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mouse anti vps35  (StressMarq)


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    StressMarq mouse anti vps35
    ( A ) HEK-293T or SH-SY5Y cells expressing TAP-tagged WT <t>VPS35</t> were subjected to TAP methodology and Western blot analysis. Inputs and TAP fractions were probed <t>with</t> <t>anti-VPS35</t> antibody. TAP purifies VPS35 more efficiently in HEK-293T cells compared to SH-SY5Y cells. ( B ) HEK-293T cells expressing TAP-tagged WT VPS35 or empty vector (EV) were subjected to TAP methodology followed by SDS-PAGE and silver staining. Endogenous VPS35 is observed slightly below VPS35-TAP band at ∼100 kDa. ( C ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. ( D ) HEK-293T cells expressing TAP-tagged WT VPS35 or EV were subjected to TAP methodology with HEPES-based buffers followed by Western blot analysis. Input and VPS35-TAP fractions were probed with anti-VPS35 or anti-VPS26 antibodies to confirm recovery of the retromer and then subjected to LC-MS/MS. ( E ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. Outside of the core retromer subunits, no known interacting proteins of VPS35 were identified. ( F ) Proportional Venn diagram demonstrating proteins identified in WT VPS35 TAP experiments using Tris– vs. HEPES-based buffers. ( G ) STRING diagram demonstrating the 7 proteins commonly identified between the two TAP experiments.
    Mouse Anti Vps35, supplied by StressMarq, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/vps35+antibody/VPS35+Antibody/bio_rxiv__64898__2026__04__09__717005-319-10-13
    Average 94 stars, based on 3 article reviews
    mouse anti vps35 - by Bioz Stars, 2026-09
    94/100 stars

    Images

    1) Product Images from "Parkinson’s disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35"

    Article Title: Parkinson’s disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35

    Journal: bioRxiv

    doi: 10.64898/2026.04.09.717005

    ( A ) HEK-293T or SH-SY5Y cells expressing TAP-tagged WT VPS35 were subjected to TAP methodology and Western blot analysis. Inputs and TAP fractions were probed with anti-VPS35 antibody. TAP purifies VPS35 more efficiently in HEK-293T cells compared to SH-SY5Y cells. ( B ) HEK-293T cells expressing TAP-tagged WT VPS35 or empty vector (EV) were subjected to TAP methodology followed by SDS-PAGE and silver staining. Endogenous VPS35 is observed slightly below VPS35-TAP band at ∼100 kDa. ( C ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. ( D ) HEK-293T cells expressing TAP-tagged WT VPS35 or EV were subjected to TAP methodology with HEPES-based buffers followed by Western blot analysis. Input and VPS35-TAP fractions were probed with anti-VPS35 or anti-VPS26 antibodies to confirm recovery of the retromer and then subjected to LC-MS/MS. ( E ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. Outside of the core retromer subunits, no known interacting proteins of VPS35 were identified. ( F ) Proportional Venn diagram demonstrating proteins identified in WT VPS35 TAP experiments using Tris– vs. HEPES-based buffers. ( G ) STRING diagram demonstrating the 7 proteins commonly identified between the two TAP experiments.
    Figure Legend Snippet: ( A ) HEK-293T or SH-SY5Y cells expressing TAP-tagged WT VPS35 were subjected to TAP methodology and Western blot analysis. Inputs and TAP fractions were probed with anti-VPS35 antibody. TAP purifies VPS35 more efficiently in HEK-293T cells compared to SH-SY5Y cells. ( B ) HEK-293T cells expressing TAP-tagged WT VPS35 or empty vector (EV) were subjected to TAP methodology followed by SDS-PAGE and silver staining. Endogenous VPS35 is observed slightly below VPS35-TAP band at ∼100 kDa. ( C ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. ( D ) HEK-293T cells expressing TAP-tagged WT VPS35 or EV were subjected to TAP methodology with HEPES-based buffers followed by Western blot analysis. Input and VPS35-TAP fractions were probed with anti-VPS35 or anti-VPS26 antibodies to confirm recovery of the retromer and then subjected to LC-MS/MS. ( E ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. Outside of the core retromer subunits, no known interacting proteins of VPS35 were identified. ( F ) Proportional Venn diagram demonstrating proteins identified in WT VPS35 TAP experiments using Tris– vs. HEPES-based buffers. ( G ) STRING diagram demonstrating the 7 proteins commonly identified between the two TAP experiments.

