Why enzymes are proficient catalysts: beyond the Pauling paradigm

Abstract

Pauling proposed that "enzymes are molecules that are complementary in structure to the activated complexes of the reactions that they catalyze, ..., [rather than] entering into reactions". This paradigm has dominated thinking in the field. While complementarity of the type proposed by Pauling can account for acceleration up to 11 orders of magnitude, most enzymes exceed that proficiency. Enzymes with proficiencies ((k(cat)/K(M))/k(uncat)) > 10(11) M(-1) achieve over 15 kcal/mol of "transition state binding" not merely by a concatenation of noncovalent effects but by covalent bond formation between enzyme or cofactor and transition state, involving a change in mechanism from that in aqueous solution. Enzymes enter into reactions with substrates and do not merely complement the transition states of the uncatalyzed reactions.