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  1. Article ; Online: Phospholipids Differentially Regulate Ca

    Lawrence, Sophie A S / Kirschbaum, Carla / Bennett, Jack L / Lutomski, Corinne A / El-Baba, Tarick J / Robinson, Carol V

    ACS chemical biology

    2024  

    Abstract: Synaptotagmin-1 (Syt-1) is a calcium sensing protein that is resident in synaptic vesicles. It is well established that Syt-1 is essential for fast and synchronous neurotransmitter release. However, the role of ... ...

    Abstract Synaptotagmin-1 (Syt-1) is a calcium sensing protein that is resident in synaptic vesicles. It is well established that Syt-1 is essential for fast and synchronous neurotransmitter release. However, the role of Ca
    Language English
    Publishing date 2024-04-02
    Publishing country United States
    Document type Journal Article
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.3c00772
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Tautomerization of H

    Beckett, Daniel / El-Baba, Tarick J / Zhang, Zhichao / Clemmer, David E / Raghavachari, Krishnan

    The journal of physical chemistry. A

    2023  Volume 127, Issue 30, Page(s) 6282–6291

    Abstract: Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of the singly protonated peptide ... ...

    Abstract Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of the singly protonated peptide H
    MeSH term(s) Hydrogen Bonding ; Peptides/chemistry ; Hydrogen/chemistry ; Models, Molecular ; Protein Structure, Tertiary ; Entropy ; Methylation
    Chemical Substances Peptides ; Hydrogen (7YNJ3PO35Z)
    Language English
    Publishing date 2023-07-25
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.3c03744
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Rationalizing the Optimization of Detergents for Membrane Protein Purification.

    Urner, Leonhard H / Junge, Florian / Fiorentino, Francesco / El-Baba, Tarick J / Shutin, Denis / Nölte, Gideon / Haag, Rainer / Robinson, Carol V

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2023  Volume 29, Issue 30, Page(s) e202300159

    Abstract: Membrane protein purification by means of detergents is key to isolating membrane-bound therapeutic targets. The role of the detergent structure in this process, however, is not well understood. Detergents are optimized empirically, leading to failed ... ...

    Abstract Membrane protein purification by means of detergents is key to isolating membrane-bound therapeutic targets. The role of the detergent structure in this process, however, is not well understood. Detergents are optimized empirically, leading to failed preparations, and thereby raising costs. Here we evaluate the utility of the hydrophilic-lipophilic balance (HLB) concept, which was introduced by Griffin in 1949, for guiding the optimization of the hydrophobic tail in first-generation, dendritic oligoglycerol detergents ([G1] OGDs). Our findings deliver qualitative HLB guidelines for rationalizing the optimization of detergents. Moreover, [G1] OGDs exhibit strongly delipidating properties, regardless of the structure of the hydrophobic tail, which delivers a methodological enabling step for investigating binding strengths of endogenous lipids and their role for membrane protein oligomerization. Our findings will facilitate the analysis of challenging drug targets in the future.
    MeSH term(s) Detergents/chemistry ; Hydrophobic and Hydrophilic Interactions ; Membrane Proteins/chemistry ; alpha-Synuclein
    Chemical Substances Detergents ; FUS protein, human ; Membrane Proteins ; alpha-Synuclein
    Language English
    Publishing date 2023-04-19
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-X
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.202300159
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Variation of CI-2 Conformers upon Addition of Methanol to Water: An IMS-MS-Based Thermodynamic Analysis.

    Pan, Hua / Raab, Shannon A / El-Baba, Tarick J / Schrecke, Samantha R / Laganowsky, Arthur / Russell, David H / Clemmer, David E

    The journal of physical chemistry. A

    2023  Volume 127, Issue 45, Page(s) 9399–9408

    Abstract: Chymotrypsin inhibitor 2 (CI-2) is a well-studied, textbook example of a cooperative, two-state, native ↔ denatured folding transition. A recent hybrid ion mobility spectrometry (IMS)/mass spectrometry (MS) thermal denaturation study of CI-2 (the well- ... ...

