Báo cáo Y học: The role of the second binding loop of the cysteine protease inhibitor, cystatin A (stefin A), in stabilizing complexes with target proteases is exerted predominantly by Leu73 pdf
Theroleofthesecondbindingloopofthecysteineprotease inhibitor,
cystatin A(stefinA),instabilizingcomplexeswithtarget proteases
is exertedpredominantlyby Leu73
Alona Pavlova, Sergio Estrada* and Ingemar Bjo¨rk
Department of Veterinary Medical Chemistry, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Sweden
The aim of this work was to elucidate the roles of individual
residues within the flexible secondbindingloopof human
cystatin Ainthe inhibition ofcysteine proteases. Four
recombinant variants oftheinhibitor, each witha single
mutation, L73G, P74G, Q76G or N77G, inthe most
exposed part of this loop were generated by PCR-based site-
directed mutagenesis. Thebindingof these variants to
papain, cathepsin L, and cathepsin B was characterized by
equilibrium and kinetic methods. Mutation of Leu73
decreased the affinity for papain, cathepsin L and cathep-
sin B by 300-fold, >10-fold and 4000-fold, respect-
ively. Mutation of Pro74 decreased the affinity for
cathepsin B by 10-fold but minimally affected the affinity
for the other two enzymes. Mutation of Gln76 and Asn77
did not alter the affinity ofcystatinA for any ofthe proteases
studied. The decreased affinities were caused exclusively by
increased dissociation rate constants. These results show that
the secondbindingloopofcystatinA plays a major role in
stabilizing thecomplexeswithproteasesby retarding their
dissociation. In contrast withcystatin B, only one amino-
acid residue ofthe loop, Leu73, isof principal importance for
this effect, Pro74 assisting to a minor extent only inthe case
of cathepsin B binding. The contribution ofthe second
binding loopofcystatinA to proteasebinding varies with
the protease, being largest, 45% ofthe total binding
energy, for inhibition of cathepsin B.
Keywords: cathepsins; cystatin; cysteine proteases; papain;
second binding loop.
Cystatins are effective protein inhibitors ofcysteine pro-
teases ofthe papain superfamily (reviewed in [1–4]). Found
both intracellularly and extracellularly, they are believed to
control the activity of normal endogenous proteases, as well
as to protect organisms from the harmful activity of
exogenous cysteineproteases [1,4–11]. They are generally
classified into three families according to their size and the
presence of internal disulfide bonds. Cystatins of family 1,
also called stefins, are small nonglycosylated proteins 11–
12 kDa in size without disulfide bonds. Family 2 cystatins
are somewhat larger, 12–14 kDa, witha structure stabi-
lized by two disulfide bonds. Kininogens, representing the
third family, are glycosylated proteins of about 50–90 kDa.
The single polypeptide chain ofa kininogen contains three
domains resembling family 2 cystatins.
Cystatins competitively inhibit the activity of papain-
like cysteineproteasesbybinding to the active site of the
latter and forming a tight, reversible protein–protein
complex. A model ofthe inhibition was initially proposed
from computer docking experiments based on the X-ray
structures of papain and chicken cystatin, a family 2
member [12]. This model was later substantiated by the
X-ray structure ofa complex ofthe family 1 cystatin,
human cystatin B (stefin B), with papain [13], the only
structure ofa cystatin–protease complex determined so
far. The N-terminal segment and two hairpin loops of the
cystatin together form a hydrophobic wedge-shaped edge
that fits well into the active-site cleft of papain. The high
degree of complementarity between the interacting surfa-
ces allows the complex to form without significant
conformational changes of either papain or the inhibitor
[12–18]. Both the similar three-dimensional structures of
cystatins of families 1 and 2 [12,13,19–21] and the
pronounced sequence homology and similar fold of
cysteine proteasesofthe papain family [4,11,22–24]
indicate that the general aspects ofthe interaction model
can be extended to complexes between cystatins and other
members of this protease family. However, certain distin-
guishing features ofthe structures of some cysteine
proteases, such as the occluding loopof cathepsin B
[25], cause the mode of inhibition to deviate somewhat for
these enzymes. Cystatins thus inhibit cathepsin B by a
two-step reaction involving displacement ofthe occluding
loop oftheproteaseinthesecond step [26,27]. Moreover,
it is apparent that theroleof an individual binding region
Correspondence to I. Bjo
¨
rk, Department of Veterinary Medical
Chemistry, Swedish University of Agricultural Sciences,
Uppsala Biomedical Centre, Box 575, SE-751 23 Uppsala, Sweden.
