On the role of the active site helix in papain, an ab initio molecular orbital study

Abstract

On the system methanethiol/imidazole/formaldehyde (modelling the active site of papain) we performed ab initio self-consistent-field molecular orbital calculations using a rather large basis of Gaussian-type functions. A point charge representation of the long central alpha-helix present in the enzyme, was added in order to establish the influence of the electric field of the helix (which amounts to 10(9) V m-1 in the active site region) on the equilibrium: RSH...Im in equilibrium RS-...ImH+, which is an essential step in a recently proposed mechanism for the catalytic action of papain. Our results show that the helix stabilizes the ion-pair by 15 kcal mole-1 more than the neutral form making the two configurations energetically equivalent and lowers the energy barrier in the reaction path by 8 kcal mole-1, thus shifting the equilibrium considerably towards the ionic situation and increasing the rate of proton transfer by several orders of magnitude. We conclude that "active site" helices, present in many enzymes, play a pertinent role in enzyme catalysis.