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  1. Article: Autoinhibited kinesin-1 adopts a hierarchical folding pattern.

    Tan, Zhenyu / Yue, Yang / da Veiga Leprevost, Felipe / Haynes, Sarah E / Basrur, Venkatesha / Nesvizhskii, Alexey I / Verhey, Kristen J / Cianfrocco, Michael A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 ... ...

    Abstract Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
    Language English
    Publishing date 2023-09-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.26.525761
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Identification of LMAN1- and SURF4-Dependent Secretory Cargoes.

    Tang, Vi T / Abbineni, Prabhodh S / Veiga Leprevost, Felipe da / Basrur, Venkatesha / Khoriaty, Rami / Emmer, Brian T / Nesvizhskii, Alexey I / Ginsburg, David

    Journal of proteome research

    2023  Volume 22, Issue 11, Page(s) 3439–3446

    Abstract: Most proteins secreted into the extracellular space are first recruited from the endoplasmic reticulum into coat protein complex II (COPII)-coated vesicles or tubules that facilitate their transport to the Golgi apparatus. Although several secreted ... ...

    Abstract Most proteins secreted into the extracellular space are first recruited from the endoplasmic reticulum into coat protein complex II (COPII)-coated vesicles or tubules that facilitate their transport to the Golgi apparatus. Although several secreted proteins have been shown to be actively recruited into COPII vesicles and tubules by the cargo receptors LMAN1 and SURF4, the full cargo repertoire of these receptors is unknown. We now report mass spectrometry analysis of conditioned media and cell lysates from HuH7 cells CRISPR targeted to inactivate the
    MeSH term(s) Humans ; Carrier Proteins/metabolism ; Endoplasmic Reticulum/metabolism ; Golgi Apparatus ; Membrane Proteins/metabolism ; Protein Transport
    Chemical Substances Carrier Proteins ; Membrane Proteins ; SURF4 protein, human
    Language English
    Publishing date 2023-10-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00259
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Identification of LMAN1 and SURF4 dependent secretory cargoes.

    Tang, Vi T / Abbineni, Prabhodh S / Leprevost, Felipe da Veiga / Basrur, Venkatesha / Emmer, Brian T / Nesvizhskii, Alexey I / Ginsburg, David

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Most proteins secreted into the extracellular space are first recruited from the endoplasmic reticulum into coat protein complex II (COPII)-coated vesicles or tubules that facilitate their transport to the Golgi apparatus. Although several secreted ... ...

    Abstract Most proteins secreted into the extracellular space are first recruited from the endoplasmic reticulum into coat protein complex II (COPII)-coated vesicles or tubules that facilitate their transport to the Golgi apparatus. Although several secreted proteins have been shown to be actively recruited into COPII vesicles/tubules by the cargo receptors LMAN1 and SURF4, the full cargo repertoire of these receptors is unknown. We now report mass spectrometry analysis of conditioned media and cell lysates from HuH7 cells CRISPR targeted to inactivate the
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.06.535922
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Autoinhibited kinesin-1 adopts a hierarchical folding pattern.

    Tan, Zhenyu / Yue, Yang / Leprevost, Felipe / Haynes, Sarah / Basrur, Venkatesha / Nesvizhskii, Alexey I / Verhey, Kristen J / Cianfrocco, Michael A

    eLife

    2023  Volume 12

    Abstract: Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 ... ...

    Abstract Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine crosslinking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer (kinesin-1 heavy chain [KHC]) and kinesin-1 heterotetramer (KHC bound to kinesin light chain 1 [KLC1]). Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled-coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
    MeSH term(s) Kinesins ; Microtubule-Associated Proteins ; Biological Transport ; Consensus ; Mass Spectrometry
    Chemical Substances Kinesins (EC 3.6.4.4) ; Microtubule-Associated Proteins
    Language English
    Publishing date 2023-11-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.86776
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Differences in Extracellular Vesicle Protein Cargo Are Dependent on Head and Neck Squamous Cell Carcinoma Cell of Origin and Human Papillomavirus Status.

