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Article ; Online: High-Throughput Protein Analysis Using Negative Stain Electron Microscopy and 2D Classification.

Arthur, Christopher P / Ciferri, Claudio

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

2019 Volume 2025, Page(s) 477–485

Abstract: High-throughput protein expression and purification allows for fast triaging of several constructs based on expression levels, protein integrity, and solubility. While this technology has been successfully adopted to prioritize constructs for structural ... ...

Abstract	High-throughput protein expression and purification allows for fast triaging of several constructs based on expression levels, protein integrity, and solubility. While this technology has been successfully adopted to prioritize constructs for structural biology, it could not inform on important biochemical properties such as domain architecture, homogeneity, and flexibility. Negative staining electron microscopy can be used to quickly evaluate these properties and, if coupled to single particle analysis, can inform on the architecture and conformational state of nearly any protein sample. Here we describe a protocol for negative stain sample preparation, imaging, and two-dimensional (2D) data analysis applicable to a variety of protein complexes. We discuss in more detail a specific application of this technology to large molecule studies to determine the binding sites of individual antibodies on target antigens.
MeSH term(s)	Animals ; Cryoelectron Microscopy/methods ; Electrophoresis, Gel, Two-Dimensional ; Epitope Mapping/methods ; Humans ; Microscopy, Electron, Transmission/methods
Language	English
Publishing date	2019-07-02
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9624-7_22
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Article ; Online: Structural basis for PRC2 engagement with chromatin.

Glancy, Eleanor / Ciferri, Claudio / Bracken, Adrian P

Current opinion in structural biology

2020 Volume 67, Page(s) 135–144

Abstract: The polycomb repressive complex 2 (PRC2) is a conserved multiprotein, repressive chromatin complex essential for development and maintenance of eukaryotic cellular identity. PRC2 comprises a trimeric core of SUZ12, EED and EZH1/2, which together with ... ...

Abstract	The polycomb repressive complex 2 (PRC2) is a conserved multiprotein, repressive chromatin complex essential for development and maintenance of eukaryotic cellular identity. PRC2 comprises a trimeric core of SUZ12, EED and EZH1/2, which together with RBBP4/7 is sufficient to catalyse mono-methylation, di-methylation and tri-methylation of histone H3 at lysine 27 (H3K27me1/2/3). These histone methyltransferase activities of PRC2 are deregulated in several human cancers and certain developmental disorders, such as Weaver Syndrome. Core PRC2 associates with several accessory proteins, which organise to define two main subassemblies, PRC2.1 and PRC2.2. Here we review new biochemical and structural studies that are providing critical insights into how core and accessory PRC2 subunits coordinate the faithful deposition of H3K27 methylations genome-wide.
MeSH term(s)	Chromatin ; Histones/metabolism ; Humans ; Methylation ; Polycomb Repressive Complex 2/genetics ; Polycomb Repressive Complex 2/metabolism ; Protein Processing, Post-Translational
Chemical Substances	Chromatin ; Histones ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
Language	English
Publishing date	2020-11-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2020.10.017
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Zs.A 3206: Show issues

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Article ; Online: Structure of the human secretory immunoglobulin M core.

Kumar, Nikit / Arthur, Christopher P / Ciferri, Claudio / Matsumoto, Marissa L

Structure (London, England : 1993)

2021 Volume 29, Issue 6, Page(s) 564–571.e3

Abstract: Immunoglobulins (Ig) A and M are the only human antibodies that form oligomers and undergo transcytosis to mucosal secretions via the polymeric Ig receptor (pIgR). When complexed with the J-chain (JC) and the secretory component (SC) of pIgR, secretory ... ...

Abstract	Immunoglobulins (Ig) A and M are the only human antibodies that form oligomers and undergo transcytosis to mucosal secretions via the polymeric Ig receptor (pIgR). When complexed with the J-chain (JC) and the secretory component (SC) of pIgR, secretory IgA and IgM (sIgA and sIgM) play critical roles in host-pathogen defense. Recently, we determined the structure of sIgA-Fc which elucidated the mechanism of polymeric IgA assembly and revealed an extensive binding interface between IgA-Fc, JC, and SC. Despite low sequence identity shared with IgA-Fc, IgM-Fc also undergoes JC-mediated assembly and binds pIgR. Here, we report the structure of sIgM-Fc and carryout a systematic comparison to sIgA-Fc. Our structural analysis reveals a remarkably conserved mechanism of JC-templated oligomerization and SC recognition of both IgM and IgA through a highly conserved network of interactions. These studies reveal the structurally conserved features of sIgM and sIgA required for function in mucosal immunity.
MeSH term(s)	Cell Line ; Humans ; Immunoglobulin A, Secretory/chemistry ; Immunoglobulin A, Secretory/metabolism ; Immunoglobulin J-Chains/metabolism ; Immunoglobulin M/chemistry ; Immunoglobulin M/metabolism ; Models, Molecular ; Protein Conformation ; Secretory Component/metabolism ; Structural Homology, Protein ; Transcytosis
Chemical Substances	Immunoglobulin A, Secretory ; Immunoglobulin J-Chains ; Immunoglobulin M ; Secretory Component ; secretory IgM
Language	English
Publishing date	2021-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2021.01.002
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Article ; Online: Structure of the secretory immunoglobulin A core.

