computer modeling in molecular biology.pdf

194 Christopher L Thorpe and David S. Mossterest of 9 A radius from the atoms of the peptide was generated. Atoms within thiscylinder were allowed to move if they were not part of the HLA-Aw68 molecule, andany atoms between the 9 A sphere and an 11 A sphere were considered passively inthe calculation in order to act as an ice-cap to prevent the solvent from boiling outof the cylinder surrounding the peptide. The system was equilibrated to 300 K anda constant pressure of 1 atm over 5 ps and was simulated for a further 100 ps underconstant temperature and pressure.Figure 7-13a and b show the plots of time versus temperature, kinetic, potentialand total energy for the dynamics trajectory. It can be readily observed thatkinetically the simulation stabilises swiftly. Thermal stabilisation of the simulationis achieved well within the first tenth of the simulation time, after which conformersare collected. In the stacked plot all four graphs demonstrate a continual plateauafter approximately 1 ps.The movements of the peptide backbone are documented in Figure 7-14. It canbe observed from the time course presented here that the majority of movements aresmall and are largely centred around the proline residue at position P5 of the peptide.In the starting structure of the interaction of the Np91-99 peptide with HLA-Aw68the region around P3, P4 and P5 of the peptide is relatively flat with a moderatebulge. Within the first 15 ps this bulge becomes more pronounced and the prolineresidue begins to orient the Ca carbon towards the MHC molecule. By 65 ps thebulge is pronounced around the P3 residue and the proline ring is pointing directlydown into the groove of HLA-Aw68. This pronounced bulge and downward facingproline are both observed in the 2.8 A structure of this HLA-Aw68 with the Np91-99peptide. The major observable difference between the model structure and the crystalstructure is the orientation of the tyrosine side chain at P7 of the peptide. Howeveras it has been observed from other crystal structures of MHC class I molecules thisposition has a dichotomy of orientations and one peptide bound structure, that ofthe mouse molecule H-2Kb with the VSV octamer peptide, displays both orientationsin the one complex with both TCR facing and MHC facing conformers beingobservable in the electron density maps. An overlay of six conformers taken at 5, 25,45,65, 85 and 105 ps shows the overall stability of the bound Np91-99 peptide structure(Figure 7-15). The orientations of the anchored side chains P2 and P9 are virtuallyunchanged throughout the simulation, whereas the more accessible side chainssuch as P1, P6 and P8 display subtle but considerable differences in their orientations(Figure 7-15 a). A comparison of the initial and final conformers from the moleculardynamics simulation with the peptide observed in HLA-B27 demonstrates the formationof the more pronounced bulge at positions P3 and P4, and the stability ofthe position of the C-terminal residue (Figure 7-15 b).