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5 protocols using leupeptin

1

Peptide Synthesis and Epigenetic Assays

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All cloning reagents were obtained from New England Biolab (Gibson assembly Master Mix, Q5-mutagenesis kit) or Thermo Scientific (Fast Digest restriction enzymes). Reagents and building blocks for the solid phase peptide synthesis (SPPS) were from Anaspec, P3Bio, ChemPep, or Aaptec. The Chem Matrix Rink Amide resin was from Sigma. Solvents for SPPS, HPLC, and LC/MS, buffering agents, and additives were from Sigma or Fisher Scientific. Antibiotics, IPTG, DTT, and protease inhibitors (leupeptin, pepstatin, aprotinin, AEBSF) were from Gold Bio. KRX E.coli cells, NanoBit, and NanoGlow luciferase assay components were from Promega, and L-rhamnose was from Chem-Implex. tRNA from yeast was purchased from Sigma. Corning 384 Well Low Volume Black Round Bottom Polystyrene NBS Microplates were from Sigma. Anti-Histone H3 (acetyl K18) antibody - ChIP Grade (ab1191) was from Abcam, Anti-Histone H3 (acetyl K9) antibody (ab4441) was from Abcam. Secondary antibodies IRDye 680RD anti-mouse and IRDye 800CW anti-rabbit were from Li-Cor.
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2

Assembly of SDS-resistant SNARE Complex

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The SNARE motifs were mixed in equimolar ratios in the following order: synaptobrevin-2 (29–93), SNAP-25A(141–203), SNAP-25A(11–82) and syntaxin-1A (191–253), in the presence of 1 M NaCl. The mixture contained the following protease inhibitors (protease inhibitor cocktail A): Antipain Dihydrochloride 0.016 mg/ml (Thermo Fischer Scientific: 50488492); Leupeptin 0.33 mg/ml (Gold Bio: L01025); Aprotinin 0.08 mg/ml (Gold Bio: A655100). The assembly reaction was incubated at room temperature overnight while rotating. The SNARE motifs that did not incorporate into complex were removed by concentration-dilution at room temperature using 30 kDa molecular weight cutoff (MWCO) Amicon centrifugation filters. The almost quantitative formation of SDS-resistant SNARE complex was verified by SDS-PAGE and Coomassie blue staining.
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Assembling SNARE Protein Complex

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The SNARE motifs were mixed in the equimolar ratio in following order: synaptobrevin-2 (29–93), SNAP-25A(141–203), SNAP-25A(11–82) and syntaxin-1A (191–253), in the presence of 1 M NaCl. The mixture contained the following protease inhibitors (protease inhibitor cocktail A): Antipain Dihydrochloride 0.016 mg/ml (Thermo Fischer Scientific: 50488492); Leupeptin 0.33 mg/ml (Gold Bio: L01025); Aprotinin 0.08 mg/ml (Gold Bio: A655100). The assembly reaction was incubated in room temperature overnight while rotating. The SNARE motifs that did not incorporate into complex were removed by concentration-dilution at room temperature using 30 kDa molecular weight cutoff (MWCO) Amicon centrifugation filters.
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4

Purification of Recombinant Proteins

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The protease inhibitor cocktail was purchased from BioVision (Mountain View, CA, USA). Deuterium oxide was purchased from Cambridge Isotope Laboratories (Tewksbury, MA, USA). Chelating sepharose resin for Ni-IDA purification was purchased from Cytiva (Uppsala, Sweden). EDTA, Tris, and NaH2PO4 were purchased from Duchefa Biochemie BV (Haarlem, The Netherlands). HEPES, IPTG, leupeptin, lysozyme, kanamycin, and TCEP were purchased from Goldbio (St. Louis, MO, USA). Acetonitrile, H2O, and MeOH were purchased from JT Baker (Phillipsburg, NJ, USA). DNase I was purchased from Roche (Basel, Switzerland). BODIPY-FL-GTP and BODIPY-FL-GTPγS were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Acetic acid, benzamidine, formic acid, GDP, phosphoric acid, imidazole, and MgCl2 were purchased from Sigma–Aldrich (St. Louis, MO, USA).
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5

Recombinant Protein Expression and Purification

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Unless otherwise indicated, all chemical reagents were obtained from Sigma or Fisher Scientific. Fluorescein di-β-D-galactopyranoside (FDG) was from Marker Gene Technologies, and the protein inhibitor mixture was from Sigma (catalog no. S8830). Leupeptin, pepstatin, and aprotinin were from Gold Biotechnology. All restriction endonucleases and E. coli strain BL21(DE3) were from Thermo Scientific. E. coli strain DH5α was purchased from New England Biolabs. Pfu ultra DNA polymerase used for site-directed mutagenesis was purchased from Agilent. [γ-32P]GTP was from Perkin Elmer. Mouse monoclonal antibodies raised against α-tubulin (T6074), FLAG tag (F1804) or His-tag (H1029) were from Sigma. Mouse monoclonal antibody raised against hemagglutinin (HA) tag (clone 12CA5, #11583816001) was obtained from Roche. Mouse monoclonal antibody raised against MYC-tag (9B11, #2276) was from Cell Signaling. Rabbit polyclonal antibody raised against Gαs (C-18, sc-383) was purchased from Santa Cruz Biotechnology. Goat anti-rabbit Alexa Fluor 680 (A21077) and goat anti-mouse IRDye 800 (#926–32210) secondary antibodies were from Life technologies and LiCor, respectively.
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