Kumar, Nikit / Arthur, Christopher P / Ciferri, Claudio / Matsumoto, Marissa L

Science (New York, N.Y.)

2020 Volume 367, Issue 6481, Page(s) 1008–1014

Abstract: Secretory immunoglobulin A (sIgA) represents the immune system's first line of defense against mucosal pathogens. IgAs are transported across the epithelium, as dimers and higher-order polymers, by the polymeric immunoglobulin receptor (pIgR). Upon ... ...

Abstract	Secretory immunoglobulin A (sIgA) represents the immune system's first line of defense against mucosal pathogens. IgAs are transported across the epithelium, as dimers and higher-order polymers, by the polymeric immunoglobulin receptor (pIgR). Upon reaching the luminal side, sIgAs mediate host protection and pathogen neutralization. In recent years, an increasing amount of attention has been given to IgA as a novel therapeutic antibody. However, despite extensive studies, sIgA structures have remained elusive. Here, we determine the atomic resolution structures of dimeric, tetrameric, and pentameric IgA-Fc linked by the joining chain (JC) and in complex with the secretory component of the pIgR. We suggest a mechanism in which the JC templates IgA oligomerization and imparts asymmetry for pIgR binding and transcytosis. This framework will inform the design of future IgA-based therapeutics.
MeSH term(s)	Humans ; Immunoglobulin A, Secretory/chemistry ; Immunoglobulin Fc Fragments/chemistry ; Immunoglobulin J-Chains/chemistry ; Protein Multimerization ; Receptors, Polymeric Immunoglobulin/chemistry ; Transcytosis
Chemical Substances	Immunoglobulin A, Secretory ; Immunoglobulin Fc Fragments ; Immunoglobulin J-Chains ; Receptors, Polymeric Immunoglobulin
Language	English
Publishing date	2020-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaz5807
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

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Article ; Online: Percutaneous closure of accidentally subclavian artery catheterization: time to change first line approach?

Discalzi, Andrea / Maglia, Claudio / Ciferri, Fernanda / Mancini, Andrea / Gibello, Lorenzo / Calandri, Marco / Varetto, Gianfranco / Fonio, Paolo

CVIR endovascular

2022 Volume 5, Issue 1, Page(s) 23

Abstract: Purpose: To present our experience and provide a literature review dissertation about the use of a suture-mediated percutaneous closure device (Perclose Proglide -PP- Abbott Vascular Inc., Santa Clara, CA, USA) to achieve hemostasis for unintended ... ...

Abstract	Purpose: To present our experience and provide a literature review dissertation about the use of a suture-mediated percutaneous closure device (Perclose Proglide -PP- Abbott Vascular Inc., Santa Clara, CA, USA) to achieve hemostasis for unintended subclavian arterial catheterization during central venous line placement. Materials & methods: Since October 2020, we have successfully treated four consecutive patients with a central venous catheter (8 to 12 French) in the subclavian artery. In each patient, we released a PP, monitoring its efficacy by performing a subclavian angiogram and placing, as a rescue strategy, an 8 mm balloon catheter near the entry point of the misplaced catheter. Primary outcome is technical and clinical success. Technical success is defined as absence of bleeding signs at completion angiography, while clinical success is a composite endpoint defined as absence of hematoma, hemoglobin loss at 12 and 24 h, and absence of procedure-related reintervention (due to vessel stenosis, pseudoaneurysm or distal embolization). Results: Technical success was obtained in 75% of cases. In one patient a mild extravasation was resolved after 3 min of balloon catheter inflation. No early complications were observed for all patients. Conclusions: PP showed a safe and effective therapeutic option in case of unintentional arterial cannulation. It can be considered as first-line strategy, as it does not preclude the possibility to use other endovascular approaches in case of vascular closure device failure.
Language	English
Publishing date	2022-05-25
Publishing country	Switzerland
Document type	Journal Article
ISSN	2520-8934
ISSN (online)	2520-8934
DOI	10.1186/s42155-022-00300-7
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Article ; Online: Cryo-EM reveals an unprecedented binding site for Na

Kschonsak, Marc / Jao, Christine C / Arthur, Christopher P / Rohou, Alexis L / Bergeron, Philippe / Ortwine, Daniel F / McKerrall, Steven J / Hackos, David H / Deng, Lunbin / Chen, Jun / Li, Tianbo / Dragovich, Peter S / Volgraf, Matthew / Wright, Matthew R / Payandeh, Jian / Ciferri, Claudio / Tellis, John C

eLife

2023 Volume 12

Abstract: The voltage-gated sodium ( ... ...

