kdel-r Search Results


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  • 88
    Thermo Fisher kdel r
    ERGIC-53 (H-245) and <t>KDEL-R</t> (FL-212) polyclonal antisera from Santa Cruz Biotechnology detect multiple protein bands. HeLa cells were infected with reovirus at a multiplicity of infection (MOI) of 1 or 10 PFU/cell. Cell lysates were prepared 24 h postinfection, resolved by SDS-PAGE, and transferred to nitrocellulose membranes. Membranes were blocked with 5% skim milk in TBS and immunoblotted using polyclonal antiserum H-245 (against ERGIC-53, left panel) or FL-212 (against KDEL-R, right panel). Anti-rabbit secondary antibody (IRDye 800CW goat anti-rabbit IgG [LI-COR]) was used for detection. Molecular mass markers (in kilodaltons) are indicated on the left.
    Kdel R, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Millipore kdel r
    Visualization of endogenous TTIs. (A–D) Vero cells growing at 37°C were fixed and immunostained for endogenous <t>KDEL-R</t> (A and B) and ERGIC-53 (C and D). A small population of the cells contained visible tubular structures (arrowheads).
    Kdel R, supplied by Millipore, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Santa Cruz Biotechnology anti kdel r
    Knockdown of secretory pathway components or proteins involved in CFTR processing impacts AAV infection. Transduction efficiency of AAV following siRNA-mediated knockdown of proteins in HEK-293 cells (A C) or HeLa cells (B D). A margin of error for nonsignificant perturbations of infection (roughly ±30% relative to controls) is indicated by dashed lines. Cells were mock transfected or transfected with non-targeting control siRNA, or siRNA targeting BiP, <t>calnexin,</t> calreticulin, <t>KDEL-R,</t> β-COP, HDAC6, dynactin, or PSMB3. Between 36 and 48 hr after transfection, cells were infected with AAV2-GFP (200 vg/cell, HEK-293; 500 vg/cell HeLa) and fixed for flow cytometry 24 hr post-infection. Data is reported as the percentage of cells infected (% GFP positive, A B) or mean fluorescence intensity (MFI, C D) from cells that are positive. Differences in cell-type specificity are apparent with β-COP, but ultimately these results suggest AAV infection can be influenced by components of the secretory pathway and the proteasome. Cells infected with lenti-GFP as a control, do not display significant differences in MFI (C D, black columns), ruling out aberrant effects on reporter gene expression. Error bars represent standard deviation and graphs are representative data sets of at least three independent experiments. Samples that were statistically different from controls are marked (*p
    Anti Kdel R, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Abcam anti kdelr
    <t>KDELR</t> mediates the association of BmCREC with COPI. A , schematic picture showing constructs of <t>EGFP-tagged</t> BmCREC fusion proteins. Red areas of the N terminus represent signal peptide (1–16 amino acids); BmCREC# indicates BmCREC without tetrapeptide
    Anti Kdelr, supplied by Abcam, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Stressgen Biotechnologies anti kdelr
    <t>KDELR</t> stimulation by Bodipy-KDEL triggers the phosphorylation of <t>cortactin</t> at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for p-cortactin (Tyr 421 of cortactin, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). p-cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to p-cortactin spots at invadopodia. (B) KDELR stimulation increases cortactin to invadopodia. A375MM cells were treated as in A, fixed, and stained for cortactin (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). Cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to cortactin spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. *** p
    Anti Kdelr, supplied by Stressgen Biotechnologies, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    OriGene human kdelr orfs
    <t>KDELR</t> stimulation by Bodipy-KDEL triggers the phosphorylation of <t>cortactin</t> at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for p-cortactin (Tyr 421 of cortactin, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). p-cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to p-cortactin spots at invadopodia. (B) KDELR stimulation increases cortactin to invadopodia. A375MM cells were treated as in A, fixed, and stained for cortactin (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). Cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to cortactin spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. *** p
    Human Kdelr Orfs, supplied by OriGene, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Becton Dickinson anti kdelr antibodies
    <t>KDELR</t> stimulation by Bodipy-KDEL triggers the phosphorylation of <t>cortactin</t> at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for p-cortactin (Tyr 421 of cortactin, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). p-cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to p-cortactin spots at invadopodia. (B) KDELR stimulation increases cortactin to invadopodia. A375MM cells were treated as in A, fixed, and stained for cortactin (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). Cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to cortactin spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. *** p
    Anti Kdelr Antibodies, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    GeneTex rabbit anti kdelr
