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Ose membrane (0.45 mm pore size, Biorad) and left to dry for at least 30 minutes at room temperature. The spotted membranes were washed three times with PBST (0.05 Tween 20 in phosphate-buffered saline or PBS pH 7.4) applying a constant vacuum flow using SNAP i.d. Protein Detection System (Millipore) and blocked for 1 h at roomNeutralizing Epitope Guiding Bacterial Clearancetemperature in PBST bu
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Ose membrane (0.45 mm pore size, Biorad) and left to dry for at least 30 minutes at room temperature. The spotted membranes were washed three times with PBST (0.05 Tween 20 in phosphate-buffered saline or PBS pH 7.4) applying a constant vacuum flow using SNAP i.d. Protein Detection System (Millipore) and blocked for 1 h at roomNeutralizing Epitope Guiding Bacterial Clearancetemperature in PBST bu
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Nto account the experimental data from Mass analysis, setting a weight of 1.5 on exposed aminoacid residues identified and on the surface area (4A) around them. Best docked complexes were selected according to energy scoring function and were finally energyminimized using the Sander program from the Amber8 package.18. During energy minimization, a Generalized Born (GB) model was employed to implic
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Engine (Matrix Science. London, UK) was used with the following parameters: one missed cleavage permission, 20 ppm measurement for MS and 0.3 Da for MS/MS tolerance. Positive identifications were accepted with p values lower than 0.05. In the searches, methionine residues modified to methionine sulfoxide were allowed. 2) Partial digestion of immunocaptured antigens. To allow the capture of conform
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R, Thr, Val) are represented by one pseudo atom and larger and more flexible side chains are represented by two pseudo atoms, to better describe the shape and dual chemical character of side chains. The contacts between pseudo atoms are described by different interaction: Lennard ones (LJ)-type potentials (A/r8-B/r6-potential), repulsive and attractive LJ-parameters describing approximately the si
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R, Thr, Val) are represented by one pseudo atom and larger and more flexible side chains are represented by two pseudo atoms, to better describe the shape and dual chemical character of side chains. The contacts between pseudo atoms are described by different interaction: Lennard ones (LJ)-type potentials (A/r8-B/r6-potential), repulsive and attractive LJ-parameters describing approximately the si
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Ds of 4.5 mm diameter coated with monoclonal human antimouse IgG antibodies) was used. The beads were washed twice with PBS using a magnet and resuspended to the initial volume.Neutralizing Epitope Guiding Bacterial Clearance1 mg of the probe (murine) mAb was added and incubated for 30 min at room temperature, after which the beads were washed twice with PBS to remove mAb excess. 0.5 ml of Proteas
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And from complete genome sequences. Codon alignments and phylogenies were constructed using the coding region for each of the 22 unique BP-2a gene sequences with MEGA5 [27]. To detect codons that show signs of adaptive evolution the program HyPhy [19] was used, as implemented in Datamonkey [28]. The codonbased maximum likelihood method REL (Random Effects Likelihood) [29] was used to estimate the