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9 protocols using trans epoxysuccinyl l leucylamido 4 guanidino butane e64

1

Fibrinolytic Enzyme Characterization

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The fibrinolytic enzyme type was determined by evaluating the effects of multifarious inhibitors on the fibrinolytic activity. Briefly, the purified enzyme solution (50 IU/ml) was pre-incubated at 37 °C for 30 min separately with each of the following inhibitors: 5.0 mM serine protease inhibitor phenylmethanesulfonyl fluoride (PMSF; Sigma, Beijing, China), 5.0 mM metalloprotease inhibitor ethylene diamine tetraacetic acid (EDTA; Sigma, Beijing, China), 10 µM aspartic protease inhibitor pepstatin A (Sigma, Beijing, China), 1.0 mM cysteine protease inhibitor trans-epoxysuccinyl-L-leucylamido-(4-guanidino) butane (E64; Sigma, Beijing, China), and 1.0 mM aminopeptidase inhibitor bestatin (Sigma, Beijing, China). To measure the effects of metal ions on the activity, the fibrinolytic enzyme (50 IU/ml) was pre-incubated separately with different metal ions (final concentration 5 mM) at pH 7.5 and 37 °C for 30 min. The enzyme solution without added ions was used as a control.
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2

Isolation of P. falciparum Parasitophorous Vacuole Membrane

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Experiments were performed with the 3D7 laboratory strain of P. falciparum. Parasitophorous-vacuole-enclosed membrane structures (PEMS) were isolated as previously described (66 (link)). Briefly, parasite cultures were routinely maintained at <10% parasitemia and 2% hematocrit. Following two rounds of synchronization by sorbitol lysis, the rings were allowed to develop into mature trophozoites and were isolated on a 65% Percoll (Sigma) density gradient. Thereafter, a cysteine protease inhibitor, trans-epoxysuccinyl-l-leucylamido(4-guanidino)butane (E-64; Sigma) was added for 8 h to allow growth of late-stage pigmented trophozoites into schizonts without rupture. The treated cultures were pelleted by low-speed centrifugation, resuspended in PBS at 1.8 × 106 schizonts/ml, and immediately frozen at −20°C to lyse the RBCs.
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3

Protein Persulfide Detection in Mouse Cortical Tissue

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Mouse cortical tissue was homogenized in a 20-fold volume of RIPA buffer containing 10 mM Tris-HCl (pH 7.4), 150 mM NaCl, 0.1% sodium deoxycholate, 0.1% SDS, 1% NP-40, 10 mM trans-Epoxysuccinyl-l-leucylamido(4-guanidino)butane (E-64) (Sigma), 10 mM Bestatin hydrochloride (Sigma), 10 mM Pepstatin A (Peptide Institute, Osaka, Japan), 10 mM Leupeptin (Peptide Institute), and either 1 mM TME-IAM or 3 mM BM. The homogenate was then centrifuged at 20,380× g at 4 °C for 15 min and incubated at 37 °C for 1 h while rotating. A part of the TME-IAM-treated samples was then diluted with RIPA buffer containing BM (final concentration 3 mM), and further incubated at 37 ℃ for 1 h while rotating. After boiling in SDS sample buffer in the absence of reductants, proteins were subjected to SDS-PAGE, followed by Coomassie Brilliant Blue (CBB) stain or Western blotting using either Poly-HRP Streptavidin (200,000 dilutions; Thermo Fisher Scientific, Waltham, MA, USA) or rat anti-TME-IAM antiserum (1:3000 dilution). The procedures for signal detection and band intensity quantification were identical to those described in Section 2.7. Protein persulfides were estimated by semi-quantitative analysis of the band intensities of samples treated with both TME-IAM and BM or only BM. The uncropped Western blotting images are shown in the original Western blotting Figure S2.
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4

Rabbit Anti-Cap Polyclonal Antibody Protocol

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The rabbit anti-Cap polyclonal antibody (pAb) was a kind gift from Prof. Zeng-Jun Lu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Monoclonal antibodies against cyclin A (CycA), GRP78, IκBα, NF-κB p65 and β-actin were purchased from Santa Cruz Biotechnology (USA). 1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid tetra(acetoxymethyl)ester (BAPTA-AM), MG132, trans-epoxysuccinyl-L-leucylamido-4-guanidino butane (E64) and ammonium chloride (NH4Cl) were purchased from Sigma-Aldrich (USA). The plasmid pMD-19T-ORF1 (our unpublished construct) (Takara) was maintained in our laboratory.
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5