    Co-purification of GRP78, <t>KDELR</t> and viral E protein from the JEV-infected cells. The BHK-21 cells were mock-infected or infected with JEV at the MOI of 0.1, and the cells were harvested by freeze-and-thaw for the disturbing of the cell membranes. The lysates were then subjected to a 30% sucrose cushion for the removal of nonspecifically interacting proteins from the virions. The JE viral particles were purified by isopycnic fractionation using a 20% to 60% linear sucrose density gradient. The JE viral E, GRP78 and KDEL receptor proteins were detected in the fraction by Western blotting using anti-JEV_E, anti-GRP78 and <t>anti-KDELR1</t> antibodies, respectively. ( A ) Mock, BHK-21 cells with mock-infected; ( B ) JEV-infected, BHK-21 cells with JEV infection; ( C ) shGRP78 with JEV-infected, the GRP78 knocked down cells infected with JEV.
    Rabbit Anti Kdelr, supplied by GeneTex, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Stressgen Biotechnologies kdelr mouse mab
    Co-purification of GRP78, <t>KDELR</t> and viral E protein from the JEV-infected cells. The BHK-21 cells were mock-infected or infected with JEV at the MOI of 0.1, and the cells were harvested by freeze-and-thaw for the disturbing of the cell membranes. The lysates were then subjected to a 30% sucrose cushion for the removal of nonspecifically interacting proteins from the virions. The JE viral particles were purified by isopycnic fractionation using a 20% to 60% linear sucrose density gradient. The JE viral E, GRP78 and KDEL receptor proteins were detected in the fraction by Western blotting using anti-JEV_E, anti-GRP78 and <t>anti-KDELR1</t> antibodies, respectively. ( A ) Mock, BHK-21 cells with mock-infected; ( B ) JEV-infected, BHK-21 cells with JEV infection; ( C ) shGRP78 with JEV-infected, the GRP78 knocked down cells infected with JEV.
    Kdelr Mouse Mab, supplied by Stressgen Biotechnologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Gallus BioPharmaceuticals gallus 7 tms kdelr receptor
    Evidence of homology between families <t>KDELR</t> and sweet. Hydropathy plots are presented across the homology transitivity path between families KDELR and Sweet. Refer to the legend of Fig 4 for a detailed description of the format. A. Hydropathy plot of KDELR member M7SWU9 (TC: 9.B.191.1.7). B. Hydropathy plot of the alignment (E-value: 1.7×10 −128 ) between KDELR member M7SWU9 and its homolog KXJ91449. C. Hydropathy plot of KDELR homolog KXJ91449. D. Hydropathy plot of Sweet member ANC68268 (TC: 2.A.123.1.27). E. Hydropathy plot of the alignment (E-value: 5.6×10 −56 ) between Sweet member ANC68268 and its homolog XP_010536596. F. Hydropathy plot of Sweet homolog XP_010536596. G. Hydropathy plot of the <t>7-TMS</t> alignment (E-value: 5.3×10 −10 ) between KDELR homologue KXJ91449 and Sweet homologue XP_010536596. The full Pfam domains of proteins KXJ91449 (PF00810) and XP_010536596 (PF03083) are included in the alignment and belong to the same clan (CL0141), further supporting the relationship between both families.
    Gallus 7 Tms Kdelr Receptor, supplied by Gallus BioPharmaceuticals, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Santa Cruz Biotechnology monoclonal anti kdel receptor kdelr antibody
    Evidence of homology between families <t>KDELR</t> and sweet. Hydropathy plots are presented across the homology transitivity path between families KDELR and Sweet. Refer to the legend of Fig 4 for a detailed description of the format. A. Hydropathy plot of KDELR member M7SWU9 (TC: 9.B.191.1.7). B. Hydropathy plot of the alignment (E-value: 1.7×10 −128 ) between KDELR member M7SWU9 and its homolog KXJ91449. C. Hydropathy plot of KDELR homolog KXJ91449. D. Hydropathy plot of Sweet member ANC68268 (TC: 2.A.123.1.27). E. Hydropathy plot of the alignment (E-value: 5.6×10 −56 ) between Sweet member ANC68268 and its homolog XP_010536596. F. Hydropathy plot of Sweet homolog XP_010536596. G. Hydropathy plot of the <t>7-TMS</t> alignment (E-value: 5.3×10 −10 ) between KDELR homologue KXJ91449 and Sweet homologue XP_010536596. The full Pfam domains of proteins KXJ91449 (PF00810) and XP_010536596 (PF03083) are included in the alignment and belong to the same clan (CL0141), further supporting the relationship between both families.
    Monoclonal Anti Kdel Receptor Kdelr Antibody, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher kdelr microplate interaction assay maxisorp 96 well plates
    Evidence of homology between families <t>KDELR</t> and sweet. Hydropathy plots are presented across the homology transitivity path between families KDELR and Sweet. Refer to the legend of Fig 4 for a detailed description of the format. A. Hydropathy plot of KDELR member M7SWU9 (TC: 9.B.191.1.7). B. Hydropathy plot of the alignment (E-value: 1.7×10 −128 ) between KDELR member M7SWU9 and its homolog KXJ91449. C. Hydropathy plot of KDELR homolog KXJ91449. D. Hydropathy plot of Sweet member ANC68268 (TC: 2.A.123.1.27). E. Hydropathy plot of the alignment (E-value: 5.6×10 −56 ) between Sweet member ANC68268 and its homolog XP_010536596. F. Hydropathy plot of Sweet homolog XP_010536596. G. Hydropathy plot of the <t>7-TMS</t> alignment (E-value: 5.3×10 −10 ) between KDELR homologue KXJ91449 and Sweet homologue XP_010536596. The full Pfam domains of proteins KXJ91449 (PF00810) and XP_010536596 (PF03083) are included in the alignment and belong to the same clan (CL0141), further supporting the relationship between both families.
    Kdelr Microplate Interaction Assay Maxisorp 96 Well Plates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    ERGIC-53 (H-245) and KDEL-R (FL-212) polyclonal antisera from Santa Cruz Biotechnology detect multiple protein bands. HeLa cells were infected with reovirus at a multiplicity of infection (MOI) of 1 or 10 PFU/cell. Cell lysates were prepared 24 h postinfection, resolved by SDS-PAGE, and transferred to nitrocellulose membranes. Membranes were blocked with 5% skim milk in TBS and immunoblotted using polyclonal antiserum H-245 (against ERGIC-53, left panel) or FL-212 (against KDEL-R, right panel). Anti-rabbit secondary antibody (IRDye 800CW goat anti-rabbit IgG [LI-COR]) was used for detection. Molecular mass markers (in kilodaltons) are indicated on the left.