    Techniques Used: Expressing, Western Blot, Plasmid Preparation, SDS Page, Silver Staining, Liquid Chromatography with Mass Spectroscopy

    ( A ) HEK-293T cells expressing TAP-tagged WT VPS35 treated with increasing concentrations of DSP were subjected to affinity purification with either streptavidin or calmodulin resin followed by Western blot analysis under reducing or non-reducing conditions. Input and purified fractions were probed with anti-VPS35 or anti-actin antibodies. Only 0.3 mM DSP treatment preserved binding of TAP-tagged VPS35 to both streptavidin and calmodulin resins. (B) HEK-293T cells expressing TAP-tagged VPS35 treated with 0.3 mM DSP were subjected to TAP methodology followed by Western blot analysis under reducing or non-reducing conditions. Input and TAP fractions were probed with anti-VPS35 or anti-WASH1 antibodies. WT VPS35-TAP eluate was subjected to LC-MS/MS analysis. ( C ) Proportional Venn diagram showing the common interacting proteins of WT VPS35 identified in Tris-based alone vs HEPES-based with DSP TAP experiments. ( D ) Proportional Venn diagram demonstrating proteins identified in HEPES-based WT VPS35-TAP assays with or without DSP treatment. The addition of reversible cross-linking greatly increased the number of interacting proteins. ( E , F ) GO and KEGG pathway analysis using the functional annotation tool DAVID of VPS35-interacting proteins identified using DSP-treated TAP assays in HEK-293T cells overexpressing TAP-tagged VPS35-WT. Top 10 GO terms for each category and top 10 KEGG Pathway terms, based on Bonferroni-corrected p-value and fold enrichment, are displayed. Bubble plots generated using SRplot. ( G ) Functional enrichment analysis using the Cytoscape plug-in ClueGo with GO biological process terms of proteins found in DSP-treated WT VPS35 TAP assays. Pathways with a p-value of <0.05 and a Kappa score of 0.4 were mapped. Two-sided hypergeometric statistical analysis test with Bonferroni step-down p-value correction was used. Node size corresponds to p-value.
    Figure Legend Snippet: ( A ) HEK-293T cells expressing TAP-tagged WT VPS35 treated with increasing concentrations of DSP were subjected to affinity purification with either streptavidin or calmodulin resin followed by Western blot analysis under reducing or non-reducing conditions. Input and purified fractions were probed with anti-VPS35 or anti-actin antibodies. Only 0.3 mM DSP treatment preserved binding of TAP-tagged VPS35 to both streptavidin and calmodulin resins. (B) HEK-293T cells expressing TAP-tagged VPS35 treated with 0.3 mM DSP were subjected to TAP methodology followed by Western blot analysis under reducing or non-reducing conditions. Input and TAP fractions were probed with anti-VPS35 or anti-WASH1 antibodies. WT VPS35-TAP eluate was subjected to LC-MS/MS analysis. ( C ) Proportional Venn diagram showing the common interacting proteins of WT VPS35 identified in Tris-based alone vs HEPES-based with DSP TAP experiments. ( D ) Proportional Venn diagram demonstrating proteins identified in HEPES-based WT VPS35-TAP assays with or without DSP treatment. The addition of reversible cross-linking greatly increased the number of interacting proteins. ( E , F ) GO and KEGG pathway analysis using the functional annotation tool DAVID of VPS35-interacting proteins identified using DSP-treated TAP assays in HEK-293T cells overexpressing TAP-tagged VPS35-WT. Top 10 GO terms for each category and top 10 KEGG Pathway terms, based on Bonferroni-corrected p-value and fold enrichment, are displayed. Bubble plots generated using SRplot. ( G ) Functional enrichment analysis using the Cytoscape plug-in ClueGo with GO biological process terms of proteins found in DSP-treated WT VPS35 TAP assays. Pathways with a p-value of <0.05 and a Kappa score of 0.4 were mapped. Two-sided hypergeometric statistical analysis test with Bonferroni step-down p-value correction was used. Node size corresponds to p-value.

