Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques

In this paper, we report the molecular mechanics and molecular dynamics studies of the hydration of papain using the AMBER and CHARMm programs. We studied papain in an environment with minimal hydration involving only the X-ray waters and also in the hydrated environment by adding an extra 9 Å layer of water around the residues. The effect of nonbond cutoff was studied by performing minimizations with 8 Å and 15 Å nonbond cutoffs using the program AMBER. Two different solvent models—a constant dielectric and a distance-dependent dielectric—were considered. The AMBER-minimized structure and the average structure obtained from the CHARMm simulations for papain solvated with X-ray waters are presented and compared with the X-ray crystal structure results. Results of a similar comparison of the hydrated structures were also presented. The calculated root mean square deviation between the minimized structure and the X-ray structure is smaller for the hydrated system than for the system hydrated with only the X-ray waters. Results of the molecular mechanics and molecular dynamics simulations were presented for the various regions of papain. The hydration of the active site of papain and the effect of hydration on the torsional motion of the active site residues are presented. © 1996 by John Wiley & Sons, Inc.