computer modeling in molecular biology.pdf

7 Major Histocompatibility Complex Class I Protein-Peptide Interactions 1937.6 Modelling and Simulationof an Influenza Virus Peptide with theHuman MHC Class I Molecule HLA-Aw68The human class I allele HLA-Aw68 provides a good basis for molecular simulations.It presents a wide variety of peptides of differing lengths, and there are X-raycrystallographic structures for the molecule both with a collection of endogenouspeptides, at 2.6 A and 1.9 A resolution and with a single peptide derived from theinfluenza virus nucleoprotein peptide (Np91-99) at 2.8 A resolution. The high resolutionstructure for HLA-Aw68 with different length multiple endogenous peptidesclearly demonstrates that the termini of the peptide are in highly similar positionsregardless of the length of the central bulge. This allows for the construction of aseries of models which have the different length peptides bound to the HLA-Aw68molecule. In addition we have constructed a model of HLA-Aw68 complexed withthe flu peptide which may be used for model validation purposes by comparison tothe recently determined crystallographic structure.The major epitope derived from the influenza virus to elicit a response from CTLwhen presented by HLA-Aw68 is a nonamer fragment (KTGGPIYKR) derived fromthe influenza virus nucleoprotein comprising of residues 91-99 [42] (Np91-99). Thispeptide has recently been studied bound in the groove of HLA-Aw68 by the groupof Don Wiley using X-ray cryo-crystallography. The resulting peptide structure hasbeen compared to that of the model nonamer peptide built into the observed densityin HLA-B27 at 2.1 A resolution, and the deviations between the two peptide modelsappear to be limited to small sequence dependant changes in the backbones of thepeptides.The peptide model and the 15 solvent molecules in the cleft of HLA-B27 weremoved into the starting structure and mutated to the sequence of the influenza viruspeptide. The waters were redefined as TIP3P waters and the assembly of MHCmolecule peptide and waters was geometry optimised. The SYBYL 5.5 implementationof the Kollman united atom force field was used with polar atoms defined astheir Kollman all atom counterparts. Charges were taken from the internal dictionaryand the 1-4 scaling term was defined to give a direct parity between the energiesgenerated by SYBYL and by Amber. Once the convergence criteria of an RMS deviationof 0.05 in the total energy term had been achieved the molecule was soaked ina bath of random water molecules comprising 2304 solvent molecules in a box whoseinitial periodic boundary size was 49.29 x 55.50 x 34.44 A (xyz). This assembly wasenergy minimised to convergence with periodic boundary conditions invoked andHLA-Aw68 held rigid. This geometry optimisation step was used to remove holesand van der Waals (VDW) clashes within the random solvent field. A sphere of in-