    Goudsmit, Christine / da Veiga Leprevost, Felipe / Basrur, Venkatesha / Peters, Lila / Nesvizhskii, Alexey / Walline, Heather

    Cancers

    2021  Volume 13, Issue 15

    Abstract: To identify potential extracellular vesicle (EV) biomarkers in head and neck squamous cell carcinoma (HNSCC), we evaluated EV protein cargo and whole cell lysates (WCL) from HPV-positive and -negative HNSCC cell lines, as well as normal oral ... ...

    Abstract To identify potential extracellular vesicle (EV) biomarkers in head and neck squamous cell carcinoma (HNSCC), we evaluated EV protein cargo and whole cell lysates (WCL) from HPV-positive and -negative HNSCC cell lines, as well as normal oral keratinocytes and HPV16-transformed cells. EVs were isolated from serum-depleted, conditioned cell culture media by polyethylene glycol (PEG) precipitation/ultracentrifugation. EV and WCL preparations were analyzed by LC-MS/MS. Candidate proteins detected at significantly higher levels in EV compared with WCL, or compared with EV from normal oral keratinocytes, were identified and confirmed by Wes Simple Western protein analysis. Our findings suggest that these proteins may be potential HNSCC EV markers as proteins that may be (1) selectively included in EV cargo for export from the cell as a strategy for metastasis, tumor cell survival, or modification of tumor microenvironment, or (2) representative of originating cell composition, which may be developed for diagnostic or prognostic use in clinical liquid biopsy applications. This work demonstrates that our method can be used to reliably detect EV proteins from HNSCC, normal keratinocyte, and transformed cell lines. Furthermore, this work has identified HNSCC EV protein candidates for continued evaluation, specifically tenascin-C, HLA-A, E-cadherin, EGFR, EPHA2, and cytokeratin 19.
    Language English
    Publishing date 2021-07-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers13153714
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Pak2-mediated phosphorylation promotes RORγt ubiquitination and inhibits colonic inflammation.

    Kathania, Mahesh / Kumar, Ritesh / Lenou, Elviche Taskem / Basrur, Venkatesha / Theiss, Arianne L / Chernoff, Jonathan / Venuprasad, K

    Cell reports

    2022  Volume 40, Issue 11, Page(s) 111345

    Abstract: Dysregulated interleukin-17 (IL-17) expression and its downstream signaling is strongly linked to inflammatory bowel diseases (IBDs). However, the molecular mechanisms by which the function of RORγt, the transcription factor of IL-17, is regulated ... ...

    Abstract Dysregulated interleukin-17 (IL-17) expression and its downstream signaling is strongly linked to inflammatory bowel diseases (IBDs). However, the molecular mechanisms by which the function of RORγt, the transcription factor of IL-17, is regulated remains elusive. By a mass spectrometry-based approach, we identify that Pak2, a serine (S)/threonine (T) kinase, directly associates with RORγt. Pak2 recognizes a conserved KRLS motif within RORγt and phosphorylates the S-316 within this motif. Genetic deletion of Pak2 in Th17 cells reduces RORγt phosphorylation, increases IL-17 expression, and induces severe colitis upon adoptive transfer to Rag1
    MeSH term(s) Animals ; Colitis ; Inflammation ; Interleukin-17/metabolism ; Mice ; Nuclear Receptor Subfamily 1, Group F, Member 3/genetics ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Phosphorylation ; Ubiquitination ; p21-Activated Kinases/metabolism
    Chemical Substances Interleukin-17 ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Pak2 protein, mouse (EC 2.7.11.1) ; p21-Activated Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2022-09-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2022.111345
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Mechanistic convergence across initiation sites for RAN translation in fragile X associated tremor ataxia syndrome.