    Techniques Used: Expressing, Affinity Purification, Western Blot, Purification, Binding Assay, Liquid Chromatography with Mass Spectroscopy, Functional Assay, Generated

    ( A ) Soluble hemi-brain extracts from 3-4 month-old WT, heterozygous and homozygous KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( B ) Correlation analysis of VPS35-interacting proteins from WT vs homozygous D620N VPS35 KI reveal a high degree of correlation (R = 0.995). ( C ) Proportional Venn diagram demonstrating the strong overlap between interacting proteins identified in WT and homozygous D620N VPS35 KI brains. ( D ) Table highlighting peptide intensities across conditions for core retromer subunits, and three interacting proteins depleted in D620N VPS35 KI brain. ( E ) Soluble striatal extracts from 3-4 month-old WT and KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( F ) Table outlining peptide intensities across conditions for core retromer subunits in striatal tissue of D620N VPS35 KI mice. ( G ) Triton-soluble fractions from striatum of adult WT or D620N VPS35 KI mice were subjected to Western blot analysis to monitor steady-state levels of core retromer subunits (VPS35, VPS26, VPS29), Rab7 and TBC1D5. ( H ) Graphs indicate densitometric analysis of protein levels normalized to actin or β-tubulin and expressed as fold-change compared to WT mice (mean ± SEM, n = 3 mice/group). Data are not significant ( P >0.05) by unpaired, two-tailed Student’s t -test.
    Figure Legend Snippet: ( A ) Soluble hemi-brain extracts from 3-4 month-old WT, heterozygous and homozygous KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( B ) Correlation analysis of VPS35-interacting proteins from WT vs homozygous D620N VPS35 KI reveal a high degree of correlation (R = 0.995). ( C ) Proportional Venn diagram demonstrating the strong overlap between interacting proteins identified in WT and homozygous D620N VPS35 KI brains. ( D ) Table highlighting peptide intensities across conditions for core retromer subunits, and three interacting proteins depleted in D620N VPS35 KI brain. ( E ) Soluble striatal extracts from 3-4 month-old WT and KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( F ) Table outlining peptide intensities across conditions for core retromer subunits in striatal tissue of D620N VPS35 KI mice. ( G ) Triton-soluble fractions from striatum of adult WT or D620N VPS35 KI mice were subjected to Western blot analysis to monitor steady-state levels of core retromer subunits (VPS35, VPS26, VPS29), Rab7 and TBC1D5. ( H ) Graphs indicate densitometric analysis of protein levels normalized to actin or β-tubulin and expressed as fold-change compared to WT mice (mean ± SEM, n = 3 mice/group). Data are not significant ( P >0.05) by unpaired, two-tailed Student’s t -test.

    Techniques Used: Control, Western Blot, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test

