MODELING PATHWAYS OF ALPHA-CHYMOTRYPSIN ACTIVATION AND DEACTIVATION

The conformational change of alpha-chymotrypsin from an inactive, chym otrypsinogen like structure at high pH to an active conformation aroun d pH 8.5 is used here as a model system to generate possible pathways for the transition by use of two different theoretical methods. One me thod, the 'targeted molecular dynamics' algorithm (TMD) adds a constra int in the direction of the target to a molecular dynamics force field and gives two different paths, one for every direction of the reactio n (Schlitter,J., Engels,M., Kruger,P.J., Mel. Graphics (1994) 12, 84-8 9). The second method, the 'self penalty walk' algorithm (SPW), refine s an initially guessed path by minimizing the sum of the energies of i ts structures (Elber,R. and Karplus,M., Chem. Phys. Lett. (1987) 139, 375-380). Thus, starting from a linear path as a first approximation, it produces a reaction coordinate of the transition. The structures of the TMD and SPW paths are similar only in the beginning while the mid dle part of the SPW path links the two TMD branches. The activation of alpha-chymotrypsin in the TMD path starts with a movement of loop VII (residues 215-225), pulling on loop VI (residues 186-194). Then the s ide chain of Met192 turns to the surface and Ile16 approaches Asp194 t o form a salt bridge. In the TMD deactivation path, loop VII also move s and pushes loop VI to the protein core. The Met192 side chain adopts three intermediate conformations, till the salt bridge Ile16-Asp194 i s broken and loop VI rearranges to its final conformation. In the SPW pathway both the formation of the salt bridge and the movement of Met1 92 happen simultaneously between two consecutive steps.