Abstract	The voltage-gated sodium (Na
MeSH term(s)	Humans ; Cryoelectron Microscopy ; Ligands ; Protein Domains ; Binding Sites ; Structure-Activity Relationship
Chemical Substances	Ligands
Language	English
Publishing date	2023-03-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.84151
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Article ; Online: Structure-guided unlocking of Na

Noland, Cameron L / Chua, Han Chow / Kschonsak, Marc / Heusser, Stephanie Andrea / Braun, Nina / Chang, Timothy / Tam, Christine / Tang, Jia / Arthur, Christopher P / Ciferri, Claudio / Pless, Stephan Alexander / Payandeh, Jian

Nature communications

2022 Volume 13, Issue 1, Page(s) 1416

Abstract: Unlike classical voltage-gated sodium ( ... ...

Abstract	Unlike classical voltage-gated sodium (Na
MeSH term(s)	Calcium/metabolism ; Cations ; Humans ; Sodium/metabolism ; Tetrodotoxin/pharmacology
Chemical Substances	Cations ; Tetrodotoxin (4368-28-9) ; Sodium (9NEZ333N27) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-03-17
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/s41467-022-28984-4
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Article ; Online: Correction to: Effectiveness and Safety of Different Vascular Closure Devices: Multicentre Prospective Observational Study.

Ierardi, Anna Maria / Coppola, Andrea / Renzulli, Matteo / Piacentino, Filippo / Fontana, Federico / Paladini, Andrea / Guzzardi, Giuseppe / Semeraro, Vittorio / Di Stasi, Carmine / Giurazza, Francesco / Niola, Raffaella / Stefanini, Matteo / Contegiacomo, Andrea / Carrubba, Claudio / Discalzi, Andrea / Ciferri, Fernanda / Carriero, Serena / Lanza, Carolina / Biondetti, Pierpaolo /

Coniglio, Giovanni / Fonio, Paolo / Venturini, Massimo / Carrafiello, Gianpaolo / Del Giudice, Costantino

Cardiovascular and interventional radiology

2023 Volume 46, Issue 9, Page(s) 1301

Language	English
Publishing date	2023-07-24
Publishing country	United States
Document type	Published Erratum
ZDB-ID	603082-8
ISSN	1432-086X ; 0342-7196 ; 0174-1551
ISSN (online)	1432-086X
ISSN	0342-7196 ; 0174-1551
DOI	10.1007/s00270-023-03513-y
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Zs.A 1378: Show issues

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Article ; Online: Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 Å Resolution.

Migl, David / Kschonsak, Marc / Arthur, Christopher P / Khin, Yadana / Harrison, Stephen C / Ciferri, Claudio / Dimitrova, Yoana N

Structure (London, England : 1993)

2020 Volume 28, Issue 3, Page(s) 363–370.e3

Abstract: Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant ... ...

Abstract	Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant Cse4
MeSH term(s)	Chromosomal Proteins, Non-Histone/chemistry ; Chromosomal Proteins, Non-Histone/metabolism ; Cryoelectron Microscopy ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Histones/chemistry ; Histones/metabolism ; Kinetochores/chemistry ; Kinetochores/metabolism ; Models, Molecular ; Nucleosomes/chemistry ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	CSE4 protein, S cerevisiae ; Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; Histones ; Nucleosomes ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2020-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2019.12.002
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Zs.A 4141: Show issues

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Article ; Online: Protein domain mapping by internal labeling and single particle electron microscopy.

Ciferri, Claudio / Lander, Gabriel C / Nogales, Eva

Journal of structural biology

2015 Volume 192, Issue 2, Page(s) 159–162

Abstract: In recent years, electron microscopy (EM) and single particle analysis have emerged as essential tools for investigating the architecture of large biological complexes. When high resolution is achievable, crystal structure docking and de-novo modeling ... ...

Abstract	In recent years, electron microscopy (EM) and single particle analysis have emerged as essential tools for investigating the architecture of large biological complexes. When high resolution is achievable, crystal structure docking and de-novo modeling allows for precise assignment of individual protein domain sequences. However, the achievable resolution may limit the ability to do so, especially when small or flexible complexes are under study. In such cases, protein labeling has emerged as an important complementary tool to characterize domain architecture and elucidate functional mechanistic details. All labeling strategies proposed to date are either focused on the identification of the position of protein termini or require multi-step labeling strategies, potentially interfering with the final labeling efficiency. Here we describe a strategy for determining the position of internal protein domains within EM maps using a recombinant one-step labeling approach named Efficient Mapping by Internal Labeling (EMIL). EMIL takes advantage of the close spatial proximity of the GFP's N- and C-termini to generate protein chimeras containing an internal GFP at desired locations along the main protein chain. We apply this method to characterize the subunit domain localization of the human Polycomb Repressive Complex 2.
MeSH term(s)	Green Fluorescent Proteins/chemistry ; Humans ; Microscopy, Electron/methods ; Models, Molecular ; Polycomb Repressive Complex 2/chemistry ; Polycomb Repressive Complex 2/ultrastructure ; Protein Structure, Tertiary ; Staining and Labeling/methods
Chemical Substances	Green Fluorescent Proteins (147336-22-9) ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
Language	English
Publishing date	2015-09-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2015.09.016
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