    ( A ) Soluble striatal extracts from 3-4 month-old WT and D620N VPS35 KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-TBC1D5 antibodies confirming a TBC1D5 binding deficit in D620N VPS35 KI brain. Arrows indicate the position of TBC1D5 in the IP VPS35 samples and two non-specific bands in the control IP V5 sample. ( B ) HEK-293T cells expressing V5-tagged VPS35 variants (WT or D620N) were subjected to IP with anti-V5 antibody followed by Western blot analysis. Inputs and IPs were probed with anti-TBC1D5 or anti-V5 antibodies. ( C ) Graph indicates densitometric analysis of TBC1D5 levels in V5 IP, normalized to endogenous levels of TBC1D5 in the input, and expressed as a percent of the WT VPS35 IP condition (mean ± SEM, n = 3-4 experiments). ( D ) Representative confocal immunofluorescent images of HEK-293T cells co-labeled for endogenous TBC1D5 (red) and V5-tagged VPS35 variants (green). ( E ) Graph indicates Pearson’s correlation coefficients for TBC1D5 with WT or D620N VPS35 (mean ± SEM, n = 50 cells/condition). Data were analyzed by unpaired, two-tailed Student’s t -test (* P <0.05).
    Figure Legend Snippet: ( A ) Soluble striatal extracts from 3-4 month-old WT and D620N VPS35 KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-TBC1D5 antibodies confirming a TBC1D5 binding deficit in D620N VPS35 KI brain. Arrows indicate the position of TBC1D5 in the IP VPS35 samples and two non-specific bands in the control IP V5 sample. ( B ) HEK-293T cells expressing V5-tagged VPS35 variants (WT or D620N) were subjected to IP with anti-V5 antibody followed by Western blot analysis. Inputs and IPs were probed with anti-TBC1D5 or anti-V5 antibodies. ( C ) Graph indicates densitometric analysis of TBC1D5 levels in V5 IP, normalized to endogenous levels of TBC1D5 in the input, and expressed as a percent of the WT VPS35 IP condition (mean ± SEM, n = 3-4 experiments). ( D ) Representative confocal immunofluorescent images of HEK-293T cells co-labeled for endogenous TBC1D5 (red) and V5-tagged VPS35 variants (green). ( E ) Graph indicates Pearson’s correlation coefficients for TBC1D5 with WT or D620N VPS35 (mean ± SEM, n = 50 cells/condition). Data were analyzed by unpaired, two-tailed Student’s t -test (* P <0.05).

    Techniques Used: Control, Western Blot, Binding Assay, Expressing, Labeling, Two Tailed Test

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    Article Title: Parkinson’s VPS35[D620N] mutation induces LRRK2-mediated lysosomal association of RILPL1 and TMEM55B
    Article Snippet: ml phospho-T73 Rab10 Abcam ab230261 (AB_2811274) 1:1000 Rab12 MRC PPU Reagents and Services, University of Dundee SA227 (AB_2921227) 1 µg/ml phospho-S106 Rab12 Abcam ab256487 (AB_2884880) 1:1000 VPS35 StressMarq SMC-602 (AB_2820301) 1:5000 LC3A/B Cell Signaling Technology 4108 (AB_2137703) 1:1000 RILPL1 Abcam Ab302492 (AB_2936945) 1:1000 TMEM55A MRC PPU Reagents and Services, University of Dundee D



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    93
    Santa Cruz Biotechnology anti vps35
    ( A ) HEK-293T or SH-SY5Y cells expressing TAP-tagged WT <t>VPS35</t> were subjected to TAP methodology and Western blot analysis. Inputs and TAP fractions were probed <t>with</t> <t>anti-VPS35</t> antibody. TAP purifies VPS35 more efficiently in HEK-293T cells compared to SH-SY5Y cells. ( B ) HEK-293T cells expressing TAP-tagged WT VPS35 or empty vector (EV) were subjected to TAP methodology followed by SDS-PAGE and silver staining. Endogenous VPS35 is observed slightly below VPS35-TAP band at ∼100 kDa. ( C ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. ( D ) HEK-293T cells expressing TAP-tagged WT VPS35 or EV were subjected to TAP methodology with HEPES-based buffers followed by Western blot analysis. Input and VPS35-TAP fractions were probed with anti-VPS35 or anti-VPS26 antibodies to confirm recovery of the retromer and then subjected to LC-MS/MS. ( E ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. Outside of the core retromer subunits, no known interacting proteins of VPS35 were identified. ( F ) Proportional Venn diagram demonstrating proteins identified in WT VPS35 TAP experiments using Tris– vs. HEPES-based buffers. ( G ) STRING diagram demonstrating the 7 proteins commonly identified between the two TAP experiments.
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    ( A ) HEK-293T or SH-SY5Y cells expressing TAP-tagged WT VPS35 were subjected to TAP methodology and Western blot analysis. Inputs and TAP fractions were probed with anti-VPS35 antibody. TAP purifies VPS35 more efficiently in HEK-293T cells compared to SH-SY5Y cells. ( B ) HEK-293T cells expressing TAP-tagged WT VPS35 or empty vector (EV) were subjected to TAP methodology followed by SDS-PAGE and silver staining. Endogenous VPS35 is observed slightly below VPS35-TAP band at ∼100 kDa. ( C ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. ( D ) HEK-293T cells expressing TAP-tagged WT VPS35 or EV were subjected to TAP methodology with HEPES-based buffers followed by Western blot analysis. Input and VPS35-TAP fractions were probed with anti-VPS35 or anti-VPS26 antibodies to confirm recovery of the retromer and then subjected to LC-MS/MS. ( E ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. Outside of the core retromer subunits, no known interacting proteins of VPS35 were identified. ( F ) Proportional Venn diagram demonstrating proteins identified in WT VPS35 TAP experiments using Tris– vs. HEPES-based buffers. ( G ) STRING diagram demonstrating the 7 proteins commonly identified between the two TAP experiments.

