Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories

Abstract

This paper explores the dependence of the molecular dynamics (MD) trajectory of a protein molecule on the titration state assigned to the molecule. Four 100-ps MD trajectories of bovine pancreatic trypsin inhibitor (BPTI) were generated, starting from two different structures, each of which was held in two different charge states. The two starting structures were the X-ray crystal structure and one of the solution structures determined by NMR, and the charge states differed only in the ionization state of N terminus.Although it is evident that the MD simulations 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 between the overall titration behavior of the protein and the charge state assumed during MD simulation: at pH 7, the total net charge of the protein resulting from the titration analysis is consistently lower for the protein with the N terminus assumed to be neutral than for the protein with the N terminus assumed to be charged.For most of the ionizable residues, the differences in the calculated pK,s among the four trajectories are statistically negligible and remain in good agreement with the data obtained by crystal structure titration and by experiment. 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 residues (Arg 1, Glu 7, Tyr 35, and Arg 42) whose pK,s reflect the initial structure and the limited trajectory lengths. This study illustrates the importance of the careful assignment of protonation states at the start of MD simulations and points to the need for simulation methods that allow for the variation of the protonation state in the calculation of equilibrium properties.

Insensitivity of Perturbed Carboxyl pKa Values in the Ovomucoid Third Domain to Charge Replacement at a Neighboring Residue

“…Some improvement in the agreement between predicted and experimental pK a values has been observed in studies that take into account possible conformational changes (53)(54)(55). The possibility of such pH-dependent conformational changes in OMTKY3 has not yet been explored in detail.…”

Analysing the pH-dependent properties of proteins using pKa calculations

“…It should be noted that many pK a calculation packages attempt to model protein flexibility implicitly or explicitly [2,6,9,10,[34][35][36][37][38] and thus remedy the sensitivity of the calculated pK a values to small perturbations in the X-ray structures used. However, even when using a pK a calculation algorithm, which models all protein dynamics explicitly, it is still of importance of assess the sensitivity of the subsystem in question to small structural perturbations.…”

Defining the Role of Salt Bridges in Protein Stability

“…(iii) The initial structure is likely to influence the results of continuum pK predictions (23), although this is not always the case (43). It appears that, again, the extent of sampling is more important.…”