Gly-7, and Lys-8 in B27(309 20). The pretty low RMSD fluctuation of DNAP(21123) soon after the first 50 ns of MD simulation and also the smaller sized RMSF values, relative to DNAP(21121) and B27(309 20), recommend a less flexible structure from the former peptide. Clustering Evaluation Reveals Distinct Peptide Flexibility and Conformations–A total of 5000 structures sampled during the final ten ns with the MD simulation have been subdivided in up to fiveSEPTEMBER 6, 2013 VOLUME 288 NUMBERclusters on the basis of similarity (RSMD) inside the peptide backbone. Two predominant clusters have been discovered for DNAP(211221), one for DNAP(21123), three for B27(309 20), and one for the x-ray template (Table 3). The distinct flexibility on the 3 peptides revealed by this evaluation was additional apparent upon taking into consideration the intracluster RMSD variability. This was calculated because the distance towards the centroid, that is the typical distance of all members of a cluster to its geometrical center. This parameter reflects the dispersion of data inside a provided cluster. Smaller sized (0.43), intermediate (0.54), and bigger values (0.7) had been identified for the important clusters of DNAP (21123),JOURNAL OF BIOLOGICAL CHEMISTRYChlamydial HLA-B27 LigandsA100 95 90 85 80b12+H2O-3NH3+3 471.Relative Abundance70 65 60 55 50 45 40 35 30 25 20 15 ten 5y9-H2O+2 b8-H2O-3NH3+2 b12-NH3+3 459.35 a12+3 455.74 b10-H2O-2NH3 350.39 b4+2 294.70 a8+3 320.43 b11+3 410.63 b9-H2O-2NH3+2 496.R R F K E G G R G G KY Ib2 by11y10y9 y8 yb8 b9 b10b11bb4-NH3+2 286.60 b2+2 157.200MH-H2O+3 MH-NH3+3 502.81 b12-NH3 688.27 b11-NH3+2 606.83 y7-NH3 b8-H2O-3NH3 918.64 b11+2 733.21 b10+2 615.70 y8 551.60 807.61 y7 y9 y10 750.36 936.35 1064.500 600 700 800 900 1000B100 95MH-NH3+2 753.b11-H2O y11 1211.Relative Abundance1200 1300 140085 80 75 70 65 60 55 50 45 40 35 30 25 20 15 10R R F K E G G R G G KY Ib2 b4 b5 b8 bb12 696.+y12 y11 y10 y9 yyb11 bm/z100 95 90 85 80b12+H2O-3NH3+3 471.00 b9-H2O-2NH3+2 497.05 y9-H2O b8-H2O-3NH3+2 b12-NH3+3 459.33 a12+3 455.72 b10-H2O-2NH3 350.48 b4+2 a +3 eight 294.91 320.17 b4-NH3+2 286.77 b2+2 157.200 300 400 500 600+b5 717.y12 684.37 y4-NH3 a8-2NH3+2 463.64 b8+2 y3-NH3 494.41 406.26 b9+2 b four 522.55 588.43 b2-NH3 296.300 400 500+Relative Abundance70 65 60 55 50 45 40 35 30 25 20 15 ten 5MH-H2O+3 MH-NH3+3 502.R R F K E G G R G G KY Ib2 by11y10y9 y8 yy12-H2O+2 y12-NH3+2 675.b8 b9 b10b11bb8-3NH3 y9 936.70 b -NH 8 970.53 3 y9-H2O y10 y8 918.52 807.Tenatoprazole Formula 41 b8 1064.Pipazethate custom synthesis 61 987.PMID:23600560 700 800 900 1000b11-H2O y11 1211.1200y12 1367.1400 1500b12-NH3 688.42 b11-NH3+2 606.98 y7-NH3 733.10 y8 807.52 b8-H2O-3NH3 918.46 b11-H2O y11 1211.Relative Abundance1200 1300 1400100 95m/zMH-NH3+2 753.b11 410.+b10+2 b11+2 551.42 615.y7 750.y9 936.900y10 1064.85 80 75 70 65 60 55 50 45 40 35 30 25 20R R F K E G G R G G KY Ib2 b4 b5 b8 by12 y11 y10 y9 yy3 b11 bm/zb12+2 697.17 y12+2 684.37 y4-NH3 a8-2NH3+2 464.00 y3-NH3 406.31 b2-NH3 296.300100 95 90 85 80b12+H2O-3NH3+3 471.b5 717.Relative Abundance70 65 60 55 50 45 40 35 30 25 20 15 10 five 0y9-H2O+2 b8-H2O-3NH3+2 b12-NH3+3 459.37 a12+3 455.80 b10-H2O-2NH3 350.48 294.b+R R F K E G G R G G KY Ib2 by11y10y9 y8 yb8 b9 b10b11by12-H2O+2 y12-NH3+2 675.b8-3NH3 y9 936.56 y8 918.55 807.41 y9-H2O b8-NH3 970.42 b8 y10 987.69 1064.1000b8+2 494.60 b9+2 b4 522.72 588.500 600b9-H2O-2NH3+2 496.78 MH-H2O+3 MH-NH3+3 502.88 b12-NH3 688.40 b11-NH3+2 607.00 y7-NH3 b8-H2O-3NH3 733.11 918.57 b10+2 b11+2 y8 551.60 615.59 807.50 y7 y9 y10 750.53 936.53 1064.500 600 700 800 900 100010 5b11-H2O y11 1211.1200y12 1367.1400 1500m/za8+3 320.55 b11+3 410.b4-.