    Abstract Chymotrypsin inhibitor 2 (CI-2) is a well-studied, textbook example of a cooperative, two-state, native ↔ denatured folding transition. A recent hybrid ion mobility spectrometry (IMS)/mass spectrometry (MS) thermal denaturation study of CI-2 (the well-studied truncated 64-residue model) in water reported evidence that this two-state transition involves numerous (∼41) unique native and non-native (denatured) solution conformations. The characterization of so many, often low-abundance, states is possible because of the very high dynamic range of IMS-MS measurements of ionic species that are produced upon electrospraying CI-2 solutions from a variable temperature electrospray ionization source. A thermodynamic analysis of these states revealed large changes in enthalpy (Δ
    Language English
    Publishing date 2023-11-07
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.3c03651
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Detergents with Scalable Properties Identify Noncanonical Lipopolysaccharide Binding to Bacterial Inner Membrane Proteins.

    Urner, Leonhard H / Fiorentino, Francesco / Shutin, Denis / Sauer, Joshua B / Agasid, Mark T / El-Baba, Tarick J / Bolla, Jani R / Stansfeld, Phillip J / Robinson, Carol V

    Journal of the American Chemical Society

    2024  

    Abstract: Lipopolysaccharide (LPS) is vital for maintaining the outer membrane barrier in Gram-negative bacteria. LPS is also frequently obtained in complex with the inner membrane proteins after detergent purification. The question of whether or not LPS binding ... ...

    Abstract Lipopolysaccharide (LPS) is vital for maintaining the outer membrane barrier in Gram-negative bacteria. LPS is also frequently obtained in complex with the inner membrane proteins after detergent purification. The question of whether or not LPS binding to inner membrane proteins not involved in outer membrane biogenesis reflects native lipid environments remains unclear. Here, we leverage the control of the hydrophilic-lipophilic balance and packing parameter concepts to chemically tune detergents that can be used to qualitatively differentiate the degree to which proteins copurify with phospholipids (PLs) and/or LPS. Given the scalable properties of these detergents, we demonstrate a detergent fine-tuning that enables the facile investigation of intact proteins and their complexes with lipids by native mass spectrometry (nMS). We conclude that LPS, a lipid that is believed to be important for outer membranes, can also affect the activity of membrane proteins that are currently not assigned to be involved in outer membrane biogenesis. Our results deliver a scalable detergent chemistry for a streamlined biophysical characterization of protein-lipid interactions, provide a rationale for the high affinity of LPS-protein binding, and identify noncanonical associations between LPS and inner membrane proteins with relevance for membrane biology and antibiotic research.
    Language English
    Publishing date 2024-04-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.3c14358
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Solution thermochemistry of concanavalin A tetramer conformers measured by variable-temperature ESI-IMS-MS.

    El-Baba, Tarick J / Clemmer, David E

    International journal of mass spectrometry

    2019  Volume 443, Page(s) 93–100

    Abstract: Variable-temperature nano-electrospray ionization coupled with ion mobility spectrometry-mass spectrometry is used to investigate the thermal denaturation of the tetrameric protein concanavalin A. As the solution temperature is increased, changes in mass ...

    Abstract Variable-temperature nano-electrospray ionization coupled with ion mobility spectrometry-mass spectrometry is used to investigate the thermal denaturation of the tetrameric protein concanavalin A. As the solution temperature is increased, changes in mass spectra and collision cross section distributions provide evidence for discrete structural changes that occur at temperatures that are ~40 to 50 degrees below the temperature required for tetramer dissociation. The subtle structural changes are associated with four distinct tetramer conformations with unique melting temperatures. Gibbs-Helmholtz analysis of the free energies determined with respect to the most abundant "native" state yields heat capacities of ΔC
    Language English
    Publishing date 2019-06-15
    Publishing country Netherlands
    Document type Journal Article
    ISSN 1387-3806
    ISSN 1387-3806
    DOI 10.1016/j.ijms.2019.06.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies.

