CMLS, Cell. Mol. Life Sci. 60 (2003) 2427 – 2444
1420-682X/03/112427-18
DOI 10.1007/s00018-003-3120-x
© Birkhäuser Verlag, Basel, 2003
CMLS
Cellular and Molecular Life Sciences
Review
Canonical protein inhibitors of serine proteases
D. Krowarsch, T. Cierpicki, F. Jelen and J. Otlewski*
Institute of Biochemistry and Molecular Biology, University of Wroclaw,
Tamka 2, 50-137 Wroclaw (Poland), Fax: + 48 71 375 26 08, e-mail: otlewski@protein.pl
Received 28 March 2003; received after revision 12 May 2003; accepted 16 May 2003
Abstract. Serine proteases and their natural protein inhibitors are among the most intensively studied protein
complexes. About 20 structurally diverse inhibitor families have been identified, comprising a-helical, b sheet,
and a/b proteins, and different folds of small disulfiderich proteins. Three different types of inhibitors can be
distinguished based on their mechanism of action: canonical (standard mechanism) and non-canonical inhibitors,
and serpins. The canonical inhibitors bind to the enzyme
through an exposed convex binding loop, which is complementary to the active site of the enzyme. The mecha-
nism of inhibition in this group is always very similar and
resembles that of an ideal substrate. The non-canonical
inhibitors interact through their N-terminal segment.
There are also extensive secondary interactions outside
the active site, contributing significantly to the strength,
speed, and specificity of recognition. Serpins, similarly to
the canonical inhibitors, interact with their target proteases in a substrate-like manner; however, cleavage of a
single peptide bond in the binding loop leads to dramatic
structural changes.
Key words. Serine protease; protein inhibitor; canonical conformation; protein-protein recognition.
Introduction to protein inhibitors of proteases
Proteases carry out an unlimited number of hydrolytic
reactions both intra- and extracellularly [1]. They are
found in viruses and in all living organisms from bacteria to mammals. Beside their physiological necessity,
proteases are potentially hazardous to their proteinaceous environment and their activity must be precisely
controlled by the respective cell or organism. When not
properly controlled, proteases can be responsible for serious diseases. The basic level of control is normally
achieved by regulated expression/secretion, by activation
of proproteases [2], and by degradation of the mature enzymes. A second level of regulation is by inhibition of
their proteolytic activity. Almost all known naturally occurring inhibitors directed toward endogenous cognate
proteases are proteins; only some microorganisms se* Corresponding author.
crete small non-proteinaceous compounds which block
the host protease activity.
Inhibition of proteases by proteins itself sounds paradoxical. Nevertheless, there are very common examples of
inhibition of proteases by structurally unrelated proteins
[3–5]. In fact, inhibitor structures, modes of inhibition
and the nature of enzyme-inhibitor complexes are surprisingly different (table 1). In the past, inhibitors were
believed to be specific for one of the four mechanistic
classes of proteases (serine, cysteine, aspartic, or metalloproteases). While this is probably true in a prevailing
number of cases, there are also known examples of proteins that are able to inhibit cysteine and aspartic protease
[6], a serine and metalloprotease [7, 8], a serine and aspartic protease [9, 10], or a serine protease and amylase
[11, 12], employing different, non-overlapping binding
sites. The latest studies, compared to older ones, include
testing of a broader range of proteases and some other hydrolases. However, very few examples of cross-protease
2428
D. Krowarsch et al.
Protein inhibitors of serine proteases
Table 1. Major features of protease inhibitors of serine, cysteine, metallo-, and aspartic proteases.
Protease
Inhibitor
Examples
Major features of inhibition
Size
Serine
canonical
inhibitors
BPTI,
OMTKY3,
eglin
3–21 kDa
per domain
noncanonical
inhibitors
hirudin,
TAP,
ornithodorin
tight, non-covalent interaction resembling enzyme-substrate
Michaelis complex, direct blockage of the active site, no conformational changes, antiparallel b sheet between enzyme
and inhibitor [3], similar mode of interaction through canonical protease-binding loop despite completely different inhibitor structures [84], important role of P1 residue, additive
effects on association energy [147]
extremely strong and specific interaction so far known for
factor Xa and thrombin only, two-step kinetics, inhibition
of the active site through N terminus of the inhibitor, two
areas of interaction [150]
irreversible covalent acyl-enzyme complex, huge conformational changes in inhibitor, disruption of protease active
site [17, 151]
serpins
Cysteine
cystatins
thyropins
IAP
chicken
cystatin,
cystatin C,
stefin B,
kininogen
p41,
equistatin
XIAP,
cIAP1
CrmA,
p35
Metallo
PCI
SMPI
Pseudomonas
aeruginosa
inhibitor,
Erwinia
chrysanthemi
inhibitor
TIMP1,
TIMP2,
TIMP3,
TIMP4
Aspartic
IA3
PI-3
6–8 kDa
per domain
45–55 kDa
extremely tight but not specific, reversible non-covalent inhibition [26], interaction through two hairpin loops and
N terminus forming a wedge, catalytic Cys25 accessible in
complex, important interactions through P2 position [29]
11 – 13 kDa, up
to 60 –120 kDa
(kininogen)
very tight inhibition, mechanism similar to cystatins but
often more specific [27, 152]
highly specific inhibition, reversible tight binding kinetics
[153], inhibition also through an interdomain flexible linker region as non-productive binding in the opposite orientation to the substrates [30– 32]
highly specific inhibition [34], similar to serpin mechanism of complexation [153]
non-specific inhibition [34], irreversible acyl-enzyme, p35
N terminus shields catalytic Cys360 from water molecules, gross conformational changes in inhibitor [33]
7 kDa
per domain
9 kDa per BIR
domain
tight enzyme-product complex, inhibition through C-terminal segment [36], key role of Val38 (P1) [154], no conformational changes in inhibitor upon complexation [155]
rather specific inhibitor, inhibition mechanism resembling standard mechanism of canonical inhibitors of serine
proteases, temporary inhibition [37], rigid protease-binding
loop [37, 156, 157]
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 [40, 158]
4 kDa
tight but not highly specific non-covalent interaction [159],
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
[160]
strong and highly specific [161], fully unfolded in free
state, forms long helix in the complex comprising only Nterminal half of inhibitor, non-covalent complex [41].
strong but not highly specific [162], antiparallel b sheet formation between enzyme and inhibitor, no conformational
changes [42]
38 kDa
35 kDa
11 kDa
15 kDa
20 – 22 kDa
8 kDa
17 kDa
BPTI, bovine pancreatic trypsin inhibitor; OMTKY3, turkey ovomucoid third domain; TAP, tick anticoagulant peptide; IAP, inhibitor of
apoptosis; XIAP, X-linked IAP; cIAP1, cellular IAP protein 1; BIR, baculoviral IAP repeat; CrmA, cytokine response modifier A; PCI,
potato carboxypeptidase inhibitor; SMPI, Streptomyces proteinaceous metalloprotease inhibitor; TIMP, tissue inhibitors of metalloproteases; IA3, inhibitor of aspartic protease from Saccharomyces cerevisiae; PI-3, Ascaris suum pepsin inhibitor 3.
CMLS, Cell. Mol. Life Sci.
Vol. 60, 2003
class inhibition at the same protease recognition site have
been reported, but their number is growing [13].
This review is devoted to canonical protein inhibitors of
serine proteases. To put serine protease inhibitors in a
broader context of possible inhibition modes, a brief outline of protein inhibitors of the four mechanistic classes
(no protein inhibitors of threonine proteases are known)
is presented below (table 1).
From a structural point of view, blocking of the enzyme
active site is almost always achieved by docking of an exposed structural element, such as a single loop or protein
terminus, either independently or in combination of two
or more such elements. Interestingly, antibodies, despite
huge structural variability of their antigen-binding loops,
cannot recognize the active site of proteases, as they only
bind to flat or convex protein surfaces [14].
There are three distinct types of serine protease inhibitors
(fig. 1). Up to the late 1980s, the majority of known protein inhibitors were those of the serine enzymes, either
substrate-like-binding canonical inhibitors blocking the
enzyme at the distorted Michaelis complex reaction stage
[4, 15, 16], or serpins (serine protease inhibitors). While
canonical inhibitors are small proteins, serpins are much
larger, typically 350–500 amino acids in size, distributed
from viruses to mammals [13, 17]. They are abundant in
human plasma and mutations in serpins lead to numerous
serious genetic diseases in humans [18]. Similarly to
canonical inhibitors, serpins interact with their target proteases in a substrate-like manner. However, while the protease-binding loop of canonical inhibitors is kept in a wellordered conformation, the binding loop of serpins is much
Review Article
2429
longer, about 17 amino acids, and able to adopt different
conformations. In the active serpin, the binding loop protrudes significantly from the serpin scaffold [19], while in
a much more stable latent conformation, this segment is
inserted into the middle of the central b sheet A (fig. 1)
[20]. In contrast to canonical inhibitors, serpins utilize the
kinetic features of a hydrolytic reaction to form a very stable acyl-enzyme intermediate. The enzyme-serpin complex is a covalent acyl-enzyme adduct and upon acylation
the protease is translocated by over 70 Å from its initial
recognition site [21]. Serpins are the only family of serine
protease inhibitors for which complex formation with
non-serine enzymes – cysteine proteases [22] and aspartyl
proteases [23] – has been demonstrated.
Non-canonical inhibitors interact through their N-terminal segment which binds to the protease active site forming a short parallel b sheet. These inhibitors also form extensive secondary interactions with the target protease
outside the active site, which provide additional buried
area and contribute significantly to strength, speed, and
specificity of recognition. The classic example is recognition of thrombin by hirudin [24]. Interestingly, such interactions are also formed by proteins possessing canonical-inhibitor-like folds or by Kazal-type inhibitors but
with a distorted conformation of the binding loop. The
non-canonical inhibitors are much less abundant than
canonical inhibitors or serpins as they only occur in
blood-sucking organisms and inhibit proteases involved
in clot formation – thrombin or factor Xa. Only a few of
them have been characterized in terms of structure and kinetics of interaction with the target protease.
Figure 1. Examples of serine protease-inhibitor complexes: canonical, CMTI:trypsin (PDB: 1ppe); non-canonical, ornithodorin:thrombin (1toc); serpin, a-1 antitrypsin:trypsin (1ezx). The binding loop and P1 side chain residue of CMTI, a-1 antitrypsin and the N terminus
of ornithodorin are marked in red. Secondary binding sites of ornithodorin are marked in orange. Secondary-structure elements are colored in blue (b sheets) and green (a helices).
