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  1. Article ; Online: Spin-Hall nano-oscillator with oblique magnetization and Dzyaloshinskii-Moriya interaction as generator of skyrmions and nonreciprocal spin-waves.

    Giordano, A / Verba, R / Zivieri, R / Laudani, A / Puliafito, V / Gubbiotti, G / Tomasello, R / Siracusano, G / Azzerboni, B / Carpentieri, M / Slavin, A / Finocchio, G

    Scientific reports

    2016  Volume 6, Page(s) 36020

    Abstract: ... Moriya interaction (i-DMI), which may lead to the nonreciprocity of the excited spin waves and ...

    Abstract Spin-Hall oscillators (SHO) are promising sources of spin-wave signals for magnonics applications, and can serve as building blocks for magnonic logic in ultralow power computation devices. Thin magnetic layers used as "free" layers in SHO are in contact with heavy metals having large spin-orbital interaction, and, therefore, could be subject to the spin-Hall effect (SHE) and the interfacial Dzyaloshinskii-Moriya interaction (i-DMI), which may lead to the nonreciprocity of the excited spin waves and other unusual effects. Here, we analytically and micromagnetically study magnetization dynamics excited in an SHO with oblique magnetization when the SHE and i-DMI act simultaneously. Our key results are: (i) excitation of nonreciprocal spin-waves propagating perpendicularly to the in-plane projection of the static magnetization; (ii) skyrmions generation by pure spin-current; (iii) excitation of a new spin-wave mode with a spiral spatial profile originating from a gyrotropic rotation of a dynamical skyrmion. These results demonstrate that SHOs can be used as generators of magnetic skyrmions and different types of propagating spin-waves for magnetic data storage and signal processing applications.
    Language English
    Publishing date 2016-10-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/srep36020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Structural Analysis of Protein Complexes by Cross-Linking and Mass Spectrometry.

    Slavin, Moriya / Kalisman, Nir

    Methods in molecular biology (Clifton, N.J.)

    2018  Volume 1764, Page(s) 173–183

    Abstract: Cross-linking and mass spectrometry is used more and more for the structural analysis of large proteins and protein complexes. Although essentially a low-resolution method, it avoids the main drawbacks of established structural techniques. Particularly, ... ...

    Abstract Cross-linking and mass spectrometry is used more and more for the structural analysis of large proteins and protein complexes. Although essentially a low-resolution method, it avoids the main drawbacks of established structural techniques. Particularly, it is largely insensitive to the inherent flexibility of the studied complexes and is applied under native conditions. It is also applicable to nearly every structural system. Therefore, cross-linking and mass spectrometry is the method of choice for elucidating the general architecture of protein complexes. Advances in instrumentation, techniques, and software now allow every lab that is working with proteins to apply the approach without much difficulty. The most specialized step in the workflow, the mass spectrometry measurement, can be done in most facilities that are performing standard proteomics. We detail here a step-by-step protocol of how to successfully apply the approach in collaboration with the mass spectrometry facility in your institution.
    MeSH term(s) Cross-Linking Reagents/metabolism ; Mass Spectrometry/methods ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Proteins/chemistry ; Proteins/metabolism
    Chemical Substances Cross-Linking Reagents ; Peptide Fragments ; Proteins
    Language English
    Publishing date 2018-03-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7759-8_11
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Open Search Strategy for Inferring the Masses of Cross-Link Adducts on Proteins.

    Slavin, Moriya / Tayri-Wilk, Tamar / Milhem, Hala / Kalisman, Nir

    Analytical chemistry

    2020  Volume 92, Issue 24, Page(s) 15899–15907

    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 ... ...

    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 C
    MeSH term(s) Animals ; Cattle ; Cross-Linking Reagents/chemistry ; Glutaral/chemistry ; Molecular Structure ; Particle Size ; Serum Albumin, Bovine/chemistry ; Surface Properties
    Chemical Substances Cross-Linking Reagents ; Serum Albumin, Bovine (27432CM55Q) ; Glutaral (T3C89M417N)
    Language English
    Publishing date 2020-11-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c03292
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: De Novo Development of Mitochondria-Targeted Molecular Probes Targeting Pink1.

    Ben-Uliel, Shulamit Fluss / Zoabi, Faten Habrat / Slavin, Moriya / Sibony-Benyamini, Hadas / Kalisman, Nir / Qvit, Nir

    International journal of molecular sciences

    2022  Volume 23, Issue 11

    Abstract: Mitochondria play central roles in maintaining cellular metabolic homeostasis, cell survival and cell death, and generate most of the cell's energy. Mitochondria maintain their homeostasis by dynamic (fission and fusion) and quality control mechanisms, ... ...