    Zhang, Yuan / Glineburg, M Rebecca / Basrur, Venkatesha / Conlon, Kevin / Wright, Shannon E / Krans, Amy / Hall, Deborah A / Todd, Peter K

    Human molecular genetics

    2022  Volume 31, Issue 14, Page(s) 2317–2332

    Abstract: Repeat associated non-AUG (RAN) translation of CGG repeats in the 5'UTR of FMR1 produces toxic proteins that contribute to fragile X-associated tremor/ataxia syndrome (FXTAS) pathogenesis. The most abundant RAN product, FMRpolyG, initiates predominantly ... ...

    Abstract Repeat associated non-AUG (RAN) translation of CGG repeats in the 5'UTR of FMR1 produces toxic proteins that contribute to fragile X-associated tremor/ataxia syndrome (FXTAS) pathogenesis. The most abundant RAN product, FMRpolyG, initiates predominantly at an ACG upstream of the repeat. Accurate FMRpolyG measurements in FXTAS patients are lacking. We used data-dependent acquisition and parallel reaction monitoring (PRM) mass spectrometry coupled with stable isotope labeled standard peptides to identify signature FMRpolyG fragments in patient samples. Following immunoprecipitation, PRM detected FMRpolyG signature peptides in transfected cells, and FXTAS tissues and cells, but not in controls. We identified two amino-terminal peptides: an ACG-initiated Ac-MEAPLPGGVR and a GUG-initiated Ac-TEAPLPGGVR, as well as evidence for RAN translation initiation within the CGG repeat itself in two reading frames. Initiation at all sites increased following cellular stress, decreased following eIF1 overexpression and was eIF4A and M7G cap-dependent. These data demonstrate that FMRpolyG is quantifiable in human samples and FMR1 RAN translation initiates via similar mechanisms for near-cognate codons and within the repeat through processes dependent on available initiation factors and cellular environment.
    MeSH term(s) Ataxia/genetics ; Fragile X Mental Retardation Protein/genetics ; Fragile X Syndrome/genetics ; Humans ; Peptides/metabolism ; Tremor/genetics ; Trinucleotide Repeat Expansion ; ran GTP-Binding Protein/genetics
    Chemical Substances FMR1 protein, human ; Peptides ; RAN protein, human ; Fragile X Mental Retardation Protein (139135-51-6) ; ran GTP-Binding Protein (EC 3.6.5.2)
    Language English
    Publishing date 2022-01-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddab353
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Identification of secreted proteins by comparison of protein abundance in conditioned media and cell lysates.

    Abbineni, Prabhodh S / Tang, Vi T / da Veiga Leprevost, Felipe / Basrur, Venkatesha / Xiang, Jie / Nesvizhskii, Alexey I / Ginsburg, David

    Analytical biochemistry

    2022  Volume 655, Page(s) 114846

    Abstract: Analysis of the full spectrum of secreted proteins in cell culture is complicated by leakage of intracellular proteins from damaged cells. To address this issue, we compared the abundance of individual proteins between the cell lysate and the conditioned ...

    Abstract Analysis of the full spectrum of secreted proteins in cell culture is complicated by leakage of intracellular proteins from damaged cells. To address this issue, we compared the abundance of individual proteins between the cell lysate and the conditioned medium, reasoning that secreted proteins should be relatively more abundant in the conditioned medium. Marked enrichment for signal-peptide-bearing proteins with increasing conditioned media to cell lysate ratio, as well loss of this signal following brefeldin A treatment, confirmed the sensitivity and specificity of this approach. The subset of proteins demonstrating increased conditioned media to cell lysate ratio in the presence of Brefeldin A identified candidates for unconventional secretion via a pathway independent of ER to Golgi trafficking.
    MeSH term(s) Brefeldin A/metabolism ; Brefeldin A/pharmacology ; Culture Media, Conditioned/metabolism ; Golgi Apparatus/metabolism ; Proteins/metabolism
    Chemical Substances Culture Media, Conditioned ; Proteins ; Brefeldin A (20350-15-6)
    Language English
    Publishing date 2022-08-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1110-1
    ISSN 1096-0309 ; 0003-2697
    ISSN (online) 1096-0309
    ISSN 0003-2697
    DOI 10.1016/j.ab.2022.114846
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Mass spectrometric profiling of HLA-B44 peptidomes provides evidence for tapasin-mediated tryptophan editing.