    Journal: bioRxiv

    Article Title: Parkinson’s disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35

    doi: 10.64898/2026.04.09.717005

    Figure Lengend Snippet: ( A ) HEK-293T or SH-SY5Y cells expressing TAP-tagged WT VPS35 were subjected to TAP methodology and Western blot analysis. Inputs and TAP fractions were probed with anti-VPS35 antibody. TAP purifies VPS35 more efficiently in HEK-293T cells compared to SH-SY5Y cells. ( B ) HEK-293T cells expressing TAP-tagged WT VPS35 or empty vector (EV) were subjected to TAP methodology followed by SDS-PAGE and silver staining. Endogenous VPS35 is observed slightly below VPS35-TAP band at ∼100 kDa. ( C ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. ( D ) HEK-293T cells expressing TAP-tagged WT VPS35 or EV were subjected to TAP methodology with HEPES-based buffers followed by Western blot analysis. Input and VPS35-TAP fractions were probed with anti-VPS35 or anti-VPS26 antibodies to confirm recovery of the retromer and then subjected to LC-MS/MS. ( E ) STRING diagram of interacting proteins identified by LC-MS/MS analysis of WT VPS35-TAP. Outside of the core retromer subunits, no known interacting proteins of VPS35 were identified. ( F ) Proportional Venn diagram demonstrating proteins identified in WT VPS35 TAP experiments using Tris– vs. HEPES-based buffers. ( G ) STRING diagram demonstrating the 7 proteins commonly identified between the two TAP experiments.

    Article Snippet: The following primary antibodies were used: mouse anti-VPS35 (ab57632, Abcam), mouse anti-VPS35 (SMC-602, stressmarq), mouse anti-V5 (Thermo Fisher), mouse anti-V5-HRP (R96125, Invitrogen), mouse anti-GFP (clone 7.1 and 13.1, Roche), rabbit anti-VPS26 (ab23892, Abcam), goat anti-VPS29 (ab10160, Abcam), rabbit anti-WASH1 (SAB4200372, Sigma-Aldrich), rabbit anti-Rab7 (ab137029, Abcam), mouse anti-actin (MAB1501, Millipore), mouse anti-β-tubulin (Sigma, T5201), rabbit anti-TBC1D5 (ab203896, Abcam) and mouse anti-TBC1D5 (sc-376296, Santa Cruz Biotechnology).

