Fractionation of bacterial cell GSK923295 clinical trial culture Fractionation of the OM fraction, IM fraction, and soluble cell (SC) components was performed according to the methods of Valle et al. [49]. P. pneumotropica ATCC 35149 cells in the mid-log phase were harvested, resuspended in 10 mM HEPES (pH 7.5) with 50 mM selleck chemicals NaCl and 0.1 mg/ml lysozyme, and disrupted by sonication. The sonicate was centrifuged at 7,000 × g for 10 min, and subsequently, the supernatant was centrifuged at 100,000 × g for 1 h by using

a Beckman Optima TL Tabletop Centrifuge (Beckman Coulter, Brea, CA, USA). The supernatant was used as the SC fraction, and the pellet containing the bacterial membrane was resuspended in a buffer containing 0.5% sarkosyl (N-laurylsarcosine) and allowed to stand for 30 min at RT.

The sarkosyl-soluble fraction was centrifuged Nutlin-3a nmr at 100,000 × g for 1 h. The supernatant was used as the IM fraction, and the pellet was resuspended in a 500 μl of 10 mM HEPES (pH 7.5) with 50 mM NaCl, 1% sarkosyl, and 10 mM EDTA and used as the OM fraction. To prepare a cell-free supernatant, the P. pneumotropica ATCC 35149 culture in the mid-log phase was centrifuged at 7,000 × g for 10 min, and the supernatant was filtered through a 0.22-μm pore size filter (Millipore) followed by a 0.45-μm pore size filter (Millipore). The filtrate was ultrafiltrated at 1000 × g for 20 min by using AmiconUltra-15 (Millipore). The resultant solution was used as the ultrafiltrated culture supernatant (UC) fraction. For SDS-PAGE analysis, the concentration of the SC, IM, OM, and UC samples were adjusted to 0.2 mg/ml, and 10 μl of each sample were subjected to 10% SDS-PAGE. Cross-linking and pull-down assay To determine the in vitro interaction of rPnxIIIA and rPnxIIIE, chemical cross-linking and IP were performed. A cross-linker for soluble proteins, bis[sulfosuccinimidyl] suberate-d0 (BS3-d0; Thermo Fisher Scientific, Waltham, MA, USA), was used for the cross-linking reaction of rPnxIIIA and rPnxIIIE according to the manufacturer’s instructions. To terminate the cross-linking reaction, 20 mM NH4HCO3

was added. Thereafter, a mixed solution was subjected to IP by using an IP kit, Dynabeads Protein G (Invitrogen), and rabbit IgG against rPnxIIIA according to the manufacturer’s instructions. The resultant 5-Fluoracil concentration solution was subjected to SDS-PAGE, and the interaction of rPnxIIIA with rPnxIIIA or rPnxIIIE was detected by Western blotting as described below. Western blotting and Southern hybridization Fractions of the P. pneumotropica cell culture, IP-treated sample, and cell lysates of P. pneumotropica reference strains were analyzed by Western blotting by using anti-rPnxIIIA IgG (1:20,000) or anti-rPnxIIIE IgG (1:20,000), followed by SDS-PAGE separation. Anti-rabbit IgG antibody conjugated to horseradish peroxidase (HRP; Thermo Fisher Scientific) for anti-rPnxIIIA IgG was used as secondary antibodies at a dilution of 1:50,000.