2430
D. Krowarsch et al.
The second largest and most carefully investigated group
are inhibitors of cysteine proteases (table 1). As with the
serine protease inhibitors, they can be divided into several
groups: cystatins, stefins, kininogen, and thyroglobulin
type 1 proteins [25, 26]. While the first three groups share
similar structural features and form the cystatin superfamily, the latter group is structurally different [27]. Interestingly, all these proteins, and probably also other inhibitors [28], share clear similarities in the mode of their
interaction with the enzymes. Members of the cystatin superfamily are reversible, extremely fast- and tight-binding competitive inhibitors, with the inhibition constants
even in a low picomolar range [26]. The crystal structures
of chicken cystatin and stefin B in complex with papain
show a precise steric fit of a hydrophobic wedge-shaped
edge of the cystatin inserted into the active site of the protease [29]. Inhibitors of caspases, the cysteine proteases
responsible for apoptosis, are surprisingly variable, structurally unrelated to the cystatin superfamily, and much
more specialized to fulfill their function. One group of
caspase inhibitors, called inhibitors of apoptosis (IAPs),
contains one or more baculoviral IAP repeat (BIR) domain that binds to the active site in a non-productive manner [30 –32]. Unexpectedly, a flexible linker connecting
the BIR domains can also serve to block the active site of
caspases 3 and 7. Another group of caspase inhibitors is
the p35 family that has only been found in some baculoviruses. These inhibitors are able to inhibit different
caspases using mechanism-based inactivation through
formation of a covalent thiol ester [33]. Although the
mechanism of inhibition in principle is similar to that of
serpins, the molecular rearrangement of the inhibitor
upon cleavage of the peptide bond is clearly different.
Caspases can also be inhibited by viral serpins. The
poxvirus CrmA serpin is able to block both caspases 1
and 8 and the serine protease granzyme B [34]. Although
the structure of the CrmA-serpin complex remains to be
determined, CrmA most probably undergoes an extensive
structural transition during complex formation [35].
There are three unrelated groups of metalloprotease inhibitors, which inhibit their cognate enzymes through
completely different mechanisms (table 1). The first discovered was potato carboxypeptidase A inhibitor (CPI), a
small 39-residue protein, forming an enzyme-product
type of complex (Gly39 is cleaved off in the crystal structure of the complex) through insertion of its C terminus
into the active site of the enzyme [36]. Subsequently, a
bacterial inhibitor, SMPI, was isolated from Streptomyces
nigrescens that, surprisingly, appeared to inhibit metalloproteases of the gluzincin family by the standard mechanism of inhibition, extremely popular among canonical
inhibitors of serine proteases [37]. Tissue inhibitors of
metalloproteases (TIMPs) fold into a continuous wedge
which blocks the active site of various matrix metalloproteases (MMPs) [38, 39]. This interaction is not highly
Protein inhibitors of serine proteases
specific and the mode of inhibition resembles the interaction between serralysins and their bacterial inhibitors
from Pseudomonas aeruginosa and Erwinia chrysanthemi [40]. Although TIMPs and the two bacterial inhibitors are structurally unrelated, both groups of inhibitors form similar coordinative bonds to the catalytic
Zn utilizing the N-terminal residue.
Protein inhibitors of aspartic proteases are rare. Currently, structures of only two inhibitors have been reported (table 1). A small yeast protein IA3, composed of
68 amino acids, is able to inhibit aspartic protease A from
the same organism in a very unusual way. While it shows
no detectable secondary structure in solution, upon complexation with the enzyme, residues 2 –32 adopt an almost perfectly helical conformation revealing that the
protease body serves as a folding template [41]. The PI-3
inhibitor from the intestinal parasite Ascaris suum presents an unrelated mode of inhibition. Its N-terminal
b strand pairs with one strand of the active-site flap,
forming an extensive eight-stranded b sheet spanning
both proteins [42].
Canonical inhibitors
The largest group of protein inhibitors are canonical inhibitors that act according to the standard mechanism of
inhibition [15]. A huge number of canonical inhibitors
have been described, isolated from various cells, tissues,
and organisms; they often accumulate in high quantities
especially in plant seeds, avian eggs, and various body
fluids. Serine proteases and their natural protein inhibitors belong to the most intensively studied models of
protein-protein recognition [14, 43]. Canonical inhibitors
are widely distributed in essentially all groups of organisms and comprise proteins from 14 to about 200 amino
acid residues. Canonical protein inhibitors do not form a
single group but can be divided into different families.
The segment responsible for protease inhibition, called
the protease-binding loop, surprisingly has always a similar, canonical conformation in all known inhibitor structures [16, 44]. This convex, extended and solvent-exposed loop is highly complementary to the concave active
site of the enzyme. The standard mechanism implies that
inhibitors are peculiar protein substrates containing the
reactive site P1-P1¢ peptide bond located in the most exposed region of the protease-binding loop (P1, P2 and P1¢,
P2¢ specify inhibitor residues amino- and carboxy-terminal to the scissile peptide bond, respectively; S1, S2 and
S1¢, S2¢ denote the corresponding subsites on the protease
[45]). The reactive site can be selectively hydrolyzed by
the enzyme, but the equilibrium value of this cleavage is
often close to 1 at neutral pH, i. e., the reactive site can be
cleaved to the extent of about 50 %. It is usually assumed,
and very often verified experimentally, that standard-
CMLS, Cell. Mol. Life Sci.
Vol. 60, 2003
mechanism inhibitors possess canonical conformation of
the binding loop. On the other hand, while loops of
canonical conformations occasionally occur in various
proteins, there is no evidence that they can block proteases according to the standard mechanism [44, 46].
Classification
A classification of canonical inhibitors was originally
proposed by Laskowski and Kato in 1980 [15]. At that
time they could distinguish eight families, based mainly
on the disulfide bond topography, location of the reactive
site, and sequence homology. Currently, 18 inhibitor families are recognized [5] (table 2). Crystal and/or solution
structures are known for representatives of almost all
families (table 2). Since the inhibitors are small, rigid,
and stable, these structures have often been determined
with high resolution and accuracy. Furthermore, serine
proteases and enzyme-inhibitor complexes crystallize
easily, often providing high-resolution data. Extensive
structural information is also available for protease-inhibitor complexes. The global structures of proteins representing different inhibitor families are completely different. Most often they comprise either purely b sheet or
mixed a/b proteins; they can also be a-helical or irregular proteins rich in disulfide cross-links. It is often
stressed that the canonical inhibitors represent the most
distinct and extensive example of convergent protein evolution, since a similar function has been implemented
many times during evolution through preservation of the
canonical loop conformation in many unrelated proteins
[5]. Examples of different folds of inhibitor structures are
shown in figure 2.
The inhibitor structure
The inhibitor scaffolds are of very different structural
types. In several inhibitor families like BPTI, Kazal,
potato 1 and 2, cereal, SSI, STI, and ecotin, typical secondary-structure elements together with the presence of a
hydrophobic core are found. In other families, including
squash, Bowman-Birk, grasshopper, hirustasin, chelonianin, and Ascaris there is essentially a lack of both hydrophobic core and extensive secondary structure. For
these inhibitors, disulfide bonds, which are usually buried
inside the molecule, are the major determinant of protein
stability and/or rigidity. With respect to the cross-links, the
most unusual is probably a cyclic peptide from sunflower
seeds that strongly inhibits trypsin (SFTI-1). This cyclic
inhibitor is homologous to the Bowman-Birk family and
consists of two antiparallel b strands additionally crosslinked with a disulfde bond and stabilized by numerous
hydrogen bonds [47]. Natural cyclic peptides also occur
Review Article
2431
among squash inhibitors [48]. Worth mentioning is that it
is possible to synthesize chemically a cyclic version of the
non-cyclic protease inhibitor BPTI [49, 50].
The presence of an inhibitory domain is usually indicative of serine protease inhibition. However, examples are
also known of naturally occurring inhibitors belonging to
ovomucoids, e.g., with Pro at P1, that are very poor inhibitors of all proteases tested including prolyl endopeptidase [51]. Sometimes other functions, not related to
canonical inhibition, could be detected for canonical domains. For example, Kazal domains occur in follistatin
[52], the squash inhibitor fold is found in the metalloprotease inhibitor PCI [53], and the BPTI domain is frequently observed in snake potassium channel blockers or
linked to the phospholipase A2 domain, Alzheimer precursor protein [54], or collagen a1 and a3 chains [55]. In
one case tested of the non-inhibitory C5 domain of collagen VI, a strong protease inhibitor could be generated
through multiple substitutions in the binding-loop region
[56]. However, in many other cases, conversion of a noninhibitory to inhibitory protein required more effort due
to severe conformational and dynamic changes in the
binding-loop region.
Two non-canonical inhibitors of coagulation proteases
from the soft tick, ornithodorin and tick anticoagulant
peptide (TAP), surprisingly show a scaffold of the archetypical canonical inhibitor BPTI (fig. 1). Ornithodorin
contains two BPTI-like domains containing insertion/
deletion in the binding-loop segments, which lead to their
major distortion [57]. In fact, this binding loop does not
contact the protease, but as in the hirudin-thrombin complex, the N-terminal tail of ornithodorin penetrates the
thrombin active site and forms a parallel b sheet with the
thrombin Ser214-Gly219 segment. Similarly, TAP, which
is a strong inhibitor of factor Xa [58], interacts through
the N terminus with the active site of factor Xa [59].
Inhibitors belonging to different families are generally
stable or even extremely stable proteins with high denaturation temperatures and resistance to chemical denaturants. At neutral pH, BPTI shows a denaturation temperature (Tden) of about 100 °C and is stable in 6 M guanidinium chloride [60, 61]. Kazal inhibitors denature with
a Tden up to 90°C and are also stable in 6 M GdmCl [62,
63], and STI unfolds at 65 °C [64]. For small inhibitors
like those from the squash family, cooperative denaturation could not be demonstrated due to a lack of secondary
structure, hydrophobic core and too small size of the cooperative unit.
Inhibitors are often heavily cross-linked with conserved
disulfide bonds. The topology of the disulfide bonds is
usually well preserved within a single family. However,
some members of the potato 1 family show either a single
disulfide [CMTI-V (Cucurbita maxima trypsin inhibitorV) and LUTI (Linum usitatissimum trypsin inhibitor)] or
no disulfide (CI-2 and eglin c). Within the STI family
2432
D. Krowarsch et al.
Protein inhibitors of serine proteases
Table 2. Representative X-ray and NMR three-dimensional structures of protein inhibitor families of serine proteases and their enzyme
complexes.