    Lutomski, Corinne A / El-Baba, Tarick J / Bolla, Jani R / Robinson, Carol V

    JACS Au

    2021  Volume 1, Issue 8, Page(s) 1147–1157

    Abstract: The SARS-CoV-2 nucleocapsid (N) protein is a highly immunogenic viral protein that plays essential roles in replication and virion assembly. Here, using native mass spectrometry, we show that dimers are the functional unit of ribonucleoprotein assembly ... ...

    Abstract The SARS-CoV-2 nucleocapsid (N) protein is a highly immunogenic viral protein that plays essential roles in replication and virion assembly. Here, using native mass spectrometry, we show that dimers are the functional unit of ribonucleoprotein assembly and that N protein binds RNA with a preference for GGG motifs, a common motif in coronavirus packaging signals. Unexpectedly, proteolytic processing of N protein resulted in the formation of additional proteoforms. The N-terminal proteoforms bind RNA, with the same preference for GGG motifs, and bind to cyclophilin A, an interaction which can be abolished by approved immunosuppressant cyclosporin A. Furthermore, N proteoforms showed significantly different interactions with IgM, IgG, and IgA antibodies from convalescent plasma. Notably, the C-terminal proteoform exhibited a heightened interaction with convalescent antibodies, suggesting the antigenic epitope is localized to the C-terminus. Overall, the different interactions of N proteoforms highlight potential avenues for therapeutic intervention and identify a stable and immunogenic proteoform as a possible candidate for immune-directed therapies.
    Language English
    Publishing date 2021-06-15
    Publishing country United States
    Document type Journal Article
    ISSN 2691-3704
    ISSN (online) 2691-3704
    DOI 10.1021/jacsau.1c00139
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Uncovering the Role of

    El-Baba, Tarick J / Lutomski, Corinne A / Burnap, Sean A / Bolla, Jani R / Baker, Lindsay A / Baldwin, Andrew J / Struwe, Weston B / Robinson, Carol V

    Journal of the American Chemical Society

    2023  Volume 145, Issue 14, Page(s) 8021–8032

    Abstract: Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address ... ...

    Abstract Interactions between the SARS-CoV-2 Spike protein and ACE2 are one of the most scrutinized reactions of our time. Yet, questions remain as to the impact of glycans on mediating ACE2 dimerization and downstream interactions with Spike. Here, we address these unanswered questions by combining a glycoengineering strategy with high-resolution native mass spectrometry (MS) to investigate the impact of
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Angiotensin-Converting Enzyme 2/chemistry ; Protein Binding ; Mass Spectrometry ; Polysaccharides
    Chemical Substances spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Polysaccharides
    Language English
    Publishing date 2023-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.3c00291
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

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  9. Article ; Online: Multiple Roles of SARS-CoV‑2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies

    Corinne A. Lutomski / Tarick J. El-Baba / Jani R. Bolla / Carol V. Robinson

    JACS Au, Vol 1, Iss 8, Pp 1147-

    2021  Volume 1157

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition.

    Noske, Gabriela Dias / Song, Yun / Fernandes, Rafaela Sachetto / Chalk, Rod / Elmassoudi, Haitem / Koekemoer, Lizbé / Owen, C David / El-Baba, Tarick J / Robinson, Carol V / Oliva, Glaucius / Godoy, Andre Schutzer

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 1545

    Abstract: The main protease from SARS-CoV-2 ( ... ...

    Abstract The main protease from SARS-CoV-2 (M
    MeSH term(s) Antiviral Agents ; Protease Inhibitors/pharmacology ; SARS-CoV-2/enzymology ; Coronavirus 3C Proteases/chemistry
    Chemical Substances 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Antiviral Agents ; Protease Inhibitors ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Language English
    Publishing date 2023-03-20
    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/s41467-023-37035-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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