    Techniques: Expressing, Western Blot, Plasmid Preparation, SDS Page, Silver Staining, Liquid Chromatography with Mass Spectroscopy

    ( A ) HEK-293T cells expressing TAP-tagged WT VPS35 treated with increasing concentrations of DSP were subjected to affinity purification with either streptavidin or calmodulin resin followed by Western blot analysis under reducing or non-reducing conditions. Input and purified fractions were probed with anti-VPS35 or anti-actin antibodies. Only 0.3 mM DSP treatment preserved binding of TAP-tagged VPS35 to both streptavidin and calmodulin resins. (B) HEK-293T cells expressing TAP-tagged VPS35 treated with 0.3 mM DSP were subjected to TAP methodology followed by Western blot analysis under reducing or non-reducing conditions. Input and TAP fractions were probed with anti-VPS35 or anti-WASH1 antibodies. WT VPS35-TAP eluate was subjected to LC-MS/MS analysis. ( C ) Proportional Venn diagram showing the common interacting proteins of WT VPS35 identified in Tris-based alone vs HEPES-based with DSP TAP experiments. ( D ) Proportional Venn diagram demonstrating proteins identified in HEPES-based WT VPS35-TAP assays with or without DSP treatment. The addition of reversible cross-linking greatly increased the number of interacting proteins. ( E , F ) GO and KEGG pathway analysis using the functional annotation tool DAVID of VPS35-interacting proteins identified using DSP-treated TAP assays in HEK-293T cells overexpressing TAP-tagged VPS35-WT. Top 10 GO terms for each category and top 10 KEGG Pathway terms, based on Bonferroni-corrected p-value and fold enrichment, are displayed. Bubble plots generated using SRplot. ( G ) Functional enrichment analysis using the Cytoscape plug-in ClueGo with GO biological process terms of proteins found in DSP-treated WT VPS35 TAP assays. Pathways with a p-value of <0.05 and a Kappa score of 0.4 were mapped. Two-sided hypergeometric statistical analysis test with Bonferroni step-down p-value correction was used. Node size corresponds to p-value.

    Journal: bioRxiv

    Article Title: Parkinson’s disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35

    doi: 10.64898/2026.04.09.717005

    Figure Lengend Snippet: ( A ) HEK-293T cells expressing TAP-tagged WT VPS35 treated with increasing concentrations of DSP were subjected to affinity purification with either streptavidin or calmodulin resin followed by Western blot analysis under reducing or non-reducing conditions. Input and purified fractions were probed with anti-VPS35 or anti-actin antibodies. Only 0.3 mM DSP treatment preserved binding of TAP-tagged VPS35 to both streptavidin and calmodulin resins. (B) HEK-293T cells expressing TAP-tagged VPS35 treated with 0.3 mM DSP were subjected to TAP methodology followed by Western blot analysis under reducing or non-reducing conditions. Input and TAP fractions were probed with anti-VPS35 or anti-WASH1 antibodies. WT VPS35-TAP eluate was subjected to LC-MS/MS analysis. ( C ) Proportional Venn diagram showing the common interacting proteins of WT VPS35 identified in Tris-based alone vs HEPES-based with DSP TAP experiments. ( D ) Proportional Venn diagram demonstrating proteins identified in HEPES-based WT VPS35-TAP assays with or without DSP treatment. The addition of reversible cross-linking greatly increased the number of interacting proteins. ( E , F ) GO and KEGG pathway analysis using the functional annotation tool DAVID of VPS35-interacting proteins identified using DSP-treated TAP assays in HEK-293T cells overexpressing TAP-tagged VPS35-WT. Top 10 GO terms for each category and top 10 KEGG Pathway terms, based on Bonferroni-corrected p-value and fold enrichment, are displayed. Bubble plots generated using SRplot. ( G ) Functional enrichment analysis using the Cytoscape plug-in ClueGo with GO biological process terms of proteins found in DSP-treated WT VPS35 TAP assays. Pathways with a p-value of <0.05 and a Kappa score of 0.4 were mapped. Two-sided hypergeometric statistical analysis test with Bonferroni step-down p-value correction was used. Node size corresponds to p-value.

    Article Snippet: The following primary antibodies were used: mouse anti-VPS35 (ab57632, Abcam), mouse anti-VPS35 (SMC-602, stressmarq), mouse anti-V5 (Thermo Fisher), mouse anti-V5-HRP (R96125, Invitrogen), mouse anti-GFP (clone 7.1 and 13.1, Roche), rabbit anti-VPS26 (ab23892, Abcam), goat anti-VPS29 (ab10160, Abcam), rabbit anti-WASH1 (SAB4200372, Sigma-Aldrich), rabbit anti-Rab7 (ab137029, Abcam), mouse anti-actin (MAB1501, Millipore), mouse anti-β-tubulin (Sigma, T5201), rabbit anti-TBC1D5 (ab203896, Abcam) and mouse anti-TBC1D5 (sc-376296, Santa Cruz Biotechnology).