    Kaur, Amanpreet / Surnilla, Avrokin / Zaitouna, Anita J / Basrur, Venkatesha / Mumphrey, Michael B / Grigorova, Irina / Cieslik, Marcin / Carrington, Mary / Nesvizhskii, Alexey I / Raghavan, Malini

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Activation of ... ...

    Abstract Activation of CD8
    Language English
    Publishing date 2023-02-27
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.26.530125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Mass Spectrometric Profiling of HLA-B44 Peptidomes Provides Evidence for Tapasin-Mediated Tryptophan Editing.

    Kaur, Amanpreet / Surnilla, Avrokin / Zaitouna, Anita J / Mumphrey, Michael B / Basrur, Venkatesha / Grigorova, Irina / Cieslik, Marcin / Carrington, Mary / Nesvizhskii, Alexey I / Raghavan, Malini

    Journal of immunology (Baltimore, Md. : 1950)

    2023  Volume 211, Issue 9, Page(s) 1298–1307

    Abstract: The extreme polymorphisms of HLA class I proteins result in structural variations in their peptide binding sites to achieve diversity in Ag presentation. External factors could independently constrict or alter HLA class I peptide repertoires. Such ... ...

    Abstract The extreme polymorphisms of HLA class I proteins result in structural variations in their peptide binding sites to achieve diversity in Ag presentation. External factors could independently constrict or alter HLA class I peptide repertoires. Such effects of the assembly factor tapasin were assessed for HLA-B*44:05 (Y116) and a close variant, HLA-B*44:02 (D116), which have low and high tapasin dependence, respectively, for their cell surface expression. Analyses of the HLA-B*44:05 peptidomes in the presence and absence of tapasin reveal that peptides with C-terminal tryptophans and higher predicted affinities are preferentially selected by tapasin, coincident with reduced frequencies of peptides with other C-terminal amino acids, including leucine. Comparisons of the HLA-B*44:05 and HLA-B*44:02 peptidomes indicate the expected structure-based alterations near the peptide C termini, but also C-terminal amino acid frequency and predicted affinity changes among the unique and shared peptide groups for B*44:02 and B*44:05. Overall, these findings indicate that the presence of tapasin and the tapasin dependence of assembly alter HLA class I peptide-binding preferences at the peptide C terminus. The particular C-terminal amino acid preferences that are altered by tapasin are expected to be determined by the intrinsic peptide-binding specificities of HLA class I allotypes. Additionally, the findings suggest that tapasin deficiency and reduced tapasin dependence expand the permissive affinities of HLA class I-bound peptides, consistent with prior findings that HLA class I allotypes with low tapasin dependence have increased breadth of CD8+ T cell epitope presentation and are more protective in HIV infections.
    MeSH term(s) Humans ; HLA-B44 Antigen/metabolism ; Tryptophan/metabolism ; HIV Infections ; Peptides/metabolism ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class I/metabolism ; Immunoglobulins/metabolism ; Protein Binding ; HLA-B Antigens/genetics ; HLA-B Antigens/metabolism
    Chemical Substances tapasin ; HLA-B44 Antigen ; Tryptophan (8DUH1N11BX) ; Peptides ; Histocompatibility Antigens Class I ; Immunoglobulins ; HLA-B Antigens
    Language English
    Publishing date 2023-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
    ZDB-ID 3056-9
    ISSN 1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
    ISSN (online) 1550-6606
    ISSN 0022-1767 ; 1048-3233 ; 1047-7381
    DOI 10.4049/jimmunol.2300232
    Database MEDical Literature Analysis and Retrieval System OnLINE

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