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  1. Book: Kras

    Stephen, Andrew G. / Esposito, Dominic

    methods and protocols

    (Methods in molecular biology ; 2789 ; Springer protocols)

    2024  

    Author's details edited by Andrew G. Stephen, Dominic Esposito
    Series title Methods in molecular biology ; 2789
    Springer protocols
    Collection
    Language English
    Size xi, 365 Seiten, Illustrationen
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT030718320
    ISBN 9781071638217 ; 1071638211
    Database Catalogue ZB MED Medicine, Health

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  2. Article ; Online: Unexpected tobacco etch virus (TEV) protease cleavage of recombinant human proteins.

    Beaumont, Lauren P / Mehalko, Jennifer / Johnson, Adam / Wall, Vanessa E / Esposito, Dominic

    Protein expression and purification

    2024  Volume 220, Page(s) 106488

    Abstract: The tobacco etch virus (TEV) protease is a commonly used reagent for removal of solubility and purification tags from recombinant proteins and is cited as being highly specific for its canonical cleavage site. Flexibility in some amino acids within this ... ...

    Abstract The tobacco etch virus (TEV) protease is a commonly used reagent for removal of solubility and purification tags from recombinant proteins and is cited as being highly specific for its canonical cleavage site. Flexibility in some amino acids within this recognition sequence has been described in the literature but researchers generally assume few native human proteins will carry off-target sequences for TEV cleavage. We report here the aberrant cleavage of three human proteins with non-canonical TEV protease cleavage sites and identify broader sequence specificity rules that can be used to predict unwanted cleavage of recombinant proteins. Using these rules, 456 human proteins were identified that could be substrates for unwanted TEV protease cleavage.
    Language English
    Publishing date 2024-04-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1055455-5
    ISSN 1096-0279 ; 1046-5928
    ISSN (online) 1096-0279
    ISSN 1046-5928
    DOI 10.1016/j.pep.2024.106488
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Material strategies and considerations for serologic testing of global infectious diseases.

    Manning, Jessica E / Duffy, Patrick E / Esposito, Dominic / Sadtler, Kaitlyn

    MRS bulletin

    2021  Volume 46, Issue 9, Page(s) 854–858

    Language English
    Publishing date 2021-09-13
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2136359-6
    ISSN 1938-1425 ; 0883-7694
    ISSN (online) 1938-1425
    ISSN 0883-7694
    DOI 10.1557/s43577-021-00167-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Polycistronic baculovirus expression of SUGT1 enables high-yield production of recombinant leucine-rich repeat proteins and protein complexes.

    Snead, Kelly / Wall, Vanessa / Ambrose, Hannah / Esposito, Dominic / Drew, Matthew

    Protein expression and purification

    2022  Volume 193, Page(s) 106061

    Abstract: The SHOC2-MRAS-PPP1CA (SMP) complex is a holoenzyme that plays a vital role in the MAP kinase signaling pathway. Previous attempts to produce this challenging three-protein complex have relied on co-infection with multiple viruses and the use of affinity ...

    Abstract The SHOC2-MRAS-PPP1CA (SMP) complex is a holoenzyme that plays a vital role in the MAP kinase signaling pathway. Previous attempts to produce this challenging three-protein complex have relied on co-infection with multiple viruses and the use of affinity tags to attempt to isolate functional recombinant protein complexes. Leucine-rich repeat containing proteins have been historically challenging to express, and we hypothesized that co-expression of appropriate chaperones may be necessary for optimal production. We describe here how the SUGT1 chaperone can, in conjunction with polycistronic protein expression in baculovirus-infected insect cells, dramatically enhance production yield and quality of recombinant SHOC2, the SMP complex, and other leucine-rich repeat proteins.
    MeSH term(s) Baculoviridae/genetics ; Leucine-Rich Repeat Proteins ; MAP Kinase Signaling System ; Recombinant Proteins/genetics
    Chemical Substances Leucine-Rich Repeat Proteins ; Recombinant Proteins
    Language English
    Publishing date 2022-02-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1055455-5
    ISSN 1096-0279 ; 1046-5928
    ISSN (online) 1096-0279
    ISSN 1046-5928
    DOI 10.1016/j.pep.2022.106061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A review of alternative promoters for optimal recombinant protein expression in baculovirus-infected insect cells.

    Grose, Carissa / Putman, Zoe / Esposito, Dominic

    Protein expression and purification

    2021  Volume 186, Page(s) 105924

    Abstract: Generating recombinant proteins in insect cells has been made possible via the use of the Baculovirus Expression Vector System (BEVS). Despite the success of many proteins via this platform, some targets remain a challenge due to issues such as ... ...

    Abstract Generating recombinant proteins in insect cells has been made possible via the use of the Baculovirus Expression Vector System (BEVS). Despite the success of many proteins via this platform, some targets remain a challenge due to issues such as cytopathic effects, the unpredictable nature of co-infection and co-expressions, and baculovirus genome instability. Many promoters have been assayed for the purpose of expressing diverse proteins in insect cells, and yet there remains a lack of implementation of those results when reviewing the landscape of commercially available baculovirus vectors. In advancing the platform to produce a greater variety of proteins and complexes, the development of such constructs cannot be avoided. A better understanding of viral gene regulation and promoter options including viral, synthetic, and insect-derived promoters will be beneficial to researchers looking to utilize BEVS by recruiting these intricate mechanisms of gene regulation for heterologous gene expression. Here we summarize some of the developments that could be utilized to improve the expression of recombinant proteins and multi-protein complexes in insect cells.
    MeSH term(s) Animals ; Baculoviridae/genetics ; Cells, Cultured ; Genetic Vectors/genetics ; Insecta/cytology ; Promoter Regions, Genetic/genetics ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sf9 Cells
    Chemical Substances Recombinant Proteins
    Language English
    Publishing date 2021-06-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1055455-5
    ISSN 1096-0279 ; 1046-5928
    ISSN (online) 1096-0279
    ISSN 1046-5928
    DOI 10.1016/j.pep.2021.105924
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  6. Article ; Online: Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties.