Fax: + 46 18 550762, Tel.: + 46 18 4714191,
E-mail: Ingemar.Bjork@vmk.slu.se
Abbreviations: app, subscript denoting an apparent equilibrium or rate
constant determined inthe presence of an enzyme substrate; E-64,
4-[(2S,3S)-3-carboxyoxiran-2-carbonyl-
L
-leucylamido]butylguani-
dine; His-tag, 10 successive histidine residues fused to an expressed
protein; k
ass
, bimolecular association rate constant; K
d
, dissociation
equilibrium constant; k
diss
, dissociation rate constant; K
i
,inhibition
constant; k
obs
, observed pseudo-first-order rate constant.
*Present address: PET-Centre, Uppsala University, University
Hospital, SE-751 85 Uppsala, Sweden.
(Received 12 July 2002, revised 16 September 2002,
accepted 20 September 2002)
Eur. J. Biochem. 269, 5649–5658 (2002) Ó FEBS 2002 doi:10.1046/j.1432-1033.2002.03273.x
of the inhibitor inproteasebinding can differ with the
target protease [28].
The contributions ofthe N-terminal region and the first
binding loopof family 1 and 2 cystatins, as well as of the
second bindingloopof family 2 cystatins, to the inhibition
of cysteineproteases have been elucidated [29–36]. Recent
work has also demonstrated the importance of two amino-
acid residues, Leu73 and His75, inthesecondbinding loop
of the family 1 inhibitor,cystatin B, for high-affinity
binding to a number ofcysteineproteases [37]. The sequence
of the corresponding hairpin loopincystatinA(stefin A),
another member of family 1, is appreciably different from
that incystatin B; in particular, His75 ofcystatin B is
substituted by Gly incystatinA [1]. Moreover, the NMR
structure ofcystatinA shows that thesecondloopof this
inhibitor is highly flexible, which might be expected to affect
the interactions withtheprotease [20]. It is thus unclear
whether thesecondbindingloopofcystatinA fulfils the
same function as thesecondbinding loops ofcystatin B and
family 2 cystatins and also what residues of this loop in
cystatin A may participate inthe interaction.
To elucidate theroleofthesecondbindingloopof human
cystatin Ainthe inhibition ofcysteine proteases, we have
characterized the contribution of four individual amino-acid
residues within the most exposed region of this loop (from
Leu73 to Asn77) to proteasebinding (see Fig. 1A). Four
recombinant cystatinA variants with Gly replacing each of
these amino acids were prepared, and their interaction with
papain, cathepsin L, and cathepsin B was characterized by
equilibrium and kinetic methods. The results clearly show
that thesecondbindingloopofcystatinAis important for
the stability ofcomplexeswithcysteine proteases. Its
quantitative roleinproteasebinding varies withthe target
enzyme, but is especially important for cathepsin B. Leu73,
which is highly conserved in family 1 cystatins, makes the
predominant contribution of all residues oftheloop to the
free energy of formation ofthe enzyme–inhibitor complex.
Pro74 isof minimal importance for the interaction with
papain and cathepsin L but participates to some extent in
cathepsin B binding. However, the roles of Gln76 and
Asn77 intheprotease inhibition are negligible.
