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Acyl group transfer processes are plentiful in enzymatic reactions. Examples may be found in ATP-dependent ligation in chapter 11, carbon-carbon bond formation in chapter 14, and fatty acid biosynthesis in chapter 18. In this chapter, we begin by presenting the basic chemistry of acyl group transfer. We then consider four major classes of proteases that catalyze acyl group transfer in the hydrolysis of peptide bonds. Acyl group transfer is so common in organic and biochemistry that the chemistry by which it occurs is often taken for granted. Early studies provided evidence for a mechanism initiated by nucleophilic addition of the acyl group acceptor to the carbonyl group to form a tetrahedral intermediate, analogous to the reversible addition of a nucleophilic molecule to the carbonyl group of an aldehyde or ketone. A mechanism of this type is shown in scheme 6-1 for acyl group transfer from a group :X to a nucleophile :G catalyzed by a general base. This mechanism is drawn from a larger family of possible mechanisms involving specific acid-base, general acid, general base, or concerted general acid-base catalysis of nucleophilic addition to an acyl carbonyl group to form a tetrahedral intermediate, followed by the elimination of :X–H to produce the new acyl compound. In enzymatic reactions the nucleophilic atom G in scheme 6-1 is normally nitrogen, oxygen, sulfur, or a carbanionic species. An acyl carbonyl group is less polar and correspondingly less reactive toward nucleophilic addition than an aldehyde or ketone. The reason is the effect on the heteroatom of nonbonding electrons, which reside in p orbitals that overlap the π orbital of the carbonyl group. The consequent delocalization of electrons stabilizes the carbonyl group and attenuates its reactivity with nucleophiles. Other factors being equal, the order of reactivity is thioester > ester > amide, which is the inverse of the degree of delocalization. Delocalization is least in thioesters because of the high energy of the sulfur p orbitals, which reside in the next higher principal quantum number relative to oxygen in the acyl carbonyl group.

Functional H-bonds are H-bonds which are significantly stronger than the surrounding ones and, for this reason, can play a specific role in the mechanism of action of important chemical or biochemical processes. This chapter reports a preliminary collection of these bonds organized in a graphic gallery of cases with little discussion, a collection of themes which have already been, or deserve to be, investigated to unravel the true role played by the H-bond in natural systems. Themes treated include: RAHB-driven processes (prototropic tautomerism in heteroconjugated systems, secondary structure of proteins, and DNA base pairing); H-bond-controlled crystal packing; bistable H-bonds in functional molecular materials (ferro/antiferroelectric crystals, excited-state proton transfer); low-barrier charge-assisted H-bonds in enzymatic catalysis (the catalytic triad of serine proteases; and proton transmission in water chains (Grotthuss mechanism, gramicidine A channel, aquaporin channels).