Crystallization screening was carried

out using the sitting-drop, vapor-diffusion technique in 96-well microplates. Trays were set using a Phenix crystallization robot (Art Robbins instrument) and commercial crystallization kits (HR-Index, HR-AMSO4, HR-Cryst1&2, HR-Cryo from Hampton Research, Nextal-JCSG + from QIAGEN, Proplex and PACT from Molecular Dimensions). The drops were set up by mixing equal volumes (0.1 μl) of the protein and the precipitant solutions equilibrated against 75 μl of the precipitant solution. The protein concentrations ranged from 10 to 80 mg/ml for PASBvg N2C3 and N2C2 and from 10 to 30 mg/ml for PASBvg N3C2 and N3C3. To prepare the membrane fractions of the various B. pertussis strains, the bacteria were grown in modified Stainer-Scholte medium (SS) [24] containing 100 μg/ml streptomycin and 10 μg/ml gentamycin. After 24 h at 37°C under rotating agitation (220 rpm) cells HDAC inhibitors list were harvested by centrifugation, resuspended in phosphate-buffered saline (PBS) to an OD600 of 5 and broken using a Hybaid Ribolyser apparatus (30 s at speed 6 in tubes containing 0.1 mm silica spheres as C188-9 ic50 the lysing

matrix). The lysates were clarified by centrifugation (8000 × g, 10 minutes), and the membrane fractions were pelleted from 1 ml of supernatants by ultracentrifugation (90 000 × g, 1 hour). The pellets were resuspended in 100 μl PBS and used for denaturing electrophoresis in 4-8% gradient polyacrylamide gels (Novex, Life Technologies). The proteins were then transferred electrophoretically to nitrocellulose membranes for immunoblotting.

Polyclonal antibodies against BvgS were raised in rats (Eurogentec, Belgium) and used at a 1:500 dilution Urocanase in PBS + 0.1% Tween 20. The secondary antibody was an anti-rat immunoglobulin- alkaline phosphatase conjugate (Promega) at a 1:7,500 dilution in the same buffer. Revelation of the blots was performed using the BCIP/NBT Color Development Substrate (Promega). Homology modeling A similarity search using PSI-BLAST [25] was performed to find suitable templates. Modeller 9v8 [26] was used to build a model of the structure of the PAS domain of BvgS based on 3BWL. The protein side-chain conformations were predicted using SCWRL4 [27]. The quality of the model was assessed using PROSA II [28]. Molecular structure inspections and illustrations were made using PyMOL (PyMOL Molecular Graphics System, version 1.3, Schrödinger). β-galactosidase activities The various B. pertussis strains harboring specific mutations in bvgS and a ptx-lacZ fusion were grown in modified SS medium containing 100 μg/ml streptomycin and 10 μg/ml gentamycin. After 24 h at 37°C under rotating agitation as above, the bacterial suspension was used to initiate cultures in 10 ml of medium either not supplemented or containing the desired concentration of modulators.