MATERIALS AND METHODS
Construction of expression vectors for cystatin A
second-loop mutants
A previously developed expression vector containing the
human cystatinA coding sequence preceded by successive
sequences for the leader peptide for the outer membrane
protein Aof Escherichia coli, a His-tag, and the recognition
site for enterokinase was used in this work [38]. This vector
has a kcl857 temperature-sensitive repressor gene, allowing
induction of expression by increasing the temperature, and
an ampicillin-resistance gene [18]. Residues Leu73, Pro74,
Gln76, and Asn77 within thesecondbindingloop of
cystatin A were substituted with Gly by PCR-based site-
directed mutagenesis [39]. Briefly, two mutagenic primers
and two standard PCR primers, the latter being comple-
mentary to regions ofthe vector flanking the cysta-
tin A-coding sequence, were used for creation of each
mutant (Table 1). The desired mutation was introduced in
two steps. First, two overlapping DNA fragments, bearing
Fig. 1. Model ofthe three-dimensional structure ofthe complex between
cystatin A and active papain. (A) Overall structure ofthe complex in
ribbon representation, withcystatinAin green and papain in blue.
Residues inthesecondbindingloopofcystatinA mutated in this work
areinred.PapainresiduesinvolvedininteractionswiththecystatinA
second-binding-loop residues are in black. (B) Close-up view of the
interactions between residues inthesecondbindingloopofcystatin A
and papain residues. The colors ofthe residues are as in (A). Inter-
molecular hydrophobic contacts within a distance of 4 A
˚
are repre-
sented as dashed lines. The model is derived from the X-ray structure
of the human C3S-cystatin B–S-(carboxymethyl)papain complex
(PDB entry 1STF) [13].
5650 A. Pavlova et al.(Eur. J. Biochem. 269) Ó FEBS 2002
the same mutation, were synthesized in two separate PCRs,
in each of which a mutagenic and a standard primer were
used and thecystatinA expression vector was the template.
In the next step, a larger DNA fragment containing the
entire mutant cystatin A-coding sequence was obtained by a
third PCR withthe standard PCR primers and with a
mixture ofthe products ofthe previous two PCRs as
template. The resulting DNA fragment was cleaved with
NcoIandBamHI, and the purified cleavage product
containing the mutant cystatinA cDNA was cloned into
the original vector between the NcoIandBamHI restriction
sites, replacing the corresponding region coding for wild-
type cystatinA [38]. The vector was then transformed into
E. coli strain MC 1061, made competent with CaCl
2
[40],
and transformants were selected by growing the bacteria on
agar plates containing ampicillin. Plasmids from a number
of colonies of each mutant were purified, and those with
the correct mutant cystatinA cDNA were identified by
sequencing in an ABI PRISMÒ 310 Genetic Analyzer
(Applied Biosystems, Foster City, CA, USA).
Expression and purification ofcystatinA mutants
Recombinant L73G, P74G, Q76G, and N77G cystatin A
variants were expressed in E. coli essentially as described
previously [18]. The recombinant proteins were purified
from periplasmic extracts by immobilized metal affinity
chromatography on HisBindÒ Resin (Novagen, Madison,
WI, USA), charged with Ni
2+
, or Ni/nitrilotriacetate
agarose (Qiagen, Hilden, Germany), as in previous work
[38]. The His-tag was cleaved off with enterokinase (EC
3.4.21.9; Biozyme Laboratories, Blaenavon, UK), and the
liberated cystatinA mutant was isolated by rechromato-
graphy on the same affinity column [38]. Intact His-tagged
fusion proteins still contaminating some preparations were
removed by absorption on a TALON
TM
Metal Affinity
Resin (Clontech, Palo Alto, CA, USA) bya hybrid batch/
gravity flow column procedure according to a protocol from
the manufacturer.
Chicken cystatin
Forms1and2ofchickencystatinwereisolatedfrom
chicken egg white [41]. The two forms have the same
sequence and are functionally identical [41], although form 2
is phosphorylated at Ser80 [42] and therefore has a lower
isoelectric point.
Proteases
Papain (EC 3.4.22.2) was purified, stored as inactive
S-(methylthio)papain and activated before use as in previ-
ous work [41]. The thiol group content ofthe activated
papain, determined by reaction with 5,5¢-dithiobis(2-nitro-
benzoic acid) [43], was 0.95–1.00 mol per mol of enzyme.