    Techniques: Expressing, Affinity Purification, Western Blot, Purification, Binding Assay, Liquid Chromatography with Mass Spectroscopy, Functional Assay, Generated

    ( A ) Soluble hemi-brain extracts from 3-4 month-old WT, heterozygous and homozygous KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( B ) Correlation analysis of VPS35-interacting proteins from WT vs homozygous D620N VPS35 KI reveal a high degree of correlation (R = 0.995). ( C ) Proportional Venn diagram demonstrating the strong overlap between interacting proteins identified in WT and homozygous D620N VPS35 KI brains. ( D ) Table highlighting peptide intensities across conditions for core retromer subunits, and three interacting proteins depleted in D620N VPS35 KI brain. ( E ) Soluble striatal extracts from 3-4 month-old WT and KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( F ) Table outlining peptide intensities across conditions for core retromer subunits in striatal tissue of D620N VPS35 KI mice. ( G ) Triton-soluble fractions from striatum of adult WT or D620N VPS35 KI mice were subjected to Western blot analysis to monitor steady-state levels of core retromer subunits (VPS35, VPS26, VPS29), Rab7 and TBC1D5. ( H ) Graphs indicate densitometric analysis of protein levels normalized to actin or β-tubulin and expressed as fold-change compared to WT mice (mean ± SEM, n = 3 mice/group). Data are not significant ( P >0.05) by unpaired, two-tailed Student’s t -test.

    Journal: bioRxiv

    Article Title: Parkinson’s disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35

    doi: 10.64898/2026.04.09.717005

    Figure Lengend Snippet: ( A ) Soluble hemi-brain extracts from 3-4 month-old WT, heterozygous and homozygous KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( B ) Correlation analysis of VPS35-interacting proteins from WT vs homozygous D620N VPS35 KI reveal a high degree of correlation (R = 0.995). ( C ) Proportional Venn diagram demonstrating the strong overlap between interacting proteins identified in WT and homozygous D620N VPS35 KI brains. ( D ) Table highlighting peptide intensities across conditions for core retromer subunits, and three interacting proteins depleted in D620N VPS35 KI brain. ( E ) Soluble striatal extracts from 3-4 month-old WT and KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-VPS26 antibodies, prior to subjecting VPS35 IP samples to LC-MS/MS analysis. ( F ) Table outlining peptide intensities across conditions for core retromer subunits in striatal tissue of D620N VPS35 KI mice. ( G ) Triton-soluble fractions from striatum of adult WT or D620N VPS35 KI mice were subjected to Western blot analysis to monitor steady-state levels of core retromer subunits (VPS35, VPS26, VPS29), Rab7 and TBC1D5. ( H ) Graphs indicate densitometric analysis of protein levels normalized to actin or β-tubulin and expressed as fold-change compared to WT mice (mean ± SEM, n = 3 mice/group). Data are not significant ( P >0.05) by unpaired, two-tailed Student’s t -test.

    Article Snippet: The following primary antibodies were used: mouse anti-VPS35 (ab57632, Abcam), mouse anti-VPS35 (SMC-602, stressmarq), mouse anti-V5 (Thermo Fisher), mouse anti-V5-HRP (R96125, Invitrogen), mouse anti-GFP (clone 7.1 and 13.1, Roche), rabbit anti-VPS26 (ab23892, Abcam), goat anti-VPS29 (ab10160, Abcam), rabbit anti-WASH1 (SAB4200372, Sigma-Aldrich), rabbit anti-Rab7 (ab137029, Abcam), mouse anti-actin (MAB1501, Millipore), mouse anti-β-tubulin (Sigma, T5201), rabbit anti-TBC1D5 (ab203896, Abcam) and mouse anti-TBC1D5 (sc-376296, Santa Cruz Biotechnology).