    Journal: mBio

    Article Title: Correction for Fernández de Castro et al., Reovirus Forms Neo-Organelles for Progeny Particle Assembly within Reorganized Cell Membranes

    doi: 10.1128/mBio.02529-14

    Figure Lengend Snippet: ERGIC-53 (H-245) and KDEL-R (FL-212) polyclonal antisera from Santa Cruz Biotechnology detect multiple protein bands. HeLa cells were infected with reovirus at a multiplicity of infection (MOI) of 1 or 10 PFU/cell. Cell lysates were prepared 24 h postinfection, resolved by SDS-PAGE, and transferred to nitrocellulose membranes. Membranes were blocked with 5% skim milk in TBS and immunoblotted using polyclonal antiserum H-245 (against ERGIC-53, left panel) or FL-212 (against KDEL-R, right panel). Anti-rabbit secondary antibody (IRDye 800CW goat anti-rabbit IgG [LI-COR]) was used for detection. Molecular mass markers (in kilodaltons) are indicated on the left.

    Article Snippet: As part of our ongoing studies of the biogenesis of reovirus inclusions, we performed immunofluorescence assays using two monoclonal antibodies specific for ERGIC-53 (C-6 [Santa Cruz Biotechnology] and G1/93 [Enzo Life Sciences]) and a monoclonal antibody specific for KDEL-R (KR-10 [Thermo Scientific]).

    Techniques: Infection, SDS Page

    Visualization of endogenous TTIs. (A–D) Vero cells growing at 37°C were fixed and immunostained for endogenous KDEL-R (A and B) and ERGIC-53 (C and D). A small population of the cells contained visible tubular structures (arrowheads).

    Journal:

    Article Title: Biogenesis of Tubular ER-to-Golgi Transport Intermediates V⃞

    doi: 10.1091/mbc.E05-06-0580

    Figure Lengend Snippet: Visualization of endogenous TTIs. (A–D) Vero cells growing at 37°C were fixed and immunostained for endogenous KDEL-R (A and B) and ERGIC-53 (C and D). A small population of the cells contained visible tubular structures (arrowheads).

    Article Snippet: Antibodies used for immunofluorescence were against COPI coatomer (CM1A10; ), the β′-subunit of COPI , the γ-adaptin subunit of AP-1, GFP, GM130 (all BD Biosciences, Heidelberg, Germany), p27 , α-tubulin (Neomarkers, Fremont, CA), KDEL-R (Calbiochem), TGN46 (Serotec, Oxford, United Kingdom), and COPII (sec23; Affinity Bioreagents, Golden, CO).

    Techniques:

    Expression levels of GFP-KDEL-R and GFP-ERGIC-53 influence TTI abundance. (A) Vero cell expressing low amounts GFP-KDEL-R showing the protein localizing to the Golgi and motile punctate structures. (B) Vero cell expressing a higher level of GFP-KDEL-R

    Journal:

    Article Title: Biogenesis of Tubular ER-to-Golgi Transport Intermediates V⃞

    doi: 10.1091/mbc.E05-06-0580

    Figure Lengend Snippet: Expression levels of GFP-KDEL-R and GFP-ERGIC-53 influence TTI abundance. (A) Vero cell expressing low amounts GFP-KDEL-R showing the protein localizing to the Golgi and motile punctate structures. (B) Vero cell expressing a higher level of GFP-KDEL-R

    Article Snippet: Antibodies used for immunofluorescence were against COPI coatomer (CM1A10; ), the β′-subunit of COPI , the γ-adaptin subunit of AP-1, GFP, GM130 (all BD Biosciences, Heidelberg, Germany), p27 , α-tubulin (Neomarkers, Fremont, CA), KDEL-R (Calbiochem), TGN46 (Serotec, Oxford, United Kingdom), and COPII (sec23; Affinity Bioreagents, Golden, CO).

    Techniques: Expressing

    Knockdown of secretory pathway components or proteins involved in CFTR processing impacts AAV infection. Transduction efficiency of AAV following siRNA-mediated knockdown of proteins in HEK-293 cells (A C) or HeLa cells (B D). A margin of error for nonsignificant perturbations of infection (roughly ±30% relative to controls) is indicated by dashed lines. Cells were mock transfected or transfected with non-targeting control siRNA, or siRNA targeting BiP, calnexin, calreticulin, KDEL-R, β-COP, HDAC6, dynactin, or PSMB3. Between 36 and 48 hr after transfection, cells were infected with AAV2-GFP (200 vg/cell, HEK-293; 500 vg/cell HeLa) and fixed for flow cytometry 24 hr post-infection. Data is reported as the percentage of cells infected (% GFP positive, A B) or mean fluorescence intensity (MFI, C D) from cells that are positive. Differences in cell-type specificity are apparent with β-COP, but ultimately these results suggest AAV infection can be influenced by components of the secretory pathway and the proteasome. Cells infected with lenti-GFP as a control, do not display significant differences in MFI (C D, black columns), ruling out aberrant effects on reporter gene expression. Error bars represent standard deviation and graphs are representative data sets of at least three independent experiments. Samples that were statistically different from controls are marked (*p