Titrations with chicken cystatin (form 1) [41] gave a cystatin
to papain stoichiometry of 0.98 ± 0.02, indicating that
the enzyme was fully active inbinding cystatins.
Cathepsin L (EC 3.4.22.15) from sheep liver was a gift from
R. W. Mason, Alfred I. du Pont Institute, Wilmington, DE,
USA. Human liver cathepsin B (EC 3.4.22.1) was obtained
from Calbiochem (San Diego, CA, USA).
Determination of protein concentration
Most protein concentrations were calculated from
A
280
measurements. Molar absorption coefficients of
55 900
M
)1
Æcm
)1
for papain and S-(methylthio)papain
[41], 8800
M
)1
Æcm
)1
for all forms ofcystatinA [18], and
11 400
M
)1
Æcm
)1
for chicken cystatin [41] were used. The
concentration of active cathepsin L was determined by
titration with 4-[(2S,3S)-3-carboxyoxiran-2-carbonyl-
L
-leu-
cylamido]butylguanidine (E-64) [44]. The concentration of
cathepsin B was provided bythe manufacturer.
Binding stoichiometries
The stoichiometries ofbindingofthecystatinA variants to
papain were determined at least in duplicate by titrations of
1 l
M
active papain or S-(methylthio)papain with the
variants. Thebinding to active papain was monitored
by following the decrease in activity ofthe enzyme with
a chromogenic substrate [38], whereas thebinding to
S-(methylthio)papain was monitored by following the
change in tryptophan fluorescence accompanying the
interaction [41]. Thebinding stoichiometries were deter-
mined by nonlinear least-squares regression analysis of the
titration curves [41].
Inhibition constants
Apparent inhibition constants, K
i
,
app
, for the inhibition of
cathepsins L and B bythecystatinA mutants were obtained
from the equilibrium rates of hydrolysis ofa fluorogenic
substrate bythe enzyme at different inhibitor concentrations
Table 1. Primers for construction of expression vectors for cystatinA second-loop mutants. All sequences are given inthe 5¢fi3¢ direction. Codons
for Gly, replacing residues to be mutated, are underlined, and base changes introducing the mutations are in bold.
Primer Mutation Direction Sequence
Standard All Forward
GCTCAGGCGACCATGGGCCATCATCATC
Reverse CTTGCATGCCCTGCAGGTCG
Mutagenic L73G Forward GTATTCAAAAGTGGTCCCGGACAAAATGAG GACTTG
Reverse TCCGGGACCACTTTTGAATACTTTCAAGTGCATATATTTATT
P74G Forward CAAAAGTCTTGGCGGACAAAATGAGGACTTGGTAC
Reverse CATTTTGTCCGCCAAGACTTTTGAATACTT TCAAGTGC
Q76G Forward CTTCCCGGAGGAAATGAGGACTTGGTACTTACTG
Reverse CCTCATTTCCTCCGGGAAGACTTTTGAATA C
N77G Forward CGGACAAGGTGAGGACTTGGTACTTACTGGATAC
Reverse CAAGTCCTCACCTTGTCCGGGAAGACTTTTG
Ó FEBS 2002 Second protease-binding loopofcystatinA (Eur. J. Biochem. 269) 5651
[28,32]. Product formation was continuously monitored in a
conventional fluorimeter (F-4000; Hitachi, Tokyo, Japan)
as in previous work [28]. The substrates were carbobenz-
oxy-
L
-phenylalanyl-
L
-arginine 4-methylcoumaryl-7-amide
(Peptide Institute, Osaka, Japan) for cathepsin L and
carbobenzoxy-
L
-arginyl-
L
-arginine 4-methylcoumaryl-
7-amide (Peptide Institute) for cathepsin B at concentra-
tions of 5 and 10 l
M
, respectively. The fluorescence never
exceeded that corresponding to 5% substrate hydrolysis.