    Whitley, Matthew J / Tran, Timothy H / Rigby, Megan / Yi, Ming / Dharmaiah, Srisathiyanarayanan / Waybright, Timothy J / Ramakrishnan, Nitya / Perkins, Shelley / Taylor, Troy / Messing, Simon / Esposito, Dominic / Nissley, Dwight V / McCormick, Frank / Stephen, Andrew G / Turbyville, Thomas / Cornilescu, Gabriel / Simanshu, Dhirendra K

    Science advances

    2024  Volume 10, Issue 7, Page(s) eadj4137

    Abstract: ... ...

    Abstract KRAS
    MeSH term(s) Humans ; Molecular Conformation ; Neoplasms ; Protein Isoforms/genetics ; Proto-Oncogene Proteins p21(ras)/genetics
    Chemical Substances Protein Isoforms ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
    Language English
    Publishing date 2024-02-14
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adj4137
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: The multidrug resistance transporter P-glycoprotein confers resistance to ferroptosis inducers.

    Frye, William J E / Huff, Lyn M / González Dalmasy, José M / Salazar, Paula / Carter, Rachel M / Gensler, Ryan T / Esposito, Dominic / Robey, Robert W / Ambudkar, Suresh V / Gottesman, Michael M

    Cancer drug resistance (Alhambra, Calif.)

    2023  Volume 6, Issue 6, Page(s) 468–480

    Abstract: Aim: ...

    Abstract Aim:
    Language English
    Publishing date 2023-07-27
    Publishing country United States
    Document type Journal Article
    ISSN 2578-532X
    ISSN (online) 2578-532X
    DOI 10.20517/cdr.2023.29
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements.

    Finci, Lorenzo I / Chakrabarti, Mayukh / Gulten, Gulcin / Finney, Joseph / Grose, Carissa / Fox, Tara / Yang, Renbin / Nissley, Dwight V / McCormick, Frank / Esposito, Dominic / Balius, Trent E / Simanshu, Dhirendra K

    Communications biology

    2024  Volume 7, Issue 1, Page(s) 260

    Abstract: RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for ... ...

    Abstract RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1's unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.
    MeSH term(s) Humans ; Cell Cycle Proteins/metabolism ; Protein Binding ; Chaperonins/chemistry ; Molecular Chaperones/metabolism ; HSP90 Heat-Shock Proteins
    Chemical Substances Cell Cycle Proteins ; Chaperonins (EC 3.6.1.-) ; Molecular Chaperones ; HSP90 Heat-Shock Proteins ; CDC37 protein, human
    Language English
    Publishing date 2024-03-02
    Publishing country England
    Document type Journal Article
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-024-05959-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases.

    Frank, Peter H / Hong, Min / Higgins, Brianna / Perkins, Shelley / Taylor, Troy / Wall, Vanessa E / Drew, Matthew / Waybright, Timothy / Gillette, William / Esposito, Dominic / Messing, Simon

    Protein expression and purification

    2024  Volume 218, Page(s) 106446

    Abstract: The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active ... ...

    Abstract The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active protein, it needs to undergo nucleotide exchange to a non-hydrolysable GTP analog. Calf intestine alkaline phosphatase bound to agarose beads (CIP-agarose) is regularly used in a nucleotide exchange protocol to replace GDP with a non-hydrolysable analog. Due to pandemic supply problems and product shortages, we found the need for an alternative to this commercially available product. Here we describe how we generated a bacterial alkaline phosphatase (BAP) with an affinity tag bound to an agarose bead. This BAP completely exchanges the nucleotide in our samples, thereby demonstrating an alternative to the commercially available product using generally available laboratory equipment.
    MeSH term(s) Monomeric GTP-Binding Proteins/metabolism ; Nucleotides ; Alkaline Phosphatase/genetics ; Alkaline Phosphatase/metabolism ; Sepharose ; Guanosine Triphosphate/metabolism ; Guanosine Diphosphate/metabolism
    Chemical Substances Monomeric GTP-Binding Proteins (EC 3.6.5.2) ; Nucleotides ; Alkaline Phosphatase (EC 3.1.3.1) ; Sepharose (9012-36-6) ; Guanosine Triphosphate (86-01-1) ; Guanosine Diphosphate (146-91-8)
    Language English
    Publishing date 2024-02-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1055455-5
    ISSN 1096-0279 ; 1046-5928
    ISSN (online) 1096-0279
    ISSN 1046-5928
    DOI 10.1016/j.pep.2024.106446
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid.

    Zhao, Huaying / Syed, Abdullah M / Khalid, Mir M / Nguyen, Ai / Ciling, Alison / Wu, Di / Yau, Wai-Ming / Srinivasan, Sanjana / Esposito, Dominic / Doudna, Jennifer A / Piszczek, Grzegorz / Ott, Melanie / Schuck, Peter

    Nucleic acids research

    2024  

    Abstract: The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high ... ...

    Abstract The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to ancestral and mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining nucleocapsid protein variants in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multivalent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
    Language English
    Publishing date 2024-04-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae256
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