Lung Caspase-3 Protein Level Quantification

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Whole lung tissue isolated from the mice were first homogenized in isotonic buffer with CHAPS detergent (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 10 mM CHAPS) with protease inhibitors (100 μM 3,4-dichloroisocoumarin (DCI), 10 μM trans-epoxysuccinyl-L-leucylamido- (4-guanidino) butane (E-64), 2 mM o-phenanthroline monohydrate (all from Sigma) and then sonicated briefly. The protein concentration of the total lung homogenates was quantified using the BCA standard protein assay kit (Thermo Fisher). Lung homogenate samples (50μgs) were separated by SDS-PAGE and transferred to PVDF membranes as described previously [37 (link)]. The membranes were blocked overnight in 5% nonfat dry milk/PBST for an hour at room temperature. The membranes were then incubated with rabbit anti-mouse caspase-3 (1:1000; Cell Signaling) overnight at 4°C followed by anti-rabbit HRP IgG (1:2000) for 1 hr at room temperature. The membranes were washed with PBST (3x for 10 min) between primary and secondary antibody incubation. The reactive bands were visualized using the chemiluminescence method (SuperSignal West Pico, Pierce). The same membranes were reprobed with GAPDH (1:500; Cell Signaling) as loading controls. Densitometric analysis was performed using ImageJ to compare protein levels and the data analyzed by unpaired two-tailed student T test.
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6

Papain Treatment of Viscous Fractions

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Prior to enzyme treatment, viscous fractions were diluted 1:1 with a modified Tyrode’s medium warmed to 37 °C and supplemented with albumin, lactate and pyruvate (TALP) [35 (link)], and 3 mg/mL BSA was added fresh on the day of collection.
Half of the sample (Exp 1) or all of the sample (Exp 2) was then incubated with Papain (0.1 mg/mL; Sigma 76216, St. Louis, MO, USA) at 37 °C for 30 min, (Papain-treated; Exp 1 and 2). In experiment 1 the remaining sample was left untreated (Viscous control; Exp 1) before being processed for cryopreservation.
Following treatment, the reaction was then suspended with the addition of an inhibitor, trans-epoxysuccinyl-L-leucylamido (4-guanidino)butane (E-64;10 μM; Sigma E3132, St. Louis, MO, USA) and incubated at 37 °C for 5 min [30 (link)].
To demonstrate the change in viscosity due to Papain treatment, the time taken for aliquots (3 μL) of treated and non-treated viscous fractions to fill a standard 20 µm Leja CASA slide (Hamilton Thorne, Beverly, MA, USA) was recorded (n = 1 bull only), as previously described [36 (link)].
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7

Valorization of Waste Hair and Sludge

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The main waste used for this research was hydrolysed hair produced during the dehairing of bovine hide and obtained from a local tanning industry located in Igualada (Barcelona, Spain). ADS from a local wastewater treatment plant were used as cosubstrate for the SSF process. The complete characterization of substrates in terms of physical, chemical and overall biological activity is presented in Table 1. For the mixture, firstly, hair waste and ADS were mixed in a weight ratio of 1:2, as described in previous studies (Abraham et al., 2014; Barrena et al., 2007a) . Afterwards, wood chips were used as bulking agent to the mixture hair: sludge in a 1:1 volumetric ratio to create the proper porosity in the mixtures (Barrena et al., 2007b) .
Protease inhibitorsphenylmethylsulfonyl fluoride (PMSF), pepstatin A and transepoxysuccinyl-L-leucylamido-(4-guanidino)butane (e64) were purchased from Sigma-Aldrich (St. Louis).
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8

Protein Purification Protocol

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Detergents (sodium dodecyl sulfate (SDS) and Triton X-100), dithiothreitol (DTT), glycerol, penicillin, streptomycin, Schneider's Drosophila medium, protein A-agarose, transepoxysuccinyl-L-leucylamido(4-guanidino)butane (E-64), the silver Stain kit Proteo Silver™, nitrocellulose membranes, and cell culture flasks were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO). The micro-bicinchoninic acid (BCA) protein assay kit was purchased from Pierce Chemical Co. (Appleton, WI). Fetal calf serum (FCS) was acquired from Gibco, Invitrogen (Brazil). A bacterial expression vector containing the T7lac promoter (pET28a) was purchased from GenScript, Inc. (Piscataway, NJ, USA). Nickel-charged (Ni-NTA) resin was obtained from Qiagen (Brazil). The full-range rainbow™ kit, 12 to 225 kDa, was purchased from GE Healthcare Life's Sciences (Little Chalfont, UK). Coupling agents [1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS)] and ethanolamide were purchased from Merck Millipore Corporation (Darmstadt, Alemanha). A carboxylated gold sensor chip (COOH1 chip) was acquired from ICx Nomadics, Inc. (Stillwater, OK). Chemiluminescence was performed using the SuperSignal West Pico Chemiluminescent kit™ Substrate (Thermo Scientific, EUA). All reagents were of analytical grade or higher.
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9

Recombinant Procathepsin K Purification

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Recombinant human procathepsin K was expressed and processed to the mature form as previously described 18 . Equine and human type II collagens were purified from fetal cartilages following pepsin digestion using standard methods 19 . Chondroitin 4-sulfate (C4-S) (chondroitin sulfate A from bovine trachea which is predominantly C4-S), trans-epoxysuccinyl-L-leucylamido-(4guanidino) butane (E-64) and trypsin (proteomic grade) were purchased from Sigma (St-Louis, Mo).
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