computer modeling in molecular biology.pdf

184 Christopher J. Thorpe and David S. Moss'.aTDark line:- RMSD calculated for superposition of whole proteinBroken line:- RMSD calculated for superposition of antigen binding domains only0.00.80.7 -0.6 -0.0 0(elFigure 7-8 (a-e).(a) Model of HLA-Aw68, built using Composer and the techniques outlined in the text fromthe structures of HLA-B27 and HLA-A2, overlaid onto the 2.6 A crystallographic structurefor HLA-Aw68 (2hla). Only the antigen binding domains were overlaid in this diagram. Theside chains of the conserved peptide binding ligands and the polymorphic position 45 aredisplayed to demonstrate the highly similar nature of the model and structure. Models ofHLA-Aw68 built from the HLA-A2 crystal structure alone give better agreement to the HLA-Aw68 crystal structure than those built from both HLA-A2 and HLA-B27, due to the slightre-arrangement in secondary structural elements and domain dispositions that occur in HLA-B27. An RMS deviation of 0.541 is observed for the Ca positions of the model and crystalstructure over all domains. For the antigen binding domains alone an RMSD of 0.507 wasobserved. This compares favourably with the RMSD value of 0.599 between the crystal structuresof HLA-A2 and HLA-Aw68 and demonstrates the bias of including HLA-A2 in thedatabase of molecules for construction.(b) RMSD values for the Composer built model of the mouse molecule H-2Kb. This modelwas built from the co-ordinates of HLA-A2, HLA-Aw68 and HLA-B27 before the publicationof the H-2Kb crystal structure. The deviation between the model and the two crystal structuresis relatively low. This suggests that the Composer built models have a high degree ofgeometrical accuracy in relating the fold of the molecules and the position of biochemicallyimportant residues.(c-e) Plots of RMSD values for Ca positions versus sequence number for the antigen bindingdomains of HLA-Aw68 (residues 1 - 182). It can be observed that slightly different profiles ofRMSDs are observed between the alignment of only the a1 and a2 domains and the alignmentof the whole protein, suggesting that the a3 and Pz-microglobulin domains are biasing theoverlay. The observation of this characteristic lead to the use of antigen binding domains onlywhen structurally superposing the model proteins with peptide bound HLA-B27 structure totransfer the peptide and solvent molecules to the model in the modelling studies performedat Birkbeck.