Family
Total
number
Free inhibitor
Enzyme-inhibitor complex
number
representative
PDB
resolution Å
number
representative
PDB
resolution Å
BPTI:
rat trypsin
OMTKY:
chymotrypsin
eglin c:
subtilisin
CPTI II:
trypsin
ecotin:
crab
collagenase
STI:
porcine
trypsin
MbBBI:
Ns3protease
SFTI-1:
trypsin
bdellastasin: porcine
trypsin
C/E-1 inhibitor: porcine elastase
PMP-C:
chymotrypsin
SSI:
subtilisin
BPN¢
PCI 1:
SGPB
1f7z
1.5
1cho
1.8
1cse
1.2
2btc
1.5
1aaz
2.3
1avw
1.75
1df9
2.1
1sfi
1.6
1eja
2.7
1eai
2.4
1gl1
2.1
2sic
1.8
4sgb
2.1
BPTI
63
28
BPTI
5pti
1.0
35
Kazal
36
16
OMSVP3
2ovo
1.5
20
Potato 1
27
16
CI-2
2ci2
2.0
11
Squash
17
9
CMTI I
1lu0
1.03
8
Ecotin
12
3
ecotin
1ifg
2.0
9
STI
11
9
STI
1avu
2.3
2
BBI
9
6
BBBI
1c2a
1.9
3
BBI (SFTI)
2
1
SFTI-1
1jbl
NMR
1
Antistasin
7
3
hirustasin
1bx7
1.2
4
Ascaris
7
6
AMCI
1ccv
NMR
1
Grasshopper
6
4
PMP-C
1pmc
NMR
2
SSI
5
1
SSI
3ssi
2.3
4
Potato 2
4
3
T1
1tih
NMR
1
Cereal
Chelonianin
4
2
4
1
CHFI
R-elafin
1bea
2rel
1.95
NMR
1
Rapeseed
1
1
ATTp
1jxc
NMR
Elafin:
porcine
elastase
1fle
1.9
Arrowhead
In the absence of X-ray structure, the representative NMR structure is indicated. Total number, total number of structures deposited in PDB
(Protein Data Bank) (free structures and complexed with protease); OMSVP3, silver pheasant ovomucoid third domain; OMTKY, turkey
ovomucoid; CI-2, chymotrypsin inhibitor 2; CMTI I, Cucurbita maxima trypsin inhibitor I; CPTI II, Cucurbita pepo trypsin inhibitor II;
STI, soybean trypsin inhibitor; BBBI, barley Bowman-Birk inhibitor; SFTI-1, sunflower trypsin inhibitor; MbBBI, mung bean BowmanBirk inhibitor; AMCI, Apis mellifera chymotrypsin inhibitor; C/E-1 inhibitor, Ascaris chymotrypsin/elastase inhibitor 1; PMP-C, Pars intercerebralis major peptide; SSI, Streptomyces subtilisin inhibitor; T1, trypsin inhibitor from Nicotiana alata; SGPB Streptomyces griseus
protease B; CHFI, corn Hageman factor inhibitor; ATTp, Arabidopsis thaliana trypsin inhibitor.
also, there is an inhibitor with a single disulfide bond instead of the two typically observed among members of
this family [65]. Worthy of note is that engineering of an
additional disulfide bond near the reactive site of the silver pheasant third domain (Kazal inhibitor) left intact its
potent inhibitory activity toward chymotrypsin, Streptomyces griseus proteases A and B, but almost abolished it
toward pancreatic elastase [66]. Selective reduction or
elimination of disulfide bond(s) in inhibitors belonging
to different families usually leads to a significant destabilization of the inhibitor molecule, to a lower association-energy and larger sensitivity to proteolysis [67–70].
The same holds for destabilizing mutation(s) introduced
into the inhibitor core [71, 72].
CMLS, Cell. Mol. Life Sci.
Vol. 60, 2003
Review Article
2433
Figure 2. Representative set of canonical inhibitor structures. The following structures are shown: hirustasin (PDB: 1bx7); AMCI (1ccv);
PI-II, protease inhibitor-II (1pi2); STFI-1 (1jbl); CHFI (1bea); R-elafin (2rel); ecotin (1ifg); PMP-C (1pmc); OMSVP3 (2ovo); BPTI
(5pti); STI (1avu); CI-2 (2ci2); T1 (1tih); ATTp (1jxc); SSI (3ssi); CMTI I (1lu0). Binding loop and P1 side chain residue are marked in
red, secondary-structure elements are colored in blue (b sheets) and green (a helices). Name of inhibitor family (in bold) and name of representative are indicated.
Domain architecture
Many inhibitors are single-domain proteins. With a possible exception for the arrowhead protease inhibitor [73],
the single inhibitory domain contains only one reactive
site responsible for protease binding [74]. This is true for
all members of the arrowhead, Ascaris, ecotin, STI,
potato 1, cereal, rapeseed, silkworm, SSI, and squash
families. In the remaining families (antistasin, BowmanBirk, BPTI, grasshopper, Kazal, chelonianin, and potato
2) the single domain can be repeated 2, 3, 4, 5, 6, 7, 9 or
even 15 times to form a multidomain, single-chain inhibitor which is able to interact independently with sev-
eral protease molecules at their reactive sites belonging to
separate domains.
The different organization observed in multidomain proteins is shown in figure 3. In the simplest case, represented by ovomucoids, three homologous Kazal domains,
each cross-linked with three disulfide bonds, are connected by short and flexible linkers. These domains are
independently able to inhibit serine proteases – for example the first domain of turkey ovomucoid inhibits Gluspecific S. griseus protease, the second domain inhibits
trypsin and the third blocks chymotrypsin, elastase and
subtilisin. Similarly, the first domain of tissue factor pathway inhibitor (TFPI) composed of three tandemly
2434
D. Krowarsch et al.
arranged BPTI domains inhibits factor VIIa/tissue factor,
the second interacts with factor Xa, and the third is without detectable inhibitory function [75]. In contrast, in the
crystal structure of bikunin, composed of two BPTI domains, the binding loop of the second domain is obstructed by the first domain, thus affecting protease binding (fig. 3) [76].
A highly unique domain topology occurs in a protein inhibitor precursor from Nicotiana alata (NaProPI). This
protein is composed of six homologous repeats; however,
their sequences do not coincide with the structural domains [77]. One of these domains comprises two chain
fragments from the first and last repeat, strongly suggesting that the precursor adopts a circular bracelet-like structure (fig. 3). In Bowman-Birk inhibitors, there are again
two independent binding loops but the presence of seven
inter- and intradomain disulfides results in a much more
compact two-domain protein. Two Kazal domains of
rhodniin serve to inhibit one enzyme – thrombin. While
the N-terminal domain binds to the active site of thrombin through its canonical loop (interestingly with His at
P1, despite strong preference of thrombin for Arg), the
binding loop of the C-terminal domain is distorted, thus
excluding canonical interaction [78]. Instead, this domain
recognizes the fibrinogen exosite on the thrombin surface
using residues located outside the binding loop region
(fig. 3). A homodimeric inhibitor from Escherichia coli,
called ecotin, although built of a single domain is active
as a dimer in which both monomers provide the proteasebinding surface (fig. 3) [79]. A comparison of the inhibitory properties of dimeric ecotin with that of an engineered monomeric form reveals a complex and non-additive interplay of binding energies provided by the binding
sites located on the two subunits [80]. Finally, several
multidomain proteins containing combinations of WAP
(whey acidic protein), Kunitz, Kazal, and thyroglobulin
domains have been identified that may control multiple
types of serine, aspartic, metallo and cysteine proteases
[81].
Protein inhibitors of serine proteases
Figure 3. Examples of multidomain serine protease inhibitors:
model of Na-Pi structure based on C1T1 and C2 NMR structures
(PDB: 1fyb and 1qh2); ecotin dimer (1ecz); model of ovomucoid
structure based on OMSVP3 crystal structure (2ovo); BBI (1bbi);
bikunin (1bik); rhodniin (1tbq). Binding loop and P1 side chain
residue are marked in red, residues involved in protease dimerization by ecotin are marked in yellow, residues from the C-terminal
domain of rhodniin interacting with thrombin are marked in cyan.
Name of inhibitor family (in bold) and name of presented structures
are indicated.
The canonical conformation of the binding loop
The convex protease-binding loop exhibits an extended
conformation, which significantly protrudes from the
protein scaffold and serves as a rather simple recognition
motif (fig. 4). The loop forms a sequential epitope spanning positions P3 to P3¢. Residues that precede or follow
this segment (e.g., P6-P4 or P4¢) and residues from a sequentially remote region, called the secondary contact region, can also contact the enzyme and influence the association energy [82 –84]. The central section of the loop
contains a solvent-exposed P1-P1¢ peptide bond, called the
reactive site. This bond is not fully inert to the proteolytic
attack by the cognate enzyme – the equilibrium value of
Figure 4. Superimposition of main chain P3-P3¢ segments (according to Schechter and Berger notation) of binding loops of:
OMSVP3, light gray (PDB: 2ovo); SSI, gray (3ssi); BPTI, dark gray
(PDB: 5pti).
CMLS, Cell. Mol. Life Sci.
Review Article
Vol. 60, 2003
the reactive-site peptide bond opening, called the
hydrolysis constant, is usually not far away from unity
[85 –87].
The conformation of the cleaved inhibitor is very similar
to the intact form with clear exceptions for the local structural changes near the P1-P1¢ peptide bond [88, 89] and increased internal mobility of the cleaved loop, but not of
the inhibitor scaffold [90, 91]. Thermodynamic analysis
reveals that hydrolysis of the reactive site in the native inhibitor does not lead to a significant increase in entropy
[92]. The full entropy gain is realized upon denaturation
of the reactive-site-cleaved inhibitor which leads to predicted values of Khyd for the hydrolysis of the reactive site
in the denatured inhibitor at between 100 and 1000 [64,
93]. However, in the case of CMTI-V, a large entropy increase was observed upon reactive-site cleavage of the
native inhibitor [94].
The main chain conformations of the binding loops of
free inhibitors representing different families are similar
and become even more alike after complex formation
with the enzyme (fig. 4) [44]. The canonical conformation is also presumed to be adopted by a productively
bound protein substrate.
The binding loops within one family (most intensively
studied for ovomucoids belonging to Kazal inhibitors
[84, 95]) often show a high level of sequential variability;
nevertheless, in all cases studied, the loops had canonical
conformation. A lack of hypervariability has been indicated for squash [96] and potato 1 families [97].
The amino acid sequences of the binding loops show
many clear amino acid preferences in different families.
For example, half cystine is present either at P3 (the
Kazal, Bowman-Birk, grasshopper, silkworm, squash,
SSI, potato 2, and Ascaris families) or at P2 (the BPTI, antistasin, arrowhead, hirustasin, and chelonianin families).
Thr is often observed at P2 (the Kazal, potato 1, BowmanBirk, SSI, ecotin, and Ascaris families) and Pro is conserved at P3 in the STI family [44]. A conserved Ile is always present at the P1¢ position in squash inhibitors. Its
mutation to Leu leads to a severe disorder of the binding
loop [98]. A similar disorder of the loop was observed
upon Asp46ÆSer substitution at the P1¢ site of eglin c
[99]. Ala and Gly are highly conserved at P1¢ in the BPTI
family. Introduction of larger side chains at this position
leads to a huge decrease in the association constants with
proteases [100]. In Bowman-Birk inhibitors, prolines are
frequently observed at P3¢ and P4¢. The Pro at P3¢ in geometry is required for strong inhibition while that at P4¢ stabilizes the P3¢ configuration [101]. Thus, the canonical
conformation may be achieved by many unrelated sequences.
