computer modeling in molecular biology.pdf

192 Christopher J# Thorpe and David S. Mosschains only. After this step the side chains of the MHC molecule within 4 A of theside chains of the peptide, the water molecules and the peptide backbone wereallowed to move. Both of the above steps were performed using the dielectric model,but with a smaller distance dependant cut-off of 4 A and an E value of 1.0. Thefinished model could then be interrogated for contacts to the MHC molecule andpotential interactions with the TCR.If simulations were to be performed on the system, the finished model producedby the methods described above was placed into a constant pressure box which wasfilled using shells of random TIP3P waters to achieve a density equivalent to thatpredicted for solvent and solute. The system was geometry optimised, with periodicboundary conditions and electrostatic effects invoked with the MHC molecule andpeptide defined as a static aggregate, to a convergence point of 0.05 RMS deviationsin the energy terms. An active zone was then defined which encompassed the peptideand any water molecules within a 9 A sphere radiating from the peptide. In additiona set of atoms was defined that included any water molecules within an 11 A sphereradiating from the peptide and any part of the protein within 9 A of the peptide. Thisset of atoms within the molecule were, unlike the active water set and the peptide,held static in the simulation. The complete set of static atoms and active atoms wereall taken into account in the energy terms of the simulation. The static water solventand any remaining water molecules in the box were only allowed to move cooperativelywith the walls of the box to relieve changes in pressure within the system.The water molecules between 9 A and 11 A effectively acted as an ice cap being fixedin their positions and possessing no velocity however due to their contribution of theenergy terms they provided an inelastic boundary to prevent the active water set boilingoff and to provide a solvent mediated restraining influence on the peptide to keepit in the cleft. The system with these sets initialised was geometry optimised to theusual convergence criteria. The sets were re-assessed following convergence and nosubstructures in any of the simulations were observed to have moved between shells.Molecular dynamics was then performed on the optimised system. Temperatureand pressure were kept close to constant by connecting the system to temperature andpressure baths at 10 fs intervals using an integrator time step of 1 fs. The system wasequilibrated to 300 K using the stability of the kinetic energy and temperature curvesas a measure of the fidelity of the equilibration. Following suitable equilibration thesystem was simulated and conformers collected at 1 ps intervals. The conformersthus obtained could then be analysed in the context of the MHC molecule in orderto look for transient interactions, new lasting interactions and the movement ofwater molecules around the cleft.