Evidence for a compact σ70 conformation in vitro and in vivo

Authors: Joron, Khalil ¹, Zamel, Joanna ¹, Kalisman, Nir ^{1, 2}, Lerner, Eitan ^{1, 2, 3, ∗}

Source: In iScience 21 June 2024 27(6)

Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Authors: Leitner, Alexander, Bonvin, Alexandre M. J. J., Borchers, Christoph H., Chalkley, Robert J., Chamot-Rooke, Julia, Combe, Colin W., Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C., Heck, Albert J. R., Hoopmann, Michael R., Huang, Lan, Ishihama, Yasushi, Jones, Andrew R., Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L., Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A., Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaino, Juan A., Wilkins, Marc R., Rappsilber, Juri

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2007.00383

Structural and dynamic insights into α-synuclein dimer conformations

Authors: Zamel, Joanna, Chen, Jiaxing, Zaer, Sofia, Harris, Paul David, Drori, Paz, Lebendiker, Mario, Kalisman, Nir, Dokholyan, Nikolay V., Lerner, Eitan

Source: In Structure 6 April 2023 31(4):411-423

Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2

Authors: 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

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Aug . 118(34), 1-9.

Access URL: https://www.jstor.org/stable/27075521

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Authors: Chen, Jiaxing, Zaer, Sofia, Drori, Paz, Zamel, Joanna, Joron, Khalil, Kalisman, Nir, Lerner, Eitan, Dokholyan, Nikolay V.

Source: In Structure 2 September 2021 29(9):1048-1064

Facilitating In Situ Cross-Linking and Mass Spectrometry by Antibody-Based Protein Enrichment

Authors: Zamel, Joanna, Cohen, Shon, Zohar, Keren, Kalisman, Nir

Source: Journal of proteome research. 20(7):3701-3708

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN627032717&indx=1&recIds=ETOCRN627032717

Structure of the Human Core Centromeric Nucleosome Complex

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

Source: In Current Biology 19 August 2019 29(16):2625-2639

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

Authors: Leitner, Alexander, Bonvin, Alexandre M.J.J., Borchers, Christoph H., Chalkley, Robert J., Chamot-Rooke, Julia, Combe, Colin W., Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C., Heck, Albert J.R., Hoopmann, Michael R., Huang, Lan, Ishihama, Yasushi, Jones, Andrew R., Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L., Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A., Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A., Wilkins, Marc R., Rappsilber, Juri

Source: STRUCTURE -CAMBRIDGE MASSACHUSETTS. 28(11):1259-1268

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100123846532.0x000001&indx=1&recIds=ETOCvdc_100123846532.0x000001

Open Search Strategy for Inferring the Masses of Cross-Link Adducts on Proteins

Authors: Slavin, Moriya, Tayri-Wilk, Tamar, Milhem, Hala, Kalisman, Nir

Source: Analytical chemistry. 92(24):15899-15907

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN625490118&indx=1&recIds=ETOCRN625490118

Automatic Inference of Sequence from Low-Resolution Crystallographic Data

Authors: Ben-Aharon, Ziv, Levitt, Michael, Kalisman, Nir

Source: In Structure 6 November 2018 26(11):1546-1554

The Neocortical Microcircuit as a tabula rasa

Authors: Kalisman, Nir, Silberberg, Gilad, Markram, Henry, Merzenich, Michael M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2005 Jan . 102(3), 880-885.

Access URL: https://www.jstor.org/stable/3374342

Integrative Structure Modeling: Overview and Assessment

Authors: Braitbard, Merav, Schneidman-Duhovny, Dina, Kalisman, Nir

Source: Annual review of biochemistry. 88:113-136

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN621233085&indx=1&recIds=ETOCRN621233085

Multifunctions of α‐Synuclein Explained by Its Dynamic Heterogeneous Conformations with a Hierarchy of Transition Times

Authors: Chen, Jiaxing, Zaer, Sofia, Drori, Paz, Zamel, Joanna, Joron, Khalil, Kalisman, Nir, Lerner, Eitan, Dokholyan, Nikolay V.

Source: FASEB journal. 36

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100196445561.0x000001&indx=1&recIds=ETOCvdc_100196445561.0x000001

Def1 interacts with TFIIH and modulates RNA polymerase II transcription

Authors: Damodaren, Nivedita, Van Eeuwen, Trevor, Zamel, Joanna, Lin-Shiao, Enrique, Kalisman, Nir, Murakami, Kenji

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Dec 01. 114(50), 13230-13235.

Access URL: https://www.jstor.org/stable/26485797

Structural Analysis of Protein Complexes by Cross-Linking and Mass Spectrometry

Authors: Slavin, Moriya, Kalisman, Nir

Source: Methods in molecular biology. 1764:173-184

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN615570021&indx=1&recIds=ETOCRN615570021

Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain

Authors: Braun, Tatjana, Vos, Matthijn R., Kalisman, Nir, Sherman, Nicholas E., Rachel, Reinhard, Wirth, Reinhard, Schröder, Gunnar F., Egelman, Edward H.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Sep . 113(37), 10352-10357.

Access URL: https://www.jstor.org/stable/26471781

Structure of an RNA polymerase II preinitiation complex

Authors: Murakami, Kenji, Tsai, Kuang-Lei, Kalisman, Nir, Bushnell, David A., Asturias, Francisco J., Kornberg, Roger D.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2015 Nov 01. 112(44), 13543-13548.

Access URL: https://www.jstor.org/stable/26465650

The Crystal Structures of the Eukaryotic Chaperonin CCT Reveal Its Functional Partitioning

Authors: Kalisman, Nir, Schröder, Gunnar F., Levitt, Michael

Source: In Structure 2 April 2013 21(4):540-549

Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins

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

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174585044.0x000001&indx=1&recIds=ETOCvdc_100174585044.0x000001

Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex

Authors: Murakami, Kenji, Elmlund, Hans, Kalisman, Nir, Bushnell, David A., Adams, Christopher M., Azubel, Maia, Elmlund, Dominika, Levi-Kalisman, Yael, Liu, Xin, Gibbons, Brian J., Levitt, Michael, Kornberg, Roger D.

Source: Science, 2013 Nov 01. 342(6159), 709-709.

Access URL: http://dx.doi.org/10.1126/science.1238724