    Journal: PLoS Pathogens

    Article Title: AAV Exploits Subcellular Stress Associated with Inflammation, Endoplasmic Reticulum Expansion, and Misfolded Proteins in Models of Cystic Fibrosis

    doi: 10.1371/journal.ppat.1002053

    Figure Lengend Snippet: Knockdown of secretory pathway components or proteins involved in CFTR processing impacts AAV infection. Transduction efficiency of AAV following siRNA-mediated knockdown of proteins in HEK-293 cells (A C) or HeLa cells (B D). A margin of error for nonsignificant perturbations of infection (roughly ±30% relative to controls) is indicated by dashed lines. Cells were mock transfected or transfected with non-targeting control siRNA, or siRNA targeting BiP, calnexin, calreticulin, KDEL-R, β-COP, HDAC6, dynactin, or PSMB3. Between 36 and 48 hr after transfection, cells were infected with AAV2-GFP (200 vg/cell, HEK-293; 500 vg/cell HeLa) and fixed for flow cytometry 24 hr post-infection. Data is reported as the percentage of cells infected (% GFP positive, A B) or mean fluorescence intensity (MFI, C D) from cells that are positive. Differences in cell-type specificity are apparent with β-COP, but ultimately these results suggest AAV infection can be influenced by components of the secretory pathway and the proteasome. Cells infected with lenti-GFP as a control, do not display significant differences in MFI (C D, black columns), ruling out aberrant effects on reporter gene expression. Error bars represent standard deviation and graphs are representative data sets of at least three independent experiments. Samples that were statistically different from controls are marked (*p

    Article Snippet: The cells were incubated with primary antibody to detect intact capsids [(monoclonal A20 (1∶10)], or cellular markers (anti-γ-tubulin (Abcam Ab16504 1∶250), anti-BiP (Abcam Ab21685 1∶1000), anti-calnexin (Abcam Ab 13504 1∶1000), anti-calreticulin (Abcam Ab2907 1∶1000), anti-KDEL-R (Santa Cruz Biotechnology sc-33806 1∶50), anti-β-COP (Abcam Ab2899 1∶1000), or anti-CFTR-570 (1∶500)] diluted in IFB, for 1 hr at 37°C or overnight at 4°C.

    Techniques: Infection, Transduction, Transfection, Flow Cytometry, Cytometry, Fluorescence, Expressing, Standard Deviation

    AAV capsids traffic to locations near Golgi/ER transport components. AAV2 virions (10,000 vg/cell) were administered to HeLa cells for 16 hr and prepped for confocal immunofluorescence with antibodies directed toward cellular markers (red) for ER-resident chaperones (BiP, calnexin, calreticulin), Golgi sorting components (KDEL-R,β-COP), or AAV2 capsids (green). Nuclei (blue) were stained with DAPI. White arrows indicate partial colocalization with KDEL-R and β-COP, yet it is difficult to assess whether colocalization occurs with ER markers.

    Journal: PLoS Pathogens

    Article Title: AAV Exploits Subcellular Stress Associated with Inflammation, Endoplasmic Reticulum Expansion, and Misfolded Proteins in Models of Cystic Fibrosis

    doi: 10.1371/journal.ppat.1002053

    Figure Lengend Snippet: AAV capsids traffic to locations near Golgi/ER transport components. AAV2 virions (10,000 vg/cell) were administered to HeLa cells for 16 hr and prepped for confocal immunofluorescence with antibodies directed toward cellular markers (red) for ER-resident chaperones (BiP, calnexin, calreticulin), Golgi sorting components (KDEL-R,β-COP), or AAV2 capsids (green). Nuclei (blue) were stained with DAPI. White arrows indicate partial colocalization with KDEL-R and β-COP, yet it is difficult to assess whether colocalization occurs with ER markers.

    Article Snippet: The cells were incubated with primary antibody to detect intact capsids [(monoclonal A20 (1∶10)], or cellular markers (anti-γ-tubulin (Abcam Ab16504 1∶250), anti-BiP (Abcam Ab21685 1∶1000), anti-calnexin (Abcam Ab 13504 1∶1000), anti-calreticulin (Abcam Ab2907 1∶1000), anti-KDEL-R (Santa Cruz Biotechnology sc-33806 1∶50), anti-β-COP (Abcam Ab2899 1∶1000), or anti-CFTR-570 (1∶500)] diluted in IFB, for 1 hr at 37°C or overnight at 4°C.

    Techniques: Immunofluorescence, Staining

    KDELR mediates the association of BmCREC with COPI. A , schematic picture showing constructs of EGFP-tagged BmCREC fusion proteins. Red areas of the N terminus represent signal peptide (1–16 amino acids); BmCREC# indicates BmCREC without tetrapeptide

    Journal: The Journal of Biological Chemistry

    Article Title: BmCREC Is an Endoplasmic Reticulum (ER) Resident Protein and Required for ER/Golgi Morphology *

    doi: 10.1074/jbc.M113.463018

    Figure Lengend Snippet: KDELR mediates the association of BmCREC with COPI. A , schematic picture showing constructs of EGFP-tagged BmCREC fusion proteins. Red areas of the N terminus represent signal peptide (1–16 amino acids); BmCREC# indicates BmCREC without tetrapeptide

    Article Snippet: Anti-silkworm α/β′/γ-COP , anti-BmKinesin-1 , anti-calnexin (Abcam), anti-EGFP (MBL), anti- Drosophila GM130 (Abcam), anti-KDELR (Abcam), anti-lamin , and anti-tubulin (Sigma) antibodies were also used.

    Techniques: Construct

    Proposed model for the ER retention mechanism of BmCREC and its function. In the PSG cells, BmCREC is recognized by KDELR and retrogradely transported from the Golgi apparatus to the ER by BmKinesin-1-driven COPI vesicles. BmCREC deficiency disrupts ER/Golgi

    Journal: The Journal of Biological Chemistry

    Article Title: BmCREC Is an Endoplasmic Reticulum (ER) Resident Protein and Required for ER/Golgi Morphology *

    doi: 10.1074/jbc.M113.463018

    Figure Lengend Snippet: Proposed model for the ER retention mechanism of BmCREC and its function. In the PSG cells, BmCREC is recognized by KDELR and retrogradely transported from the Golgi apparatus to the ER by BmKinesin-1-driven COPI vesicles. BmCREC deficiency disrupts ER/Golgi

    Article Snippet: Anti-silkworm α/β′/γ-COP , anti-BmKinesin-1 , anti-calnexin (Abcam), anti-EGFP (MBL), anti- Drosophila GM130 (Abcam), anti-KDELR (Abcam), anti-lamin , and anti-tubulin (Sigma) antibodies were also used.