The canonical loop conformation results from a rather
extensive system of disulfide bond(s), hydrogen bonds,
and/or hydrophobic interactions, which involve residues
both from the loop and the inhibitor scaffold. A scheme
2435
of the loop-maintaining interactions in different families
is shown in figure 5. For example, in the OMSVP3
(Kazal family) inhibitor, the carbonyl oxygens of P2 and
P1¢ are involved in hydrogen bonds to the side chain of
Asn33, and in CI-2 (potato 1 family), these carbonyls are
hydrogen bonded to two arginines at P6¢ and P8¢. The
LUTI inhibitor which belongs to the same family, despite
a Trp Æ Arg substitution at P8¢, is a strong inhibitor of
trypsin and its solution structure shows that loop conformation is well preserved [102]. Interestingly, mutation of
Arg at P8¢ to Lys in the homologous eglin c led to a destabilization of the binding loop [99]. There is evidence
based on changes in 15N relaxation rates for an increased
dynamics of the loop in CMTI-V mutants with eliminated side chains of Arg50 or Arg52 [103, 104]. In many
inhibitor families, there is also a common hydrogen bond
between the side chain or main chain of the P2 and P1¢ positions (fig. 5). In ovomucoid third domains, the side
chain-side chain hydrogen bond between Thr17 (P2) and
Glu19 (P1¢) is long in the free inhibitor (and therefore
not shown on fig. 5) but becomes shortened by about
0.5 Å upon complex formation, thus showing that it energetically favors the complex [105]. In Ascaris trypsin
inhibitor (ATI), there is a pH-induced structural transition in the binding-loop region observed by nuclear
magnetic resonance (NMR) – while the loop is rigid and
canonical at pH 2.4, it becomes disordered at pH 4.75
[106]. This conformational change likely results from
deprotonation of Glu32 and disruption of the hydrogen
bond between side chains of Thr30 (P2) and Glu32 (P1¢),
since in a homologous inhibitor, AMCI, which has Gln
instead of Glu, no pH-induced structural transition is observed [107]. Interestingly, replacing the CI-2 loop sequence with that of helix E from subtilisin Carlsberg led
to a protein hybrid with a well-preserved scaffold and
extended loop-like conformation of the introduced sequence [108]. This result shows that the context of the
CI-2 scaffold is sufficient to impose appropriate loop
conformation. Furthermore, a multiple mutant of BPTI
with almost all residues in the binding loop replaced
with alanines was constructed. Although this loop region
was significantly less structured compared to the wildtype protein, the binding loop still could adopt the proper conformation and interact with trypsin and chymotrypsin [109]. The inhibitor scaffold, therefore, seems
to play an active role in maintaining the loop conformation.
The standard mechanism
The canonical inhibitor-cognate protease interaction is
preserved in all cases tested and called the standard
mechanism [15]. The interaction between enzyme and inhibitor can be presented in a simplified form as a hydro-
2436
D. Krowarsch et al.
Protein inhibitors of serine proteases
Figure 5. Binding-loop structures of representatives of inhibitor families: bdellastasin (PDB :1c9p); AMCI (1ccv); BBBI (1c2a); CHFI
(1bea); elafin (1fle); ecotin (1ifg); PMP-C (1gl1); OMJPQ3, Japanese quail ovomucoid third domain (1ovo); BPTI (5pti); STI (1ba7);
eglin c (1cse); PCI-1 (4sgb); CMTI I (2sta); SSI (3ssi). The fragments comprise P3-P2¢ segments with additional residues involved in binding-loop stabilization. The backbone is shown in gray, P1 side chains in red, disulfide bridges in yellow, polar and hydrophobic side chains
in green and magenta, respectively. Additionally, hydrogen bonds are shown as black dashed lines. Amino acid residues are labeled using
one-letter codes including Schechter and Berger notations. Name of inhibitor family (in bold) and name of representative are indicated.
CMLS, Cell. Mol. Life Sci.
Review Article
Vol. 60, 2003
lysis/resynthesis reaction of the P1-P1¢ reactive-site peptide bond:
kon
E+I ¤
koff
k*off
EI ¤ E + I*
k*on
(1)
where E is the protease, I is the inhibitor, I* is the reactive-site-cleaved inhibitor, EI is the stable complex, kon
and k*on are respective second-order association rate constants, and koff and k*off are respective first-order dissociation rate constants of the complex. A recently described
bacterial inhibitor of metalloproteases appears to resemble canonical inhibitors with respect to the inhibition
mechanism [110].
Compared to peptide bond hydrolysis in a regular protein:
1) The complex EI is much more stable than the
Michaelis ES complex. Typical inhibition constant
(Ki) values are 106- to 109-fold lower than Km values.
Often, complex can be easily crystallized and shows
all typical features of protein-protein recognition [14,
43].
2) The catalytic rate constant for the hydrolysis of the reactive site is extremely low at neutral pH [87, 111].
However, there are examples of hydrolysis of reactive
sites by inhibited proteases, proceeding at much higher
rates [112, 113].
3) The conserved mode of recognition between the protease-binding loop and the active site leads to many
different serine proteases (belonging both to the chymotrypsin and subtilisin families) of different specificities being inhibited at the same reactive site in the
case of the turkey ovomucoid third domain [74]. This
is also true for other inhibitors. Eglin c (potato 1 family) inhibits 14 serine proteases with association constant values greater than 108 M–1 [5]. Furthermore, the
three-dimensional structures of BPTI complexed with
trypsin [114], chymotrypsin [115], pancreatic
kallikrein [116], thrombin [117], factor VIIa [118], and
trypsinogen [119] show extremely similar modes of
recognition, despite one billion-fold difference in their
affinities. A similar difference in the association constant exists for the interaction of trypsin with ten P1
mutants of BPTI and, again, crystal structures of the
respective complexes show virtually identical modes
of recognition [120].
4) The kcat/Km index for the hydrolysis of the reactive-site
peptide bond is often about 106 M–1 s–1, suggesting that
inhibitors are good substrates [121]. However, this parameter describes the enzyme-substrate reaction only
at low substrate concentrations ([S]<Km). Since the
Km values for hydrolysis are extremely low, the reaction rate is proportional to kcat which is known to be extremely low in the case of reactive-site hydrolysis at
neutral pH.
5) The hydrolysis reaction is reversible, i.e. the cleaved
inhibitor is active and forms the same complex with
2437
the enzyme as the intact form. During complex formation, resynthesis of the reactive-site peptide bond occurs [111]. The kinetic parameters for reactive-site
resynthesis are often similar to those of the hydrolysis
reaction. The phenomenon of hydrolysis/resynthesis
also occurs at other peptide bonds of the binding loop
and can also be catalyzed by non-serine proteases [87].
6) The equilibrium value of [I*]/[I] (hydrolysis constant,
Khyd) is often close to unity (i. e., about 50% of the inhibitor molecules have the reactive site cleaved) at pH
6 where Khyd is pH independent [86, 87, 121], but examples are known of natural ovomucoid third domain
variants with Khyd in the range of 0.4–35 [85]. Typical
Khyd values for a single peptide bond hydrolysis in a
native protein containing secondary structure are in
the neglibly low values of 10–3 to 10–8 [122]. Thus the
values of Khyd in protein inhibitors are extremely high.
Substitution of the residues which maintain the binding loop conformation affects the value of Khyd. However, the effect of a single mutation is relatively small
and does not exceed the factor 3 –5 [85].
7) While the kon values for protease-inhibitor association
are typically about 106 M–1 s–1, the koff values may differ by many orders of magnitude. The k*on values can
also differ by many orders of magnitude for the interaction of an inhibitor with different proteases [74].
8) At high concentrations of enzyme and inhibitor, the
existence of additional unstable loose complexes L
and L* can be detected by stopped-flow methods
[121]. Recent experiments revealed that the acyl-enzyme intermediate could be formed rapidly, suggesting that there is no energetic barrier to the acylation reaction [123].
The protease-inhibitor complex
The mode of recognition between different canonical inhibitors and serine proteases is always almost the same.
In the stable complex, which was a subject of numerous
crystallographic studies, a short antiparallel b sheet is
formed between the P3-P1 residues and the 214 – 216
(Ser125-Gly127 in subtilisin) segment of the enzyme
(fig. 6). The energetic contribution of one of these intermolecular main chain hydrogen bonds (donated by the
HN amide of the P1 residue of OMTKY3) was recently found to be about 1.5 kcal/mol [124]. There is an
additional antiparallel b sheet between the P4-P6 fragment and Tyr104-Gly102 residues in subtilisin complexes, which does not exist in chymotrypsin-like enzymes [125, 126]. Other very important features of
the complex include: a short (usually about 2.7 Å) contact between the P1 carbonyl carbon and the catalytic serine residue (significantly shorter in rhodniin-thrombin
[78] and mung bean trypsin inhibitor-trypsin complexes
2438
D. Krowarsch et al.
Protein inhibitors of serine proteases
Figure 6. Schematic representation of canonical inhibition based on the structure of the CMTI I:trypsin complex (PDB: 1ppe). The inhibitor [dark gray, residues marked as (I)] binds to the protease [light gray, residues marked as (E)] in a manner similar to that of a typical
substrate. Several characteristic interactions are shown: (i) antiparallel b sheet formed between residues P1-P3 of the inhibitor and residues
214 –216 of the protease; (ii) sub-van der Waals contacts between Ser195 Og and P1 carbonyl carbon, and (iii) hydrogen bonds from the
oxyanion binding hole (HN of Gly193 and Ser195) to the P1 carbonyl oxygen. Nitrogen and oxygen atoms are shown as dark and light gray
balls, respectively. Amino acid residues are labeled using three-letter codes including Schechter and Berger notation.
[127]), and two hydrogen bonds between the carbonyl
oxygen of P1 and Gly193/Ser195 amides of the oxyanion
binding hole, and the hydrogen bonds between the P1 HN
group and the side chain of Ser195 and the carbonyl of
Ser214. Conversion of the P2-P1 amide bond to an ester
bond reduces the association free energy by about 1.5
kcal/mol [124, 128]. The reactive-site peptide bond remains intact in all crystallographically studied complexes. All the above-mentioned hydrogen bonds and the
shape complementarity of interacting areas ensure very
similar recognition modes between different proteases
and inhibitors.
In the complex, about 10 –18 amino acid residues of the
inhibitor and 17 –30 residues of the protease make numerous interactions – mainly van der Waals (typically
more than 100) and hydrogen bonds (about 8–15). The
total area of the two components buried in the interface is
about 1400 Å2. According to NMR relaxation studies, the
protease-binding loop, which is often poorely structured
in free inhibitors [90, 91, 129], becomes significantly
rigidified in the complex. There are no significant conformational changes on either the enzyme or inhibitor
part accompanying complex formation, with the exception of zymogen complexes. In the trypsinogen-inhibitor
complex, major structural rearrangements are observed
in the activation domain comprising the active-site region
[130]. The organization of the activation domain in the
complex with the inhibitor is remarkably similar to one
observed in the active enzyme, but fully disordered in the
free zymogen. The association constant is about 107-fold
lower than for the active enzyme [131, 132]. Despite the
inherently low activity of the zymogen, the standard
mechanism works also for trypsinogen, which is able to
resynthesize the reactive-site peptide bond of the inhibitor [133].