    Techniques: Control, Western Blot, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test

    ( A ) Soluble striatal extracts from 3-4 month-old WT and D620N VPS35 KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-TBC1D5 antibodies confirming a TBC1D5 binding deficit in D620N VPS35 KI brain. Arrows indicate the position of TBC1D5 in the IP VPS35 samples and two non-specific bands in the control IP V5 sample. ( B ) HEK-293T cells expressing V5-tagged VPS35 variants (WT or D620N) were subjected to IP with anti-V5 antibody followed by Western blot analysis. Inputs and IPs were probed with anti-TBC1D5 or anti-V5 antibodies. ( C ) Graph indicates densitometric analysis of TBC1D5 levels in V5 IP, normalized to endogenous levels of TBC1D5 in the input, and expressed as a percent of the WT VPS35 IP condition (mean ± SEM, n = 3-4 experiments). ( D ) Representative confocal immunofluorescent images of HEK-293T cells co-labeled for endogenous TBC1D5 (red) and V5-tagged VPS35 variants (green). ( E ) Graph indicates Pearson’s correlation coefficients for TBC1D5 with WT or D620N VPS35 (mean ± SEM, n = 50 cells/condition). Data were analyzed by unpaired, two-tailed Student’s t -test (* P <0.05).

    Journal: bioRxiv

    Article Title: Parkinson’s disease-linked D620N mutation selectively alters the brain-specific protein interactome of VPS35

    doi: 10.64898/2026.04.09.717005

    Figure Lengend Snippet: ( A ) Soluble striatal extracts from 3-4 month-old WT and D620N VPS35 KI mice were subjected to IP with anti-VPS35 antibody (or isotype-matched control anti-V5 IgG) followed by Western blot analysis. Input and IP fractions were probed with anti-VPS35 and anti-TBC1D5 antibodies confirming a TBC1D5 binding deficit in D620N VPS35 KI brain. Arrows indicate the position of TBC1D5 in the IP VPS35 samples and two non-specific bands in the control IP V5 sample. ( B ) HEK-293T cells expressing V5-tagged VPS35 variants (WT or D620N) were subjected to IP with anti-V5 antibody followed by Western blot analysis. Inputs and IPs were probed with anti-TBC1D5 or anti-V5 antibodies. ( C ) Graph indicates densitometric analysis of TBC1D5 levels in V5 IP, normalized to endogenous levels of TBC1D5 in the input, and expressed as a percent of the WT VPS35 IP condition (mean ± SEM, n = 3-4 experiments). ( D ) Representative confocal immunofluorescent images of HEK-293T cells co-labeled for endogenous TBC1D5 (red) and V5-tagged VPS35 variants (green). ( E ) Graph indicates Pearson’s correlation coefficients for TBC1D5 with WT or D620N VPS35 (mean ± SEM, n = 50 cells/condition). Data were analyzed by unpaired, two-tailed Student’s t -test (* P <0.05).

    Article Snippet: The following primary antibodies were used: mouse anti-VPS35 (ab57632, Abcam), mouse anti-VPS35 (SMC-602, stressmarq), mouse anti-V5 (Thermo Fisher), mouse anti-V5-HRP (R96125, Invitrogen), mouse anti-GFP (clone 7.1 and 13.1, Roche), rabbit anti-VPS26 (ab23892, Abcam), goat anti-VPS29 (ab10160, Abcam), rabbit anti-WASH1 (SAB4200372, Sigma-Aldrich), rabbit anti-Rab7 (ab137029, Abcam), mouse anti-actin (MAB1501, Millipore), mouse anti-β-tubulin (Sigma, T5201), rabbit anti-TBC1D5 (ab203896, Abcam) and mouse anti-TBC1D5 (sc-376296, Santa Cruz Biotechnology).

    Techniques: Control, Western Blot, Binding Assay, Expressing, Labeling, Two Tailed Test