PREDICTION OF TITRATION PROPERTIES OF STRUCTURES OF A PROTEIN-DERIVEDFROM MOLECULAR-DYNAMICS TRAJECTORIES

This paper explores the dependence of the molecular dynamics (MD) traj ectory of a protein molecule on the titration state assigned to the mo lecule. Four 100-ps MD trajectories of bovine pancreatic trypsin inhib itor (BPTI) were generated, starting from two different structures, ea ch of which was held in two different charge states. The two starting structures were the X-ray crystal structure and one of the solution st ructures determined by NMR, and the charge states differed only in the ionization state of N terminus. Although it is evident that the MD si mulations were too short to sample fully the equilibrium distribution of structures in each case, standard Poisson-Boltzmann titration state analysis of the resulting configurations shows general agreement betw een the overall titration behavior of the protein and the charge state assumed during MD simulation: at pH 7, the total net charge of the pr otein resulting from the titration analysis is consistently lower for the protein with the N terminus assumed to be neutral than for the pro tein with the N terminus assumed to be charged. For most of the ioniza ble residues, the differences in the calculated pK(alpha)s among the f our trajectories are statistically negligible and remain in good agree ment with the data obtained by crystal structure titration and by expe riment. The exceptions include the N terminus, which responds directly to the change of its imposed charge; the C terminus, which in the NMR structure interacts strongly with the former; and a few other residue s (Arg 1, Glu 7, Tyr 35, and Arg 42) whose pK(alpha)s reflect the init ial structure and the limited trajectory lengths. This study illustrat es the importance of the careful assignment of protonation states at t he start of MD simulations and points to the need for simulation metho ds that allow for the variation of the protonation state in the calcul ation of equilibrium properties.