The P1 position
In canonical inhibitors, position P1 determines to a large
extent the protease-inhibitor association energy. With the
exception of Trp, Ile and Cys, all amino acids have been
observed at this position in inhibitors representing different families [134]. The plot of the substrate transitionstate energy log(kcat/Km) versus the enzyme-inhibitor association energy log(Ka) determined for a set of P1
oligopeptide substrates and protein inhibitors is a straight
line with a slope not far from unity, suggesting that interactions within the S1 pocket do not change as the reaction
proceeds from the enzyme-inhibitor complex to the transition state [51, 135, 136].
P1 Gly and particularly P1 Pro are very disfavored for
binding with most of the proteases tested [51, 137]. Also
the charged P1 side chains of Asp, Glu and His (but not
their uncharged forms), when placed in hydrophobic S1
pockets, strongly oppose complex formation [138]. The
shifts of the pK values of these side chains placed in the
hydrophobic S1 pocket of SGPB reach 5 pH units.
The P1 side chain is fully exposed in all free inhibitor
structures (fig. 7) and becomes imbedded in the S1 pocket
CMLS, Cell. Mol. Life Sci.
Vol. 60, 2003
Review Article
2439
energies of protease-inhibitor interactions were extensively
tested in the Laskowski laboratory for the interaction between ovomucoid third domains and six different serine
proteases [147]. Depending on the experimental error
analysis, the protease tested, and the number of mutations
introduced, the additivity holds for from 60 to almost
100% of the analyzed cases. Additivity offers a superb possibility of creating strong (with Ka values up to 1017 M–1) or
specific inhibitors for different proteases through careful
design of multiple mutants not only of ovomucoid third domains but also of inhibitors belonging to all other families
[147–149]. Very recently, additivity was successfully
tested in the interaction between chymotrypsin and alanine-shaved mutants of BPTI [83].
Figure 7. Solvent accessible area of CMTI I (PDB: 1lu0). Only the
main chain of the inhibitor and side chain of P1 (Arg5) are shown.
The solvent-exposed protease-binding loop (residues P3 to P3¢) and
corresponding surface is colored dark gray. Amino acid residues are
labeled using Schechter and Berger notation.
upon complex formation. It can form about 50% of the
interface contact area and provide even up to 70 % of the
association energy as deduced from comparisons with the
P1 Gly variant [51, 137, 139]. Cognate P1 side chains enter the S1 pocket preserving optimal c angles [140, 141].
An improperly matched P1-S1 interaction in terms of size,
shape, charge, polarity, or branching of the P1 side chain
leads to severe effects on the association energy [135,
137, 139, 141, 142]. Furthermore, alanine-scanning mutagenesis of BPTI [82] and theoretical calculations of the
protease-inhibitor interaction [143] clearly reveal a dominant role for the P1 residue. Since the P1 residue occupies
a central part of the canonical loop, its substitutions in
different inhibitor families often cause very similar energetic effects on the binding to the serine protease, a phenomenon called the interscaffolding additivity [137,
139]. A lack of interscaffolding additivity was observed
for the interaction of P1 Lys variants of OMTKY3 and
BPTI with chymotrypsin, and was explained based on the
crystal structures of the two complexes in which completely different conformation of the P1 side chain and its
interactions were observed upon binding in the respective
S1 pockets [115, 137, 144].
The additivity
In the simplest case, additivity assumes that the energetic
effects of two individual mutations sum up, within experimental error, in a mutant containing the two mutations
[145]. Additivity can also be applied in systems containing
a larger number of mutations. In protein chemistry, additivity is tested in various macromolecular processes almost
exclusively at the level of free energy effects [146]. Free
Acknowledgements. The research of J. Otlewski was supported by
an International Research Scholar award from the Howard Hughes
Medical Institute and by a scholarship from the Foundation for
Polish Science.
1 Neurath H. (1989) Proteolytic processing and physiological
regulation. Trends Biochem. Sci. 14: 268 – 271
2 Khan A. R. and James M. N. (1998) Molecular mechanisms
for the conversion of zymogens to active proteolytic enzymes.
Protein Sci. 7: 815 – 836
3 Bode W. and Huber R. (2000) Structural basis of the endoproteinase-protein inhibitor interaction. Biochim. Biophys. Acta
1477: 241 – 252
4 Otlewski J., Krowarsch D. and Apostoluk W. (1999) Protein
inhibitors of serine proteinases. Acta Biochim. Pol. 46:
531 – 565
5 Laskowski M. Jr, Qasim M. A. and Lu S. M. (2000) Interaction
of standard mechanism, canonical protein inhibitors with serine
proteinases. In: protein-Protein Recognition, pp. 228–279,
Kleanthous C. (ed.), Oxford University Press, Oxford
6 Strukelj B., Lenarcic B., Gruden K., Pungercar J., Rogelj B.,
Turk V. et al. (2000) Equistatin, a protease inhibitor from the
sea anemone Actinia equina, is composed of three structural
and functional domains. Biochem. Biophys. Res. Commun.
269: 732 – 736
7 Kumazaki T., Kajiwara K., Kojima S., Miura K. and Ishii S.
(1993) Interaction of Streptomyces subtilisin inhibitor (SSI)
with Streptomyces griseus metallo-endopeptidase II (SGMP
II). J. Biochem. (Tokyo) 114: 570 – 575
8 Hiraga K., Suzuki T. and Oda K. (2000) A novel doubleheaded proteinaceous inhibitor for metalloproteinase and serine proteinase. J. Biol. Chem. 275: 25173 – 25179
9 Mares M., Meloun B., Pavlik M., Kostka V. and Baudys M.
(1989) Primary structure of cathepsin D inhibitor from potatoes and its structure relationship to soybean trypsin inhibitor
family. FEBS Lett. 251: 94 – 98
10 Ritonja A., Krizaj I., Mesko P., Kopitar M., Lucovnik P.,
Strukelj B. et al. (1990) The amino acid sequence of a novel
inhibitor of cathepsin D from potato. FEBS Lett. 267: 13 – 15
11 Zemke K. J., Muller-Fahrnow A., Jany K. D., Pal G. P. and
Saenger W. (1991) The three-dimensional structure of the bifunctional proteinase K/alpha-amylase inhibitor from wheat
(PK13) at 2.5 Å resolution. FEBS Lett. 279: 240 – 242
12 Vallee F., Kadziola A., Bourne Y., Juy M., Rodenburg K. W.,
Svensson B. et al. (1998) Barley alpha-amylase bound to its
endogenous protein inhibitor BASI: crystal structure of the
complex at 1.9 Å resolution. Structure 6: 649 – 659
13 Gettins P. G. (2002) Serpin structure, mechanism, and function. Chem. Rev. 102: 4751 – 4804
2440
D. Krowarsch et al.
14 Jones S. and Thornton J. M. (1996) Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA 93: 13 – 20
15 Laskowski M. Jr and Kato I. (1980) Protein inhibitors of proteinases. Annu. Rev. Biochem. 49: 593–626
16 Bode W. and Huber R. (1992) Natural protein proteinase inhibitors and their interaction with proteinases. Eur. J.
Biochem. 204: 433–451
17 Silverman G. A., Bird P. I., Carrell R. W., Church F. C.,
Coughlin P. B., Gettins P. G. et al. (2001) The serpins are an
expanding superfamily of structurally similar but functionally
diverse proteins: evolution, mechanism of inhibition, novel
functions, and a revised nomenclature. J. Biol. Chem. 276:
33293–33296
18 Stein P. E. and Carrell R. W. (1995) What do dysfunctional
serpins tell us about molecular mobility and disease? Nat.
Struct. Biol. 2: 96–113
19 Elliott P. R., Abrahams J. P. and Lomas D. A. (1998) Wild-type
alpha 1-antitrypsin is in the canonical inhibitory conformation. J. Mol. Biol. 275: 419–425
20 Tucker H. M., Mottonen J., Goldsmith E. J. and Gerard R. D.
(1995) Engineering of plasminogen activator inhibitor-1 to reduce the rate of latency transition. Nat. Struct. Biol. 2:
442–445
21 Huntington J. A., Read R. J. and Carrell R. W. (2000) Structure of a serpin-protease complex shows inhibition by deformation. Nature 407: 923–926
22 Komiyama T., Ray C. A., Pickup D. J., Howard A. D., Thornberry N. A., Peterson E. P. et al. (1994) Inhibition of interleukin-1 beta converting enzyme by the cowpox virus serpin
CrmA: an example of cross-class inhibition. J. Biol. Chem.
269: 19331–19337
23 Mathialagan N. and Hansen T. R. (1996) Pepsin-inhibitory activity of the uterine serpins. Proc. Natl. Acad. Sci. USA 93:
13653–13658
24 Stubbs M. T., Huber R. and Bode W. (1995) Crystal structures
of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against
thrombin. FEBS Lett. 375: 103–107
25 Turk D., Sturzebecher J. and Bode W. (1991) Geometry of
binding of the N alpha-tosylated piperidides of m-amidino-,
p-amidino- and p-guanidino phenylalanine to thrombin and
trypsin: X-ray crystal structures of their trypsin complexes
and modeling of their thrombin complexes. FEBS Lett. 287:
133–138
26 Turk B., Turk V. and Turk D. (1997) Structural and functional
aspects of papain-like cysteine proteinases and their protein
inhibitors. Biol. Chem. 378: 141–150
27 Guncar G., Pungercic G., Klemencic I., Turk V. and Turk D.
(1999) Crystal structure of MHC class II-associated p41 Ii
fragment bound to cathepsin L reveals the structural basis for
differentiation between cathepsins L and S. EMBO J. 18:
793–803
28 Rigden D. J., Mosolov V. V. and Galperin M. Y. (2002) Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein
inhibitors. Protein Sci. 11: 1971–1977
29 Chai J., Shiozaki E., Srinivasula S. M., Wu Q., Datta P., Alnemri E. S. et al. (2001) Structural basis of caspase-7 inhibition by XIAP. Cell 104: 769–780
30 Huang Y., Park Y. C., Rich R. L., Segal D., Myszka D. G. and
Wu H. (2001) Structural basis of caspase inhibition by XIAP:
differential roles of the linker versus the BIR domain. Cell
104: 781–790
31 Riedl S. J., Renatus M., Schwarzenbacher R., Zhou Q., Sun C.,
Fesik S. W. et al. (2001) Structural basis for the inhibition of
caspase-3 by XIAP. Cell 104: 791–800
32 Xu G., Cirilli M., Huang Y., Rich R. L., Myszka D. G. and Wu
H. (2001) Covalent inhibition revealed by the crystal structure
of the caspase- 8/p35 complex. Nature 410: 494– 497
Protein inhibitors of serine proteases
33 Zhou Q. and Salvesen G. S. (2000) Viral caspase inhibitors
CrmA and p35. Methods Enzymol. 322: 143 – 154
34 Simonovic M., Gettins P. G. W. and Volz K. (2000) Crystal
structure of viral serpin crmA provides insights into its mechanism of cysteine proteinase inhibition. Protein Sci. 9:
1423 – 1427
35 Rees D. C. and Lipscomb W. N. (1982) Refined crystal structure of the potato inhibitor complex of carboxypeptidase A at
2.5 Å resolution. J. Mol. Biol. 160: 475 – 498
36 Seeram S. S., Hiraga K. and Oda K. (1997) Resynthesis of reactive site peptide bond and temporary inhibition of Streptomyces metalloproteinase inhibitor. J. Biochem. (Tokyo) 122:
788 – 794
37 Fernandez-Catalan C., Bode W., Huber R., Turk D., Calvete J.
J., Lichte A. et al. (1998) Crystal structure of the complex
formed by the membrane type 1-matrix metalloproteinase
with the tissue inhibitor of metalloproteinases-2, the soluble
progelatinase A receptor. EMBO J. 17: 5238 – 5248
38 Gomis-Ruth F. X., Maskos K., Betz M., Bergner A., Huber R.,
Suzuki K. et al. (1997) Mechanism of inhibition of the human
matrix metalloproteinase stromelysin-1 by TIMP-1. Nature
389: 77 – 81
39 Hege T., Feltzer R. E., Gray R. D. and Baumann U. (2001) Crystal structure of a complex between Pseudomonas aeruginosa
alkaline protease and its cognate inhibitor: inhibition by a zincNH2 coordinative bond. J. Biol. Chem. 276: 35087– 35092
40 Li M., Phylip L. H., Lees W. E., Winther J. R., Dunn B. M.,
Wlodawer A. et al. (2000) The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix. Nat.
Struct. Biol. 7: 113 – 117
41 Ng K. K., Petersen J. F., Cherney M. M., Garen C., Zalatoris J.
J., Rao-Naik C. et al. (2000) Structural basis for the inhibition
of porcine pepsin by Ascaris pepsin inhibitor-3. Nat. Struct.
Biol. 7: 653 – 657
42 Janin J. and Chothia C. (1990) The structure of protein-protein
recognition sites. J. Biol. Chem. 265: 16027 – 16030
43 Apostoluk W. and Otlewski J. (1998) Variability of the canonical loop conformations in serine proteinases inhibitors and
other proteins. Proteins 32: 459 – 474
44 Schechter I. and Berger A. (1967) On the size of the active site
in proteases. I. Papain. Biochem. Biophys. Res. Commun. 27:
157 – 162
45 Jackson R. M. and Russell R. B. (2000) The serine protease inhibitor canonical loop conformation: examples found in extracellular hydrolases, toxins, cytokines and viral proteins. J.
Mol. Biol. 296: 325 – 334
46 Korsinczky M. L., Schirra H. J., Rosengren K. J., West J.,
Condie B. A., Otvos L. et al. (2001) Solution structures by 1H
NMR of the novel cyclic trypsin inhibitor SFTI-1 from sunflower seeds and an acyclic permutant. J. Mol. Biol. 311:
579 – 591
47 Felizmenio-Quimio M. E., Daly N. L. and Craik D. J. (2001)
Circular proteins in plants: solution structure of a novel
macrocyclic trypsin inhibitor from Momordica cochinchinensis. J. Biol. Chem. 276: 22875 – 22882
48 Goldenberg D. P. and Creighton T. E. (1983) Circular and circularly permuted forms of bovine pancreatic trypsin inhibitor.
J. Mol. Biol. 165: 407 – 413
49 Botos I., Wu Z., Lu W. and Wlodawer A. (2001) Crystal structure of a cyclic form of bovine pancreatic trypsin inhibitor.
FEBS Lett. 509: 90 – 94
50 Lu W., Apostol I., Qasim M. A., Warne N., Wynn R., Zhang W.
L. et al. (1997) Binding of amino acid side-chains to S1 cavities of serine proteinases. J. Mol. Biol. 266: 441 – 461
51 Hohenester E., Maurer P. and Timpl R. (1997) Crystal structure of a pair of follistatin-like and EF-hand calcium-binding
domains in BM-40. EMBO J. 16: 3778 – 3786
52 Bode W., Greyling H. J., Huber R., Otlewski J. and Wilusz T.
(1989) The refined 2.0 Å X-ray crystal structure of the com-
CMLS, Cell. Mol. Life Sci.
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
Vol. 60, 2003
plex formed between bovine beta-trypsin and CMTI-I, a
trypsin inhibitor from squash seeds (Cucurbita maxima):
topological similarity of the squash seed inhibitors with the
carboxypeptidase A inhibitor from potatoes. FEBS Lett. 242:
285–292
Pritchard L. and Dufton M. J. (1999) Evolutionary trace
analysis of the Kunitz/BPTI family of proteins: functional divergence may have been based on conformational adjustment.
J. Mol. Biol. 285: 1589–1607
Zweckstetter M., Czisch M., Mayer U., Chu M. L., Zinth W.,
Timpl R. et al. (1996) Structure and multiple conformations of
the kunitz-type domain from human type VI collagen alpha3(VI) chain in solution. Structure 4: 195–209
Kohfeldt E., Gohring W., Mayer U., Zweckstetter M., Holak
T. A., Chu M. L. et al. (1996) Conversion of the Kunitztype module of collagen VI into a highly active trypsin inhibitor by site-directed mutagenesis. Eur. J. Biochem. 238:
333 – 340
Locht A. van de, Stubbs M. T., Bode W., Friedrich T.,
Bollschweiler C., Hoffken W. et al. (1996) The ornithodorinthrombin crystal structure, a key to the TAP enigma? EMBO
J. 15: 6011–6017
Waxman L., Smith D. E., Arcuri K. E. and Vlasuk G. P. (1990)
Tick anticoagulant peptide (TAP) is a novel inhibitor of blood
coagulation factor Xa. Science 248: 593–596
Wei A., Alexander R. S., Duke J., Ross H., Rosenfeld S. A. and
Chang C. H. (1998) Unexpected binding mode of tick anticoagulant peptide complexed to bovine factor Xa. J. Mol. Biol.
283: 147–154
Moses E. and Hinz H. J. (1983) Basic pancreatic trypsin inhibitor has unusual thermodynamic stability parameters. J.
Mol. Biol. 170: 765–776
Makhatadze G. I., Kim K. S., Woodward C. and Privalov P. L.
(1993) Thermodynamics of BPTI folding. Protein Sci. 2:
2028–2036
Wieczorek M., Otlewski J., Cook J., Parks K., Leluk J., Wilimowska-Pelc A. et al. (1985) The squash family of serine proteinase inhibitors: amino acid sequences and association equilibrium constants of inhibitors from squash, summer squash,
zucchini, and cucumber seeds. Biochem. Biophys. Res. Commun. 126: 646–652
Otlewski J. and Laskowski M. Jr (1985) Calorimetric investigation of the reactive site of turkey ovomucoid third domain.
Fed. Proc. Fed. Am. Soc. Exp. Biol. 44: 1807
Krokoszynska I. and Otlewski J. (1996) Thermodynamic stability effects of single peptide bond hydrolysis in protein inhibitors of serine proteinases. J. Mol. Biol. 256: 793– 802
Socorro M. C. M. do, Oliva M. L., Fritz H., Jochum M.,
Mentele R., Sampaio M. et al. (2002) Characterization of a
Kunitz trypsin inhibitor with one disulfide bridge purified
from Swartzia pickellii. Biochem. Biophys. Res. Commun.
291: 635–639
Hemmi H., Kumazaki T., Yamazaki T., Kojima S., Yoshida T.,
Kyogoku Y. et al. (2003) Inhibitory specificity change of the
ovomucoid third domain of the silver pheasant upon introduction of an engineered Cys14-Cys39 bond. Biochemistry 42:
2524–2534
Hurle M. R., Marks C. B., Kosen P. A., Anderson S. and Kuntz
I. D. (1990) Denaturant-dependent folding of bovine pancreatic trypsin inhibitor mutants with two intact disulfide bonds.
Biochemistry 29: 4410–4419
Krokoszynska I., Dadlez M. and Otlewski J. (1998) Structure
of single-disulfide variants of bovine pancreatic trypsin inhibitor (BPTI) as probed by their binding to bovine betatrypsin. J. Mol. Biol. 275: 503–513
Rolka K., Kupryszewski G., Rozycki J., Ragnarsson U.,
Zbyryt T. and Otlewski J. (1992) New analogues of Cucurbita
maxima trypsin inhibitor III (CMTI III) with simplified structure. Biol. Chem. Hoppe Seyler 373: 1055–1060
Review Article
2441
69 Yu M. H., Weissman J. S. and Kim P. S. (1995) Contribution
of individual side-chains to the stability of BPTI examined by
alanine-scanning mutagenesis. J. Mol. Biol. 249: 388 – 397
70 Tamura A., Kanaori K., Kojima S., Kumagai I., Miura K. and
Akasaka K. (1991) Mechanisms of temporary inhibition in
Streptomyces subtilisin inhibitor induced by an amino acid
substitution, tryptophan 86 replaced by histidine. Biochemistry 30: 5275 – 5286
71 Beeser S. A., Goldenberg D. P. and Oas T. G. (1997) Enhanced
protein flexibility caused by a destabilizing amino acid replacement in BPTI. J. Mol. Biol. 269: 154 – 164
72 Xie Z. W., Luo M. J., Xu W. F. and Chi C. W. (1997) Two reactive site locations and structure-function study of the arrowhead proteinase inhibitors, A and B, using mutagenesis.
Biochemistry 36: 5846 – 5852
73 Ardelt W. and Laskowski M. Jr (1985) Turkey ovomucoid
third domain inhibits eight different serine proteinases of varied specificity on the same ...Leu18-Glu19... reactive site.
Biochemistry 24: 5313 – 5320
74 Petersen L. C., Bjorn S. E., Olsen O. H., Nordfang O., Norris
F. and Norris K. (1996) Inhibitory properties of separate recombinant Kunitz-type-protease-inhibitor domains from tissue-factor-pathway inhibitor. Eur. J. Biochem. 235: 310 – 316
75 Xu Y., Carr P. D., Guss J. M. and Ollis D. L. (1998) The crystal structure of bikunin from the inter-alpha-inhibitor complex: a serine protease inhibitor with two Kunitz domains. J.
Mol. Biol. 276: 955 – 966
76 Schirra H. J., Scanlon M. J., Lee M. C., Anderson M. A. and
Craik D. J. (2001) The solution structure of C1-T1, a two-domain proteinase inhibitor derived from a circular precursor
protein from Nicotiana alata. J. Mol. Biol. 306: 69 – 79
77 Locht A. van de, Lamba D., Bauer M., Huber R., Friedrich T.,
Kroger B. et al. (1995) Two heads are better than one: crystal
structure of the insect derived double domain Kazal inhibitor
rhodniin in complex with thrombin. EMBO J. 14: 5149 – 5157
78 McGrath M. E., Erpel T., Bystroff C. and Fletterick R. J.
(1994) Macromolecular chelation as an improved mechanism
of protease inhibition: structure of the ecotin-trypsin complex.