    Abstract Mitochondria play central roles in maintaining cellular metabolic homeostasis, cell survival and cell death, and generate most of the cell's energy. Mitochondria maintain their homeostasis by dynamic (fission and fusion) and quality control mechanisms, including mitophagy, the removal of damaged mitochondria that is mediated mainly by the Pink1/Parkin pathway. Pink1 is a serine/threonine kinase which regulates mitochondrial function, hitherto many molecular mechanisms underlying Pink1 activity in mitochondrial homeostasis and cell fate remain unknown. Peptides are vital biological mediators that demonstrate remarkable potency, selectivity, and low toxicity, yet they have two major limitations, low oral bioavailability and poor stability. Herein, we rationally designed a linear peptide that targets Pink1 and, using straightforward chemistry, we developed molecular probes with drug-like properties to further characterize Pink1. Initially, we conjugated a cell-penetrating peptide and a cross-linker to map Pink1's 3D structure and its interaction sites. Next, we conjugated a fluorescent dye for cell-imaging. Finally, we developed cyclic peptides with improved stability and binding affinity. Overall, we present a facile approach to converting a non-permeable linear peptide into a research tool possessing important properties for therapeutics. This is a general approach using straightforward chemistry that can be tailored for various applications by numerous laboratories.
    MeSH term(s) Mitochondria/metabolism ; Mitophagy ; Molecular Probes/metabolism ; Protein Kinases/metabolism ; Protein Serine-Threonine Kinases ; Ubiquitin-Protein Ligases/metabolism
    Chemical Substances Molecular Probes ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Protein Kinases (EC 2.7.-) ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2022-05-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23116076
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: De Novo Development of Mitochondria-Targeted Molecular Probes Targeting Pink1

    Shulamit Fluss Ben-Uliel / Faten Habrat Zoabi / Moriya Slavin / Hadas Sibony-Benyamini / Nir Kalisman / Nir Qvit

    International Journal of Molecular Sciences, Vol 23, Iss 6076, p

    2022  Volume 6076

    Abstract: Mitochondria play central roles in maintaining cellular metabolic homeostasis, cell survival and cell death, and generate most of the cell’s energy. Mitochondria maintain their homeostasis by dynamic (fission and fusion) and quality control mechanisms, ... ...

    Abstract Mitochondria play central roles in maintaining cellular metabolic homeostasis, cell survival and cell death, and generate most of the cell’s energy. Mitochondria maintain their homeostasis by dynamic (fission and fusion) and quality control mechanisms, including mitophagy, the removal of damaged mitochondria that is mediated mainly by the Pink1/Parkin pathway. Pink1 is a serine/threonine kinase which regulates mitochondrial function, hitherto many molecular mechanisms underlying Pink1 activity in mitochondrial homeostasis and cell fate remain unknown. Peptides are vital biological mediators that demonstrate remarkable potency, selectivity, and low toxicity, yet they have two major limitations, low oral bioavailability and poor stability. Herein, we rationally designed a linear peptide that targets Pink1 and, using straightforward chemistry, we developed molecular probes with drug-like properties to further characterize Pink1. Initially, we conjugated a cell-penetrating peptide and a cross-linker to map Pink1’s 3D structure and its interaction sites. Next, we conjugated a fluorescent dye for cell-imaging. Finally, we developed cyclic peptides with improved stability and binding affinity. Overall, we present a facile approach to converting a non-permeable linear peptide into a research tool possessing important properties for therapeutics. This is a general approach using straightforward chemistry that can be tailored for various applications by numerous laboratories.
    Keywords Pink1 ; mitophagy ; bioactive peptides ; peptidomimetics ; backbone cyclization ; protein-protein interactions ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 540 ; 571
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The double homeodomain protein DUX4c is associated with regenerating muscle fibers and RNA-binding proteins.

    Claus, Clothilde / Slavin, Moriya / Ansseau, Eugénie / Lancelot, Céline / Bah, Karimatou / Lassche, Saskia / Fiévet, Manon / Greco, Anna / Tomaiuolo, Sara / Tassin, Alexandra / Dudome, Virginie / Kusters, Benno / Declèves, Anne-Emilie / Laoudj-Chenivesse, Dalila / van Engelen, Baziel G M / Nonclercq, Denis / Belayew, Alexandra / Kalisman, Nir / Coppée, Frédérique

    Skeletal muscle

    2023  Volume 13, Issue 1, Page(s) 5

    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 ... ...

