we describe a refinement protocol that is able to consistently refine submitted predictions for all categories at CASP7. The protocol uses direct energy minimization of the knowledge-based potential of mean force that is based on the interaction statistics of 167 atom types (Summa and Levitt, Proc Natl Acad Sci USA 2007; 104:3177-3182). Our protocol is thus computationally very efficient; it only takes a few minutes of CPU time to run typical protein models (300 residues). We observe an average structural improvement of 1% in GDT_TS, for predictions that have low and medium homology to known PDB structures (Global Distance Test score or GDT_TS between 50 and 80%). We also observe a marked improvement in the stereochemistry of the models. The level of improvement varies amongst the various participants at CASP, but we see large improvements (>10% increase in GDT_TS) even for models predicted by the best performing groups at CASP7. In addition, our protocol consistently improved the best predicted models in the refinement category at CASP7 and CASP8. These improvements in structure and stereochemistry prove the usefulness of our computationally inexpensive, powerful and automatic refinement protocol.
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Affiliation(s)
- Gaurav Chopra
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
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17
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Amir EAD, Kalisman N, Keasar C. Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities. Proteins 2008; 72:62-73. [PMID: 18186478 DOI: 10.1002/prot.21896] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Rotatable torsion angles are the major degrees of freedom in proteins. Adjacent angles are highly correlated and energy terms that rely on these correlations are intensively used in molecular modeling. However, the utility of torsion based terms is not yet fully exploited. Many of these terms do not capture the full scale of the correlations. Other terms, which rely on lookup tables, cannot be used in the context of force-driven algorithms because they are not fully differentiable. This study aims to extend the usability of torsion terms by presenting a set of high-dimensional and fully-differentiable energy terms that are derived from high-resolution structures. The set includes terms that describe backbone conformational probabilities and propensities, side-chain rotamer probabilities, and an elaborate term that couples all the torsion angles within the same residue. The terms are constructed by cubic spline interpolation with periodic boundary conditions that enable full differentiability and high computational efficiency. We show that the spline implementation does not compromise the accuracy of the original database statistics. We further show that the side-chain relevant terms are compatible with established rotamer probabilities. Despite their very local characteristics, the new terms are often able to identify native and native-like structures within decoy sets. Finally, force-based minimization of NMR structures with the new terms improves their torsion angle statistics with minor structural distortion (0.5 A RMSD on average). The new terms are freely available in the MESHI molecular modeling package. The spline coefficients are also available as a documented MATLAB file.
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Affiliation(s)
- El-Ad David Amir
- Department of Computer Science, Ben-Gurion University of the Negev, Israel
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18
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Noy K, Kalisman N, Keasar C. Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials. BMC Struct Biol 2008; 8:27. [PMID: 18510728 PMCID: PMC2427033 DOI: 10.1186/1472-6807-8-27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Accepted: 05/29/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution. RESULTS We tested the new approach on four families of short beta-hairpin peptides: TrpZip, MBH, bhpW and EPO, whose structural stabilities have been experimentally measured in previous studies. For all four families, both computational techniques show considerable correlation (r > 0.65) with the experimentally measured stabilities. The consensus of the two techniques shows higher correlation (r > 0.82). CONCLUSION Our results suggest a prediction scheme that can be used to estimate the relative structural stability within a peptide family. We discuss the applicability of this predictive approach for in-silico screening of combinatorial peptide libraries.
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Affiliation(s)
- Karin Noy
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel.
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19
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Abstract
UNLABELLED Adapting a modular and object-oriented approach in the design of molecular modeling packages may reduce the software development barrier between ideas and their programed applications. Towards this goal we developed MESHI, a new, strictly object-oriented, molecular modeling suite written in Java. MESHI provides a comprehensive library of extendable classes for all the essential components of molecular modeling: molecular and geometry elements, energy functions and optimization methods. AVAILABILITY MESHI and its related documentation are freely available at http://www.cs.bgu.ac.il/~meshi; the MESHI API is available at http://www.cs.bgu.ac.il/~meshi/API CONTACT: keasar@cs.bgu.ac.il SUPPLEMENTARY INFORMATION The Supplementary information includes (1) a detailed description of several key packages and classes, and (2) a brief presentation of results achieved by using the MESHI application--Beautify--in the CASP6 experiment.
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Affiliation(s)
- Nir Kalisman
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
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20
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Abstract
The neocortex has a high capacity for plasticity. To understand the full scope of this capacity, it is essential to know how neurons choose particular partners to form synaptic connections. By using multineuron whole-cell recordings and confocal microscopy we found that axons of layer V neocortical pyramidal neurons do not preferentially project toward the dendrites of particular neighboring pyramidal neurons; instead, axons promiscuously touch all neighboring dendrites without any bias. Functional synaptic coupling of a small fraction of these neurons is, however, correlated with the existence of synaptic boutons at existing touch sites. These data provide the first direct experimental evidence for a tabula rasa-like structural matrix between neocortical pyramidal neurons and suggests that pre- and postsynaptic interactions shape the conversion between touches and synapses to form specific functional microcircuits. These data also indicate that the local neocortical microcircuit has the potential to be differently rewired without the need for remodeling axonal or dendritic arbors.
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Affiliation(s)
- Nir Kalisman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
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21
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Abstract
A model is presented that allows prediction of the probability for the formation of appositions between the axons and dendrites of any two neurons based only on their morphological statistics and relative separation. Statistics of axonal and dendritic morphologies of single neurons are obtained from 3D reconstructions of biocytin-filled cells, and a statistical representation of the same cell type is obtained by averaging across neurons according to the model. A simple mathematical formulation is applied to the axonal and dendritic statistical representations to yield the probability for close appositions. The model is validated by a mathematical proof and by comparison of predicted appositions made by layer 5 pyramidal neurons in the rat somatosensory cortex with real anatomical data. The model could be useful for studying microcircuit connectivity and for designing artificial neural networks.
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Affiliation(s)
- Nir Kalisman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
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