EMBO J. 13: 1502 – 1507
79 Eggers C. T., Wang S. X., Fletterick R. J. and Craik C. S.
(2001) The role of ecotin dimerization in protease inhibition.
J. Mol. Biol. 308: 975 – 991
80 Trexler M., Banyai L. and Patthy L. (2001) A human protein
containing multiple types of protease-inhibitory modules.
Proc. Natl. Acad. Sci. USA 98: 3705 – 3709
81 Castro M. J. and Anderson S. (1996) Alanine point-mutations
in the reactive region of bovine pancreatic trypsin inhibitor:
effects on the kinetics and thermodynamics of binding to betatrypsin and alpha-chymotrypsin. Biochemistry 35: 11435 –
11446
82 Buczek O., Koscielska-Kasprzak K., Krowarsch D., Dadlez
M. and Otlewski J. (2002) Analysis of serine proteinase-inhibitor interaction by alanine shaving. Protein Sci. 11: 806 –
819
83 Laskowski M. and Qasim M. A. (2000) What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme substrate complexes? Biochim. Biophys. Acta
1477: 324 – 337
84 Ardelt W. and Laskowski M. Jr (1991) Effect of single amino
acid replacements on the thermodynamics of the reactive site
peptide bond hydrolysis in ovomucoid third domain. J. Mol.
Biol. 220: 1041 – 1053
85 Siekmann J., Wenzel H. R., Matuszak E., Goldammer E. von
and Tschesche H. (1988) The pH dependence of the equilibrium constant KHyd for the hydrolysis of the Lys15-Ala16 reactive-site peptide bond in bovine pancreatic trypsin inhibitor
(aprotinin). J. Protein Chem. 7: 633 – 640
86 Otlewski J. and Zbyryt T. (1994) Single peptide bond hydrolysis/resynthesis in squash inhibitors of serine proteinases. 1.
2442
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
D. Krowarsch et al.
Kinetics and thermodynamics of the interaction between
squash inhibitors and bovine beta-trypsin. Biochemistry 33:
200–207
Musil D., Bode W., Huber R., Laskowski M. Jr, Lin T. Y. and
Ardelt W. (1991) Refined X-ray crystal structures of the reactive site modified ovomucoid inhibitor third domains from silver pheasant (OMSVP3*) and from Japanese quail
(OMJPQ3*). J. Mol. Biol. 220: 739–755
Betzel C., Dauter Z., Genov N., Lamzin V., Navaza J.,
Schnebli H. P. et al. (1993) Structure of the proteinase inhibitor eglin c with hydrolysed reactive centre at 2.0 Å resolution. FEBS Lett. 317: 185–188
Shaw G. L., Davis B., Keeler J. and Fersht A. R. (1995) Backbone dynamics of chymotrypsin inhibitor 2: effect of breaking
the active site bond and its implications for the mechanism of
inhibition of serine proteases. Biochemistry 34: 2225 – 2233
Liu J., Prakash O., Huang Y., Wen L., Wen J. J., Huang J. K. et
al. (1996) Internal mobility of reactive-site-hydrolyzed recombinant Cucurbita maxima trypsin inhibitor-V characterized by NMR spectroscopy: evidence for differential stabilization of newly formed C- and N-termini. Biochemistry 35:
12503–12510
Krishnamoorthi R., Lin C. L. and VanderVelde D. (1992)
Structural consequences of the natural substitution, E9K, on
reactive-site-hydrolyzed squash (Cucurbita maxima) trypsin
inhibitor (CMTI), as studied by two-dimensional NMR. Biochemistry 31: 4965–4969
Laskowski M. Jr and Sealock R. W. (1971) Protein proteinase
inhibitors – molecular aspects. In: the Enzymes, vol. 3, pp.
376 – 457, Boyer P. D. (ed.), Academic Press, New York
Cai M., Gong Y., Prakash O. and Krishnamoorthi R. (1995)
Reactive-site hydrolyzed Cucurbita maxima trypsin inhibitorV: function, thermodynamic stability, and NMR solution
structure. Biochemistry 34: 12087–12094
Laskowski M. Jr, Kato I., Ardelt W., Cook J., Denton A., Empie M. W. et al. (1987) Ovomucoid third domains from 100
avian species: isolation, sequences, and hypervariability of enzyme-inhibitor contact residues. Biochemistry 26: 202 – 221
Otlewski J. and Krowarsch D. (1996) Squash inhibitor family
of serine proteinases. Acta Biochim. Pol. 43: 431 – 444
Beuning L. L., Spriggs T. W. and Christeller J. T. (1994) Evolution of the proteinase inhibitor I family and apparent lack of
hypervariability in the proteinase contact loop. J. Mol. Evol.
39: 644–654
Nielsen K. J., Alewood D., Andrews J., Kent S. B. and Craik D.
J. (1994) An 1H NMR determination of the three-dimensional
structures of mirror-image forms of a Leu-5 variant of the
trypsin inhibitor from Ecballium elaterium (EETI-II). Protein
Sci. 3: 291–302
Heinz D. W., Hyberts S. G., Peng J. W., Priestle J. P., Wagner
G. and Grutter M. G. (1992) Changing the inhibitory specificity and function of the proteinase inhibitor eglin c by sitedirected mutagenesis: functional and structural investigation.
Biochemistry 31: 8755–8766
Grzesiak A., Helland R., Smalas A. O., Krowarsch D., Dadlez
M. and Otlewski J. (2000) Substitutions at the P(1) position in
BPTI strongly affect the association energy with serine proteinases. J. Mol. Biol. 301: 205–217
Brauer A. B., Domingo G. J., Cooke R. M., Matthews S. J. and
Leatherbarrow R. J. (2002) A conserved cis peptide bond is
necessary for the activity of Bowman-Birk inhibitor protein.
Biochemistry 41: 10608–10615
Cierpicki T. and Otlewski J. (2000) Determination of a high
precision structure of a novel protein, Linum usitatissimum
trypsin inhibitor (LUTI), using computer-aided assignment of
NOESY cross-peaks. J. Mol. Biol. 302: 1179–1192
Cai M., Huang Y., Prakash O., Wen L., Dunkelbarger S. P.,
Huang J. K. et al. (1996) Differential modulation of binding
loop flexibility and stability by Arg50 and Arg52 in Cucurbita
Protein inhibitors of serine proteases
103
104
105
106
107
108
109
110
111
112
113
114
115
116
maxima trypsin inhibitor-V deduced by trypsin-catalyzed hydrolysis and NMR spectroscopy. Biochemistry 35: 4784 –
4794
Cai M., Gong Y. X., Wen L. and Krishnamoorthi R. (2002)
Correlation of binding-loop internal dynamics with stability
and function in potato I inhibitor family: relative contributions
of Arg(50) and Arg(52) in Cucurbita maxima trypsin inhibitor-V as studied by site-directed mutagenesis and NMR
spectroscopy. Biochemistry 41: 9572 – 9579
Fujinaga M., Sielecki A. R., Read R. J., Ardelt W., Laskowski
M. Jr and James M. N. (1987) Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor
turkey ovomucoid third domain at 1.8 Å resolution. J. Mol.
Biol. 195: 397 – 418
Grasberger B. L., Clore G. M. and Gronenborn A. M. (1994)
High-resolution structure of Ascaris trypsin inhibitor in solution: direct evidence for a pH-induced conformational transition in the reactive site. Structure 2: 669 – 678
Cierpicki T., Bania J. and Otlewski J. (2000) NMR solution
structure of Apis mellifera chymotrypsin/cathepsin G inhibitor-1 (AMCI-1): structural similarity with Ascaris protease inhibitors. Protein Sci. 9: 976 – 984
Osmark P., Sorensen P. and Poulsen F. M. (1993) Context dependence of protein secondary structure formation: the threedimensional structure and stability of a hybrid between chymotrypsin inhibitor 2 and helix E from subtilisin Carlsberg.
Biochemistry 32: 11007 – 11014
Cierpicki T. and Otlewski J. (2002) NMR structures of two
variants of bovine pancreatic trypsin inhibitor (BPTI) reveal
unexpected influence of mutations on protein structure and
stability. J. Mol. Biol. 321: 647 – 658
Seeram S. S., Hiraga K., Saji A., Tashiro M. and Oda K.
(1997) Identification of reactive site of a proteinaceous metalloproteinase inhibitor from Streptomyces nigrescens TK-23. J.
Biochem. (Tokyo) 121: 1088 – 1095
Finkenstadt W. R. and Laskowski M. Jr (1967) Resynthesis by
trypsin of the cleaved peptide bond in modified soybean
trypsin inhibitor. J. Biol. Chem. 242: 771 – 773
Estell D. A., Wilson K. A. and Laskowski M. Jr (1980) Thermodynamics and kinetics of the hydrolysis of the reactive-site
peptide bond in pancreatic trypsin inhibitor (Kunitz) by Dermasterias imbricata trypsin 1. Biochemistry 19: 131 – 137
Ardelt W. and Laskowski M. Jr (1983) Thermodynamics and
kinetics of the hydrolysis and resynthesis of the reactive site
peptide bond in turkey ovomucoid third domain by aspergillopeptidase B. Acta Biochim. Pol. 30: 115 – 126
Huber R., Kukla D., Bode W., Schwager P., Bartels K., Deisenhofer J. et al. (1974) Structure of the complex formed by
bovine trypsin and bovine pancreatic trypsin inhibitor. II.
Crystallographic refinement at 1.9 Å resolution. J. Mol. Biol.
89: 73 – 101
Scheidig A. J., Hynes T. R., Pelletier L. A., Wells J. A. and Kossiakoff A. A. (1997) Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of
Alzheimer’s amyloid beta-protein precursor (APPI) and basic
pancreatic trypsin inhibitor (BPTI): engineering of inhibitors
with altered specificities. Protein Sci. 6: 1806 – 1824
Chen Z. and Bode W. (1983) Refined 2.5 Å X-ray crystal
structure of the complex formed by porcine kallikrein A and
the bovine pancreatic trypsin inhibito: crystallization, Patterson search, structure determination, refinement, structure and
comparison with its components and with the bovine trypsinpancreatic trypsin inhibitor complex. J. Mol. Biol. 164:
283 – 311
Locht A. van de, Bode W., Huber R., Le Bonniec B. F., Stone
S. R., Esmon C. T. et al. (1997) The thrombin E192Q-BPTI
complex reveals gross structural rearrangements: implications
for the interaction with antithrombin and thrombomodulin.
EMBO J. 16: 2977 – 2984
CMLS, Cell. Mol. Life Sci.
