Structural basis of serine protease action
the fourth dimension
pp. 139-148
in: Robert Zwilling (ed), Natural sciences and human thought, Berlin, Springer, 1995Abstract
The enormous advances in site-directed mutagenesis of proteins have led to a renewed and rising interest in the molecular mechanisms of enzyme catalysis. Approaches to the more than 50-year-old scientific puzzle of enzyme catalysis include, in more or less chronological order, enzyme kinetics using a wide variety of natural and synthetic substrates, chemical modification of enzymes combined with kinetic analysis, X-ray and neutron crystallography of enzyme- inhibitor complexes, site-directed mutagenesis methods combined with crystal-lographic, nuclear magnetic resonance (NMR) and kinetic studies and computer-aided molecular design based on theoretical considerations. Despite this large variety of approaches, or perhaps because of their diversity, debate still continues about the role of various structural and functional features in catalysis. This is well illustrated by four reviews [1–4] which have focused on quite different aspects of the molecular and energetic bases of enzyme catalysis, leaving the question as to how enzymes work still unanswered. Practically all concepts are based on Pauling's transition state theory [5]. According to this theory, enzymes provide templates which are complementary to the reactants in their activated transition state rather than to the substrates in their ground state. Consequently, the driving force for catalysis originates from the increase in the binding energy as the structure of the substrate changes to that of the transition state [6]. However, the molecular mechanism of conversion from the ground state to transition state is not clear at all. As Warshel and co-workers [3] put it: "The real question and the real puzzle do not boil down to whether or not enzymes reduce activation barriers, but to how do they accomplish it? This problem is far from being trivial, and cannot be resolved quantitatively by saying that enzymes provide templates that bind the transition state." Warshel's suggestion is that "enzymes work by providing electrostatic complementarity to the changes in charge distribution occurring during the reactions they catalyze." No matter whether electrostatic and/or other kinds of complementarities are involved, the structures of the enzymes must undergo some changes to complement changes of the substrate throughout the catalytic reactions.