. 2005 Mar 3;24(7):1303–1310. doi: 10.1038/sj.emboj.7600611

Table 1.

Structural and mechanistic features of protein inhibitors of proteases

Protease type	Inhibitor	Representatives	Major features of inhibition	Inhibitor size
Serine	Canonical inhibitors	BPTI, OMTKY3, eglin c, CMTI I	Often extremely tight and fast, noncovalent interaction resembling Michaelis complex, direct blockage of the active site, no conformational changes, antiparallel β-sheet between enzyme and inhibitor, similar mode of interaction through canonical protease binding loop in 18 different inhibitor scaffolds, moderate size of interface, utmost role of P₁ residue, additive effects on association energy	3–21 kDa per domain
	Noncanonical inhibitors	Hirudin, TAP, ornithodorin	Extremely strong, fast and specific interaction so far known for factor X_a and thrombin only, two-step kinetics, inhibition of the active site through inhibitor's N-terminus forming parallel β-sheet with enzyme active site, large interface composed of two interaction areas	6–8 kDa per domain
	Serpins	α-1-Antitrypsin, antithrombin	Irreversible covalent acyl–enzyme complex, mouse-trap mechanism, huge conformational changes in inhibitor, important role of P₁ position, suicide inhibition, disruption of protease active site	45–55 kDa

Cysteine	Cystatins	Chicken cystatin, cystatin C, stefin B, kininogen	Extremely tight but not specific, reversible and noncovalent inhibition, interaction through a wedge formed by two hairpin loops and N-terminus, catalytic Cys25 accessible in complex, important interactions through P₂ position	11–13 kDa, up to 60–120 kDa (kininogen)
	Thyropins	p41, equistatin	Very tight inhibition, mechanism similar to cystatins but often more specific, unusual inhibition of cysteine and aspartic proteases at different domains of equistatin	7 kDa per domain
	Bromelain inhibitors	BI-VI	Moderately strong inhibition at low pH and no inhibition at neutral pH, structural resemblance to canonical inhibitors of Bowman–Birk family	6–8 kDa
	Staphostatins	Staphostatin B	Moderately strong inhibition, inhibition mechanism resembling that of canonical inhibitors, inhibitor structure different from cystatins, unusual conformation of conserved Gly at P₁, substrate-like orientation of inhibitor, large area of interaction, importance of P₁′ position	11 kDa
	IAP	XIAP, cIAP1	Highly specific inhibition, reversible tight binding kinetics, inhibition also through interdomain flexible linker region as nonproductive binding in orientation opposite to that of substrates	9 kDa per BIR domain
		CrmA, PI-9	Highly specific inhibition, similar to serpin mechanism-based inactivation	38 kDa
		p35	Nonspecific inhibition, irreversible acyl-enzyme, distortion of active site, p35 N-terminus shields catalytic Cys360 from water molecules, gross conformational changes in inhibitor	35 kDa

Metallo		PCI, LCI	Tight enzyme–product complex, inhibition through C-terminal segment, key role of Val38 (P₁), no conformational changes in inhibitor upon complexation	4 kDa
		SMPI	Moderately specific inhibitor, inhibition mechanism resembling standard mechanism of canonical inhibitors of serine proteases, temporary inhibition, rigid protease binding loop	11 kDa
		P. aeruginosa inhibitor, E. chrysanthemi inhibitor	Both tight and weak inhibition observed, major interactions through five N-terminal residues, N-terminal amino group forms a coordinative bond to catalytic Zn, in analogy to TIMPs	15 kDa
		TIMP1–4	Tight but not highly specific noncovalent interaction, N-terminus and five inhibitor loops form wedge contacting the active site, bidental coordination of catalytic Zn through N-terminus, major interactions through P₁′ residue, moderate conformational changes in inhibitor upon complexation	20–22 kDa

Aspartic		IA₃	Strong, highly specific and fully unique type of inhibition, fully unfolded in free state, forms long helix in the complex comprising only N-terminal half of inhibitor, noncovalent complex	8 kDa
		PI-3	Strong but not highly specific, antiparallel β-sheet formed between enzyme and inhibitor, no conformational changes	17 kDa
BPTI: bovine pancreatic trypsin inhibitor; OMTKY3: turkey ovomucoid third domain; CMTI I: Cucurbita maxima trypsin inhibitor 1; TAP: tick anticoagulant peptide; BI-VI, bromelain inhibitor VI from pineapple; IAP: inhibitor of apoptosis; XIAP: X-linked IAP; cIAP1: cellular inhibitor of apoptosis protein 1; BIR: baculoviral IAP repeat; CrmA: cytokine response modifier A; PI-9: protease inhibitor 9; PCI: potato carboxypeptidase inhibitor; LCI: leech carboxypeptidase inhibitor; SMPI: Streptomyces proteinaceous metalloprotease inhibitor; TIMP: tissue inhibitors of metalloproteases; IA₃: inhibitor of aspartic protease from yeast; PI-3, Ascaris suum pepsin inhibitor 3.