Vol. 60, 2003
117 Zhang E., St Charles R. and Tulinsky A. (1999) Structure of
extracellular tissue factor complexed with factor VIIa inhibited with a BPTI mutant. J. Mol. Biol. 285: 2089–2104
118 Bode W., Schwager P. and Huber R. (1978) The transition of
bovine trypsinogen to a trypsin-like state upon strong ligand
binding: the refined crystal structures of the bovine trypsinogenpancreatic trypsin inhibitor complex and of its ternary complex
with Ile-Val at 1.9 Å resolution. J. Mol. Biol. 118: 99–112
119 Helland R., Otlewski J., Sundheim O., Dadlez M. and Smalas
A. O. (1999) The crystal structures of the complexes between
bovine beta-trypsin and ten P1 variants of BPTI. J. Mol. Biol.
287: 923–942
120 Finkenstadt W. R., Hamid M. A., Mattis J. A., Schrode J. A.,
Sealock R. W. and Laskowski M. J. (1974) Kinetics and thermodynamics of the interaction of proteinases with protein inhibitors. In: Bayer-Symposium V, pp. 389 – 411, Fritz H.,
Tschesche H., Greene L. J. and Truscheit E. (eds), Springer,
Berlin
121 Buczek O., Krowarsch D. and Otlewski J. (2002) Thermodynamics of single peptide bond cleavage in bovine pancreatic
trypsin inhibitor (BPTI). Protein Sci. 11: 924–932
122 Radisky E. S. and Koshland D. E. Jr (2002) A clogged gutter
mechanism for protease inhibitors. Proc. Natl. Acad. Sci.
USA 99: 10316–10321
123 Lu W., Qasim M. A., Laskowski M. Jr and Kent S. B. (1997)
Probing intermolecular main chain hydrogen bonding in serine proteinase-protein inhibitor complexes: chemical synthesis of backbone-engineered turkey ovomucoid third domain.
Biochemistry 36: 673–679
124 McPhalen C. A. and James M. N. (1988) Structural comparison of two serine proteinase-protein inhibitor complexes:
eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo. Biochemistry 27: 6582–6598
125 Takeuchi Y., Satow Y., Nakamura K. T. and Mitsui Y. (1991)
Refined crystal structure of the complex of subtilisin BPN¢
and Streptomyces subtilisin inhibitor at 1.8 Å resolution. J.
Mol. Biol. 221: 309–325
126 Lin G., Bode W., Huber R., Chi C. and Engh R. A. (1993) The
0.25-nm X-ray structure of the Bowman-Birk-type inhibitor
from mung bean in ternary complex with porcine trypsin. Eur.
J. Biochem. 212: 549–555
127 Bateman K. S., Huang K., Anderson S., Lu W., Qasim M. A.,
Laskowski M. Jr et al. (2001) Contribution of peptide bonds
to inhibitor-protease binding: crystal structures of the turkey
ovomucoid third domain backbone variants OMTKY3-Pro18I
and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the
free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I. J. Mol.
Biol. 305: 839–849
128 Peng J. W. and Wagner G. (1992) Mapping of the spectral densities of N-H bond motions in eglin c using heteronuclear relaxation experiments. Biochemistry 31: 8571–8586
129 Bode W. and Huber R. (1978) Crystal structure analysis and
refinement of two variants of trigonal trypsinogen: trigonal
trypsin and PEG (polyethylene glycol) trypsinogen and their
comparison with orthorhombic trypsin and trigonal trypsinogen. FEBS Lett. 90: 265–269
130 Bode W. (1979) The transition of bovine trypsinogen to a
trypsin-like state upon strong ligand binding. II. The binding
of the pancreatic trypsin inhibitor and of isoleucine-valine and
of sequentially related peptides to trypsinogen and to p-guanidinobenzoate-trypsinogen. J. Mol. Biol. 127: 357–374
131 Antonini E., Ascenzi P., Bolognesi M., Gatti G., Guarneri M.
and Menegatti E. (1983) Interaction between serine (pro)enzymes, and Kazal and Kunitz inhibitors. J. Mol. Biol. 165:
543–558
132 Zbyryt T. and Otlewski J. (1991) Interaction between squash
inhibitors and bovine trypsinogen. Biol. Chem. Hoppe Seyler
372: 255–262
Review Article
2443
133 Laskowski M. Jr (1986) Protein inhibitors of serine proteinases – mechanism and classification. Adv. Exp. Med. Biol.
199: 1 – 17
134 Kojima S., Nishiyama Y., Kumagai I. and Miura K. (1991) Inhibition of subtilisin BPN¢ by reaction site P1 mutants of
Streptomyces subtilisin inhibitor. J. Biochem. (Tokyo) 109:
377 – 382
135 Polanowska J., Krokoszynska I., Czapinska H., Watorek W.,
Dadlez M. and Otlewski J. (1998) Specificity of human
cathepsin G. Biochim. Biophys. Acta 1386: 189 – 198
136 Krowarsch D., Dadlez M., Buczek O., Krokoszynska I.,
Smalas A. O. and Otlewski J. (1999) Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases. J. Mol. Biol. 289: 175 – 186
137 Abul Qasim M., Ranjbar M. R., Wynn R., Anderson S. and
Laskowski M., Jr. (1995) Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation. J. Biol. Chem. 270: 27419 – 27422
138 Qasim M. A., Ganz P. J., Saunders C. W., Bateman K. S.,
James M. N. and Laskowski M. Jr (1997) Interscaffolding additivity: association of P1 variants of eglin c and of turkey
ovomucoid third domain with serine proteinases. Biochemistry 36: 1598 – 1607
139 Huang K., Lu W., Anderson S., Laskowski M. Jr and James M.
N. (1995) Water molecules participate in proteinase-inhibitor
interactions: crystal structures of Leu18, Ala18, and Gly18
variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B. Protein Sci. 4:
1985 – 1997
140 Helland R., Berglund G. I., Otlewski J., Apostoluk W., Andersen O. A., Willassen N. P. et al. (1999) High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
Acta Crystallogr. D Biol. Crystallogr. 55: 139 – 148
141 Beckmann J., Mehlich A., Schroder W., Wenzel H. R. and
Tschesche H. (1988) Preparation of chemically ‘mutated’
aprotinin homologues by semisynthesis: P1 substitutions
change inhibitory specificity. Eur. J. Biochem. 176: 675 – 682
142 Krystek S., Stouch T. and Novotny J. (1993) Affinity and
specificity of serine endopeptidase-protein inhibitor interactions: empirical free energy calculations based on X-ray crystallographic structures. J. Mol. Biol. 234: 661 – 679
143 Qasim M. A., Lu S. M., Ding J., Bateman K. S., James M. N.,
Anderson S. et al. (1999) Thermodynamic criterion for the
conformation of P1 residues of substrates and of inhibitors in
complexes with serine proteinases. Biochemistry 38: 7142 –
7150
144 Wells J. A. (1990) Additivity of mutational effects in proteins.
Biochemistry 29: 8509 – 8517
145 Dill K. A. (1997) Additivity principles in biochemistry. J. Biol.
Chem. 272: 701 – 704
146 Lu S. M., Lu W., Qasim M. A., Anderson S., Apostol I., Ardelt
W. et al. (2001) Predicting the reactivity of proteins from their
sequence alone: Kazal family of protein inhibitors of serine
proteinases. Proc. Natl. Acad. Sci. USA 98: 1410 – 1415
147 Lu W., Zhang W., Molloy S. S., Thomas G., Ryan K., Chiang
Y. et al. (1993) Arg15-Lys17-Arg18 turkey ovomucoid third
domain inhibits human furin. J. Biol. Chem. 268: 14583 –
14585
148 Laskowski M. Jr, Qasim M. A. and Yi Z. (2003) Additivitybased prediction of equilibrium constants for some proteinprotein associations. Curr. Opin. Struct. Biol. 13: 130 – 139
149 Stubbs M. T. and Bode W. (1994) Coagulation factors and
their inhibitors. Curr. Opin. Struct. Biol. 4: 823 – 832
150 Huntington J. A. and Carrell R. W. (2001) The serpins: nature’s
molecular mousetraps. Sci. Prog. 84: 125 – 136
151 Stubbs M. T., Laber B., Bode W., Huber R., Jerala R., Lenarcic B. et al. (1990) The refined 2.4 Å X-ray crystal structure
of recombinant human stefin B in complex with the cysteine
2444
152
153
154
155
156
157
D. Krowarsch et al.
proteinase papain: a novel type of proteinase inhibitor interaction. EMBO J. 9: 1939–1947
Lenarcic B. and Bevec T. (1998) Thyropins – new structurally
related proteinase inhibitors. Biol. Chem. 379: 105 – 111
Stennicke H. R., Ryan C. A. and Salvesen G. S. (2002) Reprieval from execution: the molecular basis of caspase inhibition. Trends. Biochem. Sci. 27: 94–101
Molina M. A., Marino C., Oliva B., Aviles F. X. and Querol E.
(1994) C-tail valine is a key residue for stabilization of complex between potato inhibitor and carboxypeptidase A. J. Biol.
Chem. 269: 21467–21472
Clore G. M., Gronenborn A. M., Nilges M. and Ryan C. A.
(1987) Three-dimensional structure of potato carboxypeptidase inhibitor in solution: a study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics. Biochemistry 26: 8012–8023
Tate S., Ohno A., Seeram S. S., Hiraga K., Oda K. and Kainosho M. (1998) Elucidation of the mode of interaction of thermolysin with a proteinaceous metalloproteinase inhibitor,
SMPI, based on a model complex structure and a structural
dynamics analysis. J. Mol. Biol. 282: 435–446
Ohno A., Tate S., Seeram S. S., Hiraga K., Swindells M. B.,
Oda K. et al. (1998) NMR structure of the Streptomyces met-
Protein inhibitors of serine proteases
158
159
160
161
162
alloproteinase inhibitor, SMPI, isolated from Streptomyces nigrescens TK-23: another example of an ancestral beta gammacrystallin precursor structure. J. Mol. Biol. 282: 421 – 433
Baumann U., Bauer M., Letoffe S., Delepelaire P. and Wandersman C. (1995) Crystal structure of a complex between
Serratia marcescens metallo-protease and an inhibitor from
Erwinia chrysanthemi. J. Mol. Biol. 248: 653 – 661
Gomez D. E., Alonso D. F., Yoshiji H. and Thorgeirsson U. P.
(1997) Tissue inhibitors of metalloproteinases: structure, regulation and biological functions. Eur. J. Cell Biol. 74: 111 –
122
Gomis-Ruth F. X., Gomez-Ortiz M., Vendrell J., Ventura S.,
Bode W., Huber R. et al. (1997) Crystal structure of an
oligomer of proteolytic zymogens: detailed conformational
analysis of the bovine ternary complex and implications for
their activation. J. Mol. Biol. 269: 861 – 880
Dreyer T., Valler M. J., Kay J., Charlton P. and Dunn B. M.
(1985) The selectivity of action of the aspartic-proteinase inhibitor IA3 from yeast (Saccharomyces cerevisiae). Biochem.
J. 231: 777 – 779
Kageyama T. (1998) Molecular cloning, expression and characterization of an Ascaris inhibitor for pepsin and cathepsin E.
Eur. J. Biochem. 253: 804 – 809