Inhibitor concentrations were at least 10-fold higher than
enzyme concentrations. The inhibition ofthe enzymes by
L73G-cystatin A was analysed at cystatin concentrations
ranging from (0.1–0.5) · K
i,app
to (6–10) · K
i,app
. Corres-
ponding measurements with P74G-cystatin A were per-
formed at inhibitor concentrations varying from
(0.5–2) · K
i,app
to (10–14) · K
i,app
, whereas the range was
from (3–4) · K
i,app
to (10–30) · K
i,app
for Q76G-cystatin A
and N77G-cystatin A. Values of K
i,app
were derived by
nonlinear regression analyses of plots ofthe ratio between
the inhibited and uninhibited rates of substrate hydrolysis
against inhibitor concentration [32]. True inhibition con-
stants, K
i
, were obtained after correction for substrate
competition [32,45,46].
Association kinetics
Association rate constants, k
ass,
for the inhibition of papain
and cathepsins L and B bythecystatinA mutants were
determined by continuously monitoring the loss of enzyme
activity inthe presence ofa fluorogenic substrate in either a
conventional fluorimeter (see above) or a stopped-flow
fluorimeter (SX-17
MV
; Applied Biophysics, Leatherhead,
UK) [28,38]. The substrate for papain was 10 l
M
carbo-
benzoxy-
L
-phenylalanyl-
L
-arginine 4-methylcoumaryl-7-
amide (Peptide Institute), and the substrates for cathepsins
L and B and their concentrations were the same as those
used to determine K
i
(see above). The fluorescence was
always lower than that given by 5% substrate hydrolysis.
The concentrations ofthe inhibitors were at least 10-fold
higher than those ofthe enzymes and were varied ina 10–
20-fold range. The highest inhibitor concentrations in
reactions with papain and cathepsin L were 10–20 n
M
,
whereas reactions with cathepsin B were analyzed at
inhibitor concentrations up to 30 l
M
for L73G-cystatin A
andupto0.3–0.5l
M
for the other mutants. Apparent
pseudo-first-order rate constants, k
obs,app
, were obtained by
nonlinear least-squares regression analysis ofthe progress
curves [28]. Apparent association rate constants, k
ass,app
,
were calculated from the slopes of plots of k
obs,app
vs.
inhibitor concentration and were corrected for substrate
competition to give the true association rate constants, k
ass
[28,45–47].
Dissociation kinetics
Dissociation rate constants, k
diss
, for thecomplexesof the
cystatin A mutants with papain were determined by dis-
placement experiments, essentially as detailed previously
[14,16]. Papain dissociating from thecomplexes was trapped
by a high excess of chicken cystatin (form 2), which binds
faster and more tightly to papain than cystatinA or the
cystatin A mutants do [14,18] (see also Results) and thereby
prevents reassociation ofthecystatinA variants with the
enzyme. The concentration ofthecystatinA mutant–
papain complexes was 2.5–5.0 l
M
, and the molar ratio of
the displacing chicken cystatin to thecomplexes varied
between 10-fold and 50-fold. The progress ofthe reaction
was monitored for 100–150 h by following the appearance
of the newly formed complex between papain and chicken
cystatin, analyzed by ion-exchange chromatography on
a MonoQ
TM
column (Amersham Biosciences, Uppsala,
Sweden). Form 2 of chicken cystatin was used because its
lower isoelectric point allows the complex with papain to be
well separated and thus easily quantified in this analysis.
k
diss
was calculated as described previously [14].
k
diss
for the complex between L73G-cystatin A and
cathepsin L was determined by trapping the enzyme
dissociated from the complex bya high concentration of
the substrate, carbobenzoxy-
L
-phenylalanyl-
L
-arginine
4-methylcoumaryl-7-amide, which binds tightly to cathep-
sin L witha K
m
of 1.8 l
M
[45]. In most experiments, the
complex was formed by incubating 0.04 n
M
cathepsin L
with 0.4 n
M
L73G-cystatin A for 90 min, which resulted in
an essentially complete reaction, with 80% ofthe enzyme
being saturated withthe inhibitor. The substrate was then
added to a final concentration of 100 l
M
with minimal
dilution ofthe complex. Alternatively, the complex was
formed by incubation of 1 n
M
cathepsin L with 10 n
M
L73G-cystatin A