What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme substrate complexes?

Proteinases perform many beneficial functions that are essential to life, b ut they are also dangerous and must be controlled. Here we focus on one of the control mechanisms: the ubiquitous presence of protein proteinase inhib itors. We deal only with a subset of these: the standard mechanism, canonic al protein inhibitors of serine proteinases. Each of the inhibitory domains of such inhibitors has one reactive site peptide bond, which serves all th e cognate enzymes as a substrate. The reactive site peptide bond is in a co mbining loop which has an identical conformation in all inhibitors and in a ll enzyme-inhibitor complexes. There are at least 18 families of such inhib itors. They all share the conformation of the combining loops but each has its own global three-dimensional structure. Many three-dimensional structur es of enzyme-inhibitor complexes were determined. They are frequently used to predict the conformation of substrates in very short-lived enzyme-substr ate transition state complexes. Turkey ovomucoid third domain and eglin c h ave a Leu residue at P-1. In complexes with chymotrypsin, these P1 Leu resi dues assume the same conformation. The relative free energies of binding of P1 Leu (relative to either PI Gly or P1 Ala) are within experimental error , the same for complexes of turkey ovomucoid third domain, eglin c, PI Leu variant of bovine pancreatic trypsin inhibitor and of a substrate with chym otrypsin. Therefore, the PI Leu conformation in transition state complexes is predictable. In contrast, the conformation of PI Lys(+) is strikingly di fferent in the complexes of Lys(18) turkey ovomucoid third domain and of bo vine pancreatic trypsin inhibitor with chymotrypsin. The relative free ener gies of binding are also quite different. Yet, the relative free energies o f binding are nearly identical for Lys(+) in turkey ovomucoid third domain and in a substrate, thus allowing us to know the structure of the latter. S imilar reasoning is applied to a few other systems. (C) 2000 Elsevier Scien ce B.V. All rights reserved.