    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.
    MeSH term(s) Humans ; Carrier Proteins ; Cytoplasm ; Desmin ; Homeodomain Proteins/genetics ; Mitochondrial Proteins ; Muscle Fibers, Skeletal ; Muscular Dystrophy, Facioscapulohumeral/genetics ; Transcription Factors/genetics ; RNA-Binding Proteins/genetics
    Chemical Substances C1QBP protein, human ; Carrier Proteins ; Desmin ; Homeodomain Proteins ; Mitochondrial Proteins ; DUX4L9 protein, human ; Transcription Factors ; RNA-Binding Proteins
    Language English
    Publishing date 2023-03-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2595637-1
    ISSN 2044-5040 ; 2044-5040
    ISSN (online) 2044-5040
    ISSN 2044-5040
    DOI 10.1186/s13395-022-00310-y
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  7. Article ; Online: Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2.

    Slavin, Moriya / Zamel, Joanna / Zohar, Keren / Eliyahu, Tsiona / Braitbard, Merav / Brielle, Esther / Baraz, Leah / Stolovich-Rain, Miri / Friedman, Ahuva / Wolf, Dana G / Rouvinski, Alexander / Linial, Michal / Schneidman-Duhovny, Dina / Kalisman, Nir

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 34

    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 ... ...

    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.
    MeSH term(s) Cross-Linking Reagents/chemistry ; HEK293 Cells ; Humans ; Mass Spectrometry ; Models, Molecular ; Protein Domains ; SARS-CoV-2/chemistry ; Viral Proteins/chemistry
    Chemical Substances Cross-Linking Reagents ; Viral Proteins
    Language English
    Publishing date 2021-08-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2103554118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins

    Tamar Tayri-Wilk / Moriya Slavin / Joanna Zamel / Ayelet Blass / Shon Cohen / Alex Motzik / Xue Sun / Deborah E. Shalev / Oren Ram / Nir Kalisman

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 9

    Abstract: Formaldehyde (FA) is a popular cross-linking reagent, but applying it for cross-linking mass spectrometry (XLMS) has been largely unsuccessful. Here, the authors show that cross-links in structured proteins are the product of two FA molecules and ... ...

    Abstract Formaldehyde (FA) is a popular cross-linking reagent, but applying it for cross-linking mass spectrometry (XLMS) has been largely unsuccessful. Here, the authors show that cross-links in structured proteins are the product of two FA molecules and identify hundreds of FA cross-links by XLMS in vitro and in situ.
    Keywords Science ; Q
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins.

    Tayri-Wilk, Tamar / Slavin, Moriya / Zamel, Joanna / Blass, Ayelet / Cohen, Shon / Motzik, Alex / Sun, Xue / Shalev, Deborah E / Ram, Oren / Kalisman, Nir

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 3128

    Abstract: Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate ... ...

    Abstract Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies.
    MeSH term(s) Amino Acids/chemistry ; Cell Line, Tumor ; Cross-Linking Reagents/chemistry ; Formaldehyde/chemistry ; Humans ; Mass Spectrometry ; Molecular Docking Simulation ; Protein Interaction Mapping/methods ; Proteins/chemistry ; Proteins/metabolism
    Chemical Substances Amino Acids ; Cross-Linking Reagents ; Proteins ; Formaldehyde (1HG84L3525)
    Language English
    Publishing date 2020-06-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-16935-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Structure of the Human Core Centromeric Nucleosome Complex.

    Allu, Praveen Kumar / Dawicki-McKenna, Jennine M / Van Eeuwen, Trevor / Slavin, Moriya / Braitbard, Merav / Xu, Chen / Kalisman, Nir / Murakami, Kenji / Black, Ben E

    Current biology : CB

    2019  Volume 29, Issue 16, Page(s) 2625–2639.e5

    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 ( ... ...

    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-C
    MeSH term(s) Centromere/ultrastructure ; Chromosomal Proteins, Non-Histone/ultrastructure ; Cryoelectron Microscopy ; Humans ; Mitosis/physiology ; Nucleosomes/ultrastructure
    Chemical Substances CENPN protein, human ; Chromosomal Proteins, Non-Histone ; Nucleosomes ; centromere protein C
    Language English
    Publishing date 2019-07-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2019.06.062
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