Preparation of whole cell protein extract For differential proteomic analysis, C. perfringens ATCC13124 was anaerobically grown on TPYG and CMM agar at 37°C for 24 hrs (corresponding to stationary

phase of growth) and the surface growth was harvested using 50 mM Tris/HCl, pH 7.2. Care was taken to avoid contamination CFTRinh-172 concentration from agar medium and the cells were buy NVP-BSK805 washed in 50 mM Tris/HCl, pH 7.2. The cells were resuspended in the same buffer supplemented with protease inhibitor (Protease inhibitor cocktail, Sigma). Cell lysis was performed by sonication and the un-disrupted cells were removed by centrifugation (10000 × g; 15 min; 4°C). Preparation of cell surface and cell envelope protein Cell surface protein was prepared by the method reported earlier for another Gram positive bacterium [46]. Briefly, C. perfringens cells were grown on TPYG broth at 37°C and twenty milliliter of culture was harvested in the exponential growth phase (OD600 nm~0.8). The harvested cells were washed twice with pre-cooled 50 mM Tris-HCl buffer, pH 7.2 and resuspended in 50 mM Tris-HCl buffer, pH 7.2 containing 2% (w/v) CHAPS. The protein preparation was placed on LY333531 order ice for 2 h, followed by centrifugation at 3500 × g at 4°C for 30 min to separate the cell surface proteins. The supernatant was filtered through a 0.22 μm syringe filter (Milipore, India) to obtain a cell free

surface protein preparation. For preparation of cell envelope (structure-associated) protein, the cells were grown on TPYG broth at 37°C and twenty

milliliter of culture was harvested mafosfamide in the exponential growth phase (OD600 nm~0.8). The harvested cells were washed twice with pre-cooled 50 mM Tris-HCl buffer, pH 7.2 and resuspended in the same buffer. Cell lysis was performed by sonication and the un-disrupted cells were removed by centrifugation (10,000 × g; 15 min; 4°C). Cell envelope proteins were then collected by centrifugation (40,000 × g; 30 min; 4°C) and washed three times with distilled water. The pellet was resuspended in distilled water, divided into aliquots and stored at -80°C until use. Total protein concentration was determined according to the method of Bradford [47] using Quick Start Bradford Protein Assay kit (Bio-Rad, USA) as per manufacturer’s instructions. The protein concentration was calculated using bovine serum albumin (BSA) as standard. 2-DE In order to improve focusing, proteins samples were purified using 2D-cleanup kit (Bio-Rad) and the protein pellet was finally resuspended in sample rehydration buffer (8 M urea, 2% w/v CHAPS, 15 mM DTT and 0.5% v/v IPG buffer pH 3–10). The isoelectric focusing was performed using immobilized pH gradient (IPG) strips (Bio-Rad, USA). IPG strips with a pH range from 5–8 were used for all the experiments except for the separation of surface proteins where strips of pH range 3–10 were used.