    Techniques:

    KDELR stimulation by Bodipy-KDEL triggers the phosphorylation of cortactin at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for p-cortactin (Tyr 421 of cortactin, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). p-cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to p-cortactin spots at invadopodia. (B) KDELR stimulation increases cortactin to invadopodia. A375MM cells were treated as in A, fixed, and stained for cortactin (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). Cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to cortactin spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. *** p

    Journal: Oncotarget

    Article Title: A Golgi-based KDELR-dependent signalling pathway controls extracellular matrix degradation

    doi:

    Figure Lengend Snippet: KDELR stimulation by Bodipy-KDEL triggers the phosphorylation of cortactin at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for p-cortactin (Tyr 421 of cortactin, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). p-cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to p-cortactin spots at invadopodia. (B) KDELR stimulation increases cortactin to invadopodia. A375MM cells were treated as in A, fixed, and stained for cortactin (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). Cortactin immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red green and blue signals). White arrows point to cortactin spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. *** p

    Article Snippet: Antibodies and constructs The antibodies used were: anti-pSrc (p-Tyr 418; Invitrogen); anti-Src (SC18; Santa Cruz Biotechnology); anti-pASAP1 (p-Tyr782; Rockland Immunochemicals); anti-ASAP1 (Transduction Laboratories); anti-cortactin and anti p-cortactin (p-Tyr 421; Merck Millipore) anti-KDELR (Stressgen Biotechnology); anti PDI (Assay Designs); anti-KDELR 2, anti-KDELR 3, and anti-HRP antibodies (Abcam); anti-myc (Invitrogen), anti-actin (Sigma Aldrich); fluorophore-conjugated antibodies and fluorophore-conjugated actin (Molecular Probes); anti-HRP (Abcam) and HRP-conjugated antibodies (Calbiochem).

    Techniques: Incubation, Staining, Immunofluorescence

    ASAP1 is involved in KDELR-dependent ECM degradation (A) KDELR stimulation increases the levels of phosphorylated ASAP1 in areas of ECM degradation. A375MM cells were transfected with the empty vector (Mock) or ssHRP KDEL , and grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h and then fixed and stained for pASAP1 (pTyr 782, green). An anti-HRP antibody (blue) was used to visualise ssHRP KDEL -transfected cells. Merged images of red and green (Mock) and red, green and blue signals are also shown (Merge). pASAP1 immunofluorescence overlapping the degradation patches are shown in the enlargements of the boxed regions (small right panels: red and green signals). The images are representative of three independent experiments. (B) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments. In each experiment, at least 100 cells were quantified. (C) KDELR stimulation increases ASAP1 recruitment to areas of degradation. A375MM cells were treated as in A, fixed, and stained for ASAP1 (green). An anti-HRP antibody (blue) was used to visualise ssHRP KDEL -transfected cells. Merged images of red and green (Mock) and red, green and blue signals are also shown (Merge). ASAP1 immunofluorescence overlapping the degradation patches are shown in the enlargements of the boxed regions (small right panels: red and green signals). The images are representative of three independent experiments. (D) Quantification of pASAP1 immunofluorescence in the cell regions overlapping the ECM degradation patches. Data are means ±SEM of pASAP1 immunofluorescence per cell (% of control), of three independent experiments. In each experiment at least 100 cells were quantified. (A, C) Scale bars, 10 μm. (E) The ASAP1 Y782F mutant inhibit ECM degradation. A375MM cells were transfected with empty vector (Mock), Flag-tagged ASAP1-wt or the Flag-tagged ASAP1 Y782F mutant. The cells were also transfected with myc-tagged ssHRP KDEL , myc-tagged ssHRP KDEL and ASAP1-wt, or myc-tagged ssHRP KDEL and ASAP1 Y782F. Following BB94wash-out, the cells were incubated for a further 3 h, then fixed, stained and scored for degradation of the ECM. Quantification of the degradation area per cell. Data are means ±SEM, as indicated for B. ***p

    Journal: Oncotarget

    Article Title: A Golgi-based KDELR-dependent signalling pathway controls extracellular matrix degradation

    doi:

    Figure Lengend Snippet: ASAP1 is involved in KDELR-dependent ECM degradation (A) KDELR stimulation increases the levels of phosphorylated ASAP1 in areas of ECM degradation. A375MM cells were transfected with the empty vector (Mock) or ssHRP KDEL , and grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h and then fixed and stained for pASAP1 (pTyr 782, green). An anti-HRP antibody (blue) was used to visualise ssHRP KDEL -transfected cells. Merged images of red and green (Mock) and red, green and blue signals are also shown (Merge). pASAP1 immunofluorescence overlapping the degradation patches are shown in the enlargements of the boxed regions (small right panels: red and green signals). The images are representative of three independent experiments. (B) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments. In each experiment, at least 100 cells were quantified. (C) KDELR stimulation increases ASAP1 recruitment to areas of degradation. A375MM cells were treated as in A, fixed, and stained for ASAP1 (green). An anti-HRP antibody (blue) was used to visualise ssHRP KDEL -transfected cells. Merged images of red and green (Mock) and red, green and blue signals are also shown (Merge). ASAP1 immunofluorescence overlapping the degradation patches are shown in the enlargements of the boxed regions (small right panels: red and green signals). The images are representative of three independent experiments. (D) Quantification of pASAP1 immunofluorescence in the cell regions overlapping the ECM degradation patches. Data are means ±SEM of pASAP1 immunofluorescence per cell (% of control), of three independent experiments. In each experiment at least 100 cells were quantified. (A, C) Scale bars, 10 μm. (E) The ASAP1 Y782F mutant inhibit ECM degradation. A375MM cells were transfected with empty vector (Mock), Flag-tagged ASAP1-wt or the Flag-tagged ASAP1 Y782F mutant. The cells were also transfected with myc-tagged ssHRP KDEL , myc-tagged ssHRP KDEL and ASAP1-wt, or myc-tagged ssHRP KDEL and ASAP1 Y782F. Following BB94wash-out, the cells were incubated for a further 3 h, then fixed, stained and scored for degradation of the ECM. Quantification of the degradation area per cell. Data are means ±SEM, as indicated for B. ***p

    Article Snippet: Antibodies and constructs The antibodies used were: anti-pSrc (p-Tyr 418; Invitrogen); anti-Src (SC18; Santa Cruz Biotechnology); anti-pASAP1 (p-Tyr782; Rockland Immunochemicals); anti-ASAP1 (Transduction Laboratories); anti-cortactin and anti p-cortactin (p-Tyr 421; Merck Millipore) anti-KDELR (Stressgen Biotechnology); anti PDI (Assay Designs); anti-KDELR 2, anti-KDELR 3, and anti-HRP antibodies (Abcam); anti-myc (Invitrogen), anti-actin (Sigma Aldrich); fluorophore-conjugated antibodies and fluorophore-conjugated actin (Molecular Probes); anti-HRP (Abcam) and HRP-conjugated antibodies (Calbiochem).

    Techniques: Transfection, Plasmid Preparation, Incubation, Staining, Immunofluorescence, Mutagenesis

    KDELR stimulation by overexpression of the KDELR ligand ssHRP KDEL increases degradation of the ECM (A) A375MM cells were grown in complete medium (with 10% serum) on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h, and then fixed and stained with phalloidin (blue) and cortactin (green). Merged images of blue green and red signals are also shown (Merge). Invadopodia are evident in the enlargement of the boxed region (small right panel: green, blue and red signals). (B) A375MM cells were transfected with empty vector (Mock), ssHRP (2 μg), or ssHRP-KDEL (2 μg), and treated as in A. The cells were then fixed and stained with an anti-HRP antibody (green) and phalloidin (blue). Merged images of red and blue(Mock) and red, blue and green signals (ssHRP and ssHRP ssHRP KDEL ) are also shown (Merge). Invadopodia are shown in the enlargements of the boxed regions (small right panels: blue and red signals). (A, B). Scale bars, 10 μm. The images are representative of three independent experiments. (C) Cells transfected with increasing concentrations (0.5, 1, 2 μg) ssHRP or ssHRP KDEL were processed as in A. Data are degradation area per cell (% of control), as means ±SEM from three independent experiments, with at least 100 cells quantified per experiment. *p

    Journal: Oncotarget

    Article Title: A Golgi-based KDELR-dependent signalling pathway controls extracellular matrix degradation

    doi:

    Figure Lengend Snippet: KDELR stimulation by overexpression of the KDELR ligand ssHRP KDEL increases degradation of the ECM (A) A375MM cells were grown in complete medium (with 10% serum) on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h, and then fixed and stained with phalloidin (blue) and cortactin (green). Merged images of blue green and red signals are also shown (Merge). Invadopodia are evident in the enlargement of the boxed region (small right panel: green, blue and red signals). (B) A375MM cells were transfected with empty vector (Mock), ssHRP (2 μg), or ssHRP-KDEL (2 μg), and treated as in A. The cells were then fixed and stained with an anti-HRP antibody (green) and phalloidin (blue). Merged images of red and blue(Mock) and red, blue and green signals (ssHRP and ssHRP ssHRP KDEL ) are also shown (Merge). Invadopodia are shown in the enlargements of the boxed regions (small right panels: blue and red signals). (A, B). Scale bars, 10 μm. The images are representative of three independent experiments. (C) Cells transfected with increasing concentrations (0.5, 1, 2 μg) ssHRP or ssHRP KDEL were processed as in A. Data are degradation area per cell (% of control), as means ±SEM from three independent experiments, with at least 100 cells quantified per experiment. *p

    Article Snippet: Antibodies and constructs The antibodies used were: anti-pSrc (p-Tyr 418; Invitrogen); anti-Src (SC18; Santa Cruz Biotechnology); anti-pASAP1 (p-Tyr782; Rockland Immunochemicals); anti-ASAP1 (Transduction Laboratories); anti-cortactin and anti p-cortactin (p-Tyr 421; Merck Millipore) anti-KDELR (Stressgen Biotechnology); anti PDI (Assay Designs); anti-KDELR 2, anti-KDELR 3, and anti-HRP antibodies (Abcam); anti-myc (Invitrogen), anti-actin (Sigma Aldrich); fluorophore-conjugated antibodies and fluorophore-conjugated actin (Molecular Probes); anti-HRP (Abcam) and HRP-conjugated antibodies (Calbiochem).

    Techniques: Over Expression, Incubation, Staining, Transfection, Plasmid Preparation

    KDELR stimulation by Bodipy-KDEL triggers the phosphorylation of ASAP1 at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for pASAP1 (pTyr 782, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). pASAP1 immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red, green and blue signals).. White arrows point to pASAP1 spots at invadopodia. (B) KDELR stimulation increases ASAP1 to invadopodia. A375MM cells were treated as in A, fixed, and stained for ASAP1 (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). ASAP1 immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red, green and blue signals). White arrows point to ASAP1 spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. (D) Quantification of pASAP1 immunofluorescence levels at invadopodia. Data are means ±SEM of pASAP1 immunofluorescence per cell (% of control), from three independent experiments, with at least 50 cells quantified per experiment. (E) Quantification of ASAP1 immunofluorescence levels at invadopodia. Data are means ±SEM, as indicated for D. (C, D, E) ***p

    Journal: Oncotarget

    Article Title: A Golgi-based KDELR-dependent signalling pathway controls extracellular matrix degradation

    doi:

    Figure Lengend Snippet: KDELR stimulation by Bodipy-KDEL triggers the phosphorylation of ASAP1 at invadopodia (A) A375MM cells were grown on rhodamine-conjugated crosslinked gelatine (red) for 16 h in the presence of BB94. Following BB94 wash-out, the cells were incubated for a further 3 h with the membrane permeant KDELR agonist Bodipy-KDEL (3 μM) or with vehicle alone (Vehicle) as a control. After fixing, the cells were stained for pASAP1 (pTyr 782, green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). pASAP1 immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red, green and blue signals).. White arrows point to pASAP1 spots at invadopodia. (B) KDELR stimulation increases ASAP1 to invadopodia. A375MM cells were treated as in A, fixed, and stained for ASAP1 (green) and phalloidin (blue). Merged images of red, green and blue signals are also shown (Merge). ASAP1 immunofluorescence overlapping the invadopodia are shown in the enlargements of the boxed regions (small right panels: red, green and blue signals). White arrows point to ASAP1 spots at invadopodia. (A, B) The images are representative of three independent experiments. Scale bars, 10 μm. (C) Quantification of the degradation area per cell. Data are degradation area per cell (% of control), as means ±SEM of three independent experiments, with at least 50 cells quantified per experiment. (D) Quantification of pASAP1 immunofluorescence levels at invadopodia. Data are means ±SEM of pASAP1 immunofluorescence per cell (% of control), from three independent experiments, with at least 50 cells quantified per experiment. (E) Quantification of ASAP1 immunofluorescence levels at invadopodia. Data are means ±SEM, as indicated for D. (C, D, E) ***p

    Article Snippet: Antibodies and constructs The antibodies used were: anti-pSrc (p-Tyr 418; Invitrogen); anti-Src (SC18; Santa Cruz Biotechnology); anti-pASAP1 (p-Tyr782; Rockland Immunochemicals); anti-ASAP1 (Transduction Laboratories); anti-cortactin and anti p-cortactin (p-Tyr 421; Merck Millipore) anti-KDELR (Stressgen Biotechnology); anti PDI (Assay Designs); anti-KDELR 2, anti-KDELR 3, and anti-HRP antibodies (Abcam); anti-myc (Invitrogen), anti-actin (Sigma Aldrich); fluorophore-conjugated antibodies and fluorophore-conjugated actin (Molecular Probes); anti-HRP (Abcam) and HRP-conjugated antibodies (Calbiochem).

    Techniques: Incubation, Staining, Immunofluorescence

    Co-purification of GRP78, KDELR and viral E protein from the JEV-infected cells. The BHK-21 cells were mock-infected or infected with JEV at the MOI of 0.1, and the cells were harvested by freeze-and-thaw for the disturbing of the cell membranes. The lysates were then subjected to a 30% sucrose cushion for the removal of nonspecifically interacting proteins from the virions. The JE viral particles were purified by isopycnic fractionation using a 20% to 60% linear sucrose density gradient. The JE viral E, GRP78 and KDEL receptor proteins were detected in the fraction by Western blotting using anti-JEV_E, anti-GRP78 and anti-KDELR1 antibodies, respectively. ( A ) Mock, BHK-21 cells with mock-infected; ( B ) JEV-infected, BHK-21 cells with JEV infection; ( C ) shGRP78 with JEV-infected, the GRP78 knocked down cells infected with JEV.

    Journal: Viruses

    Article Title: A KDEL Retrieval System for ER-Golgi Transport of Japanese Encephalitis Viral Particles

    doi: 10.3390/v8020044

    Figure Lengend Snippet: Co-purification of GRP78, KDELR and viral E protein from the JEV-infected cells. The BHK-21 cells were mock-infected or infected with JEV at the MOI of 0.1, and the cells were harvested by freeze-and-thaw for the disturbing of the cell membranes. The lysates were then subjected to a 30% sucrose cushion for the removal of nonspecifically interacting proteins from the virions. The JE viral particles were purified by isopycnic fractionation using a 20% to 60% linear sucrose density gradient. The JE viral E, GRP78 and KDEL receptor proteins were detected in the fraction by Western blotting using anti-JEV_E, anti-GRP78 and anti-KDELR1 antibodies, respectively. ( A ) Mock, BHK-21 cells with mock-infected; ( B ) JEV-infected, BHK-21 cells with JEV infection; ( C ) shGRP78 with JEV-infected, the GRP78 knocked down cells infected with JEV.

    Article Snippet: The following antibodies were primarily used: mouse anti-JEV NS1/E/prM (1:3000 dilution) [ , ] (YaoHong Biotechnology, Inc., New Taipei City, Taiwan), mouse anti-KDELR1 (Novus Biologicals, Littleton, CO, USA), rabbit anti-KDELR (GeneTex, Irvine, CA, USA), rat anti-GPR94 (NeoMarkers, Fremont, CA, USA), rabbit anti-PDI (Santa Cruz Biotechnology) and rabbit anti-β-actin antiserum (Sigma, St. Louis, MO, USA).

    Techniques: Copurification, Infection, Purification, Fractionation, Western Blot

    Evidence of homology between families KDELR and sweet. Hydropathy plots are presented across the homology transitivity path between families KDELR and Sweet. Refer to the legend of Fig 4 for a detailed description of the format. A. Hydropathy plot of KDELR member M7SWU9 (TC: 9.B.191.1.7). B. Hydropathy plot of the alignment (E-value: 1.7×10 −128 ) between KDELR member M7SWU9 and its homolog KXJ91449. C. Hydropathy plot of KDELR homolog KXJ91449. D. Hydropathy plot of Sweet member ANC68268 (TC: 2.A.123.1.27). E. Hydropathy plot of the alignment (E-value: 5.6×10 −56 ) between Sweet member ANC68268 and its homolog XP_010536596. F. Hydropathy plot of Sweet homolog XP_010536596. G. Hydropathy plot of the 7-TMS alignment (E-value: 5.3×10 −10 ) between KDELR homologue KXJ91449 and Sweet homologue XP_010536596. The full Pfam domains of proteins KXJ91449 (PF00810) and XP_010536596 (PF03083) are included in the alignment and belong to the same clan (CL0141), further supporting the relationship between both families.

    Journal: PLoS ONE

    Article Title: Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families

    doi: 10.1371/journal.pone.0231085

    Figure Lengend Snippet: Evidence of homology between families KDELR and sweet. Hydropathy plots are presented across the homology transitivity path between families KDELR and Sweet. Refer to the legend of Fig 4 for a detailed description of the format. A. Hydropathy plot of KDELR member M7SWU9 (TC: 9.B.191.1.7). B. Hydropathy plot of the alignment (E-value: 1.7×10 −128 ) between KDELR member M7SWU9 and its homolog KXJ91449. C. Hydropathy plot of KDELR homolog KXJ91449. D. Hydropathy plot of Sweet member ANC68268 (TC: 2.A.123.1.27). E. Hydropathy plot of the alignment (E-value: 5.6×10 −56 ) between Sweet member ANC68268 and its homolog XP_010536596. F. Hydropathy plot of Sweet homolog XP_010536596. G. Hydropathy plot of the 7-TMS alignment (E-value: 5.3×10 −10 ) between KDELR homologue KXJ91449 and Sweet homologue XP_010536596. The full Pfam domains of proteins KXJ91449 (PF00810) and XP_010536596 (PF03083) are included in the alignment and belong to the same clan (CL0141), further supporting the relationship between both families.

    Article Snippet: Similarly, in the structure of the Gallus gallus 7-TMS KDELR receptor (PDB: 6I6H) locked in the apo ER state, KDEL retrieval signal-bound Golgi state, and in complex with an antagonistic synthetic nanobody [ ], the MEME profile again maps to TMSs 1–2.

    Techniques:

    Basic repeat unit of 4 TMSs in family KDELR (TC: 9.B.191). A representative alignment between 8-TMS KDELR homologs XP_020093034 and GAQ80789, illustrates the 4-TMS repeat unit in KDELR as identified by AncientRep [ 32 ]. Thin black vertical lines with wedges delimit the regions involved in the alignment of the two full-length proteins. Orange and cyan bars highlight hydrophobicity peaks (i.e., inferred TMSs), respectively, for both proteins. A. Hydropathy plot of protein XP_020093034. TMSs 1–4 (shaded in dark gray) participate in the alignment shown in panel D. B. Hydropathy plot of protein GAQ80789. Hydrophobic peaks 5–8 (shaded in dark gray) participate in the alignment shown in panel D. C. Hydropathy plot of the alignment (E-value: 9.4×10 −102 ) between the full proteins. D. Hydropathy plot of the 4-TMS alignment (E-value: 5.0×10 −4 ) that provides evidence for the repeat. Interruptions in the hydropathy curves of panels C and D indicate gaps in the corresponding sequence alignments.

    Journal: PLoS ONE

    Article Title: Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families

    doi: 10.1371/journal.pone.0231085

    Figure Lengend Snippet: Basic repeat unit of 4 TMSs in family KDELR (TC: 9.B.191). A representative alignment between 8-TMS KDELR homologs XP_020093034 and GAQ80789, illustrates the 4-TMS repeat unit in KDELR as identified by AncientRep [ 32 ]. Thin black vertical lines with wedges delimit the regions involved in the alignment of the two full-length proteins. Orange and cyan bars highlight hydrophobicity peaks (i.e., inferred TMSs), respectively, for both proteins. A. Hydropathy plot of protein XP_020093034. TMSs 1–4 (shaded in dark gray) participate in the alignment shown in panel D. B. Hydropathy plot of protein GAQ80789. Hydrophobic peaks 5–8 (shaded in dark gray) participate in the alignment shown in panel D. C. Hydropathy plot of the alignment (E-value: 9.4×10 −102 ) between the full proteins. D. Hydropathy plot of the 4-TMS alignment (E-value: 5.0×10 −4 ) that provides evidence for the repeat. Interruptions in the hydropathy curves of panels C and D indicate gaps in the corresponding sequence alignments.

    Article Snippet: Similarly, in the structure of the Gallus gallus 7-TMS KDELR receptor (PDB: 6I6H) locked in the apo ER state, KDEL retrieval signal-bound Golgi state, and in complex with an antagonistic synthetic nanobody [ ], the MEME profile again maps to TMSs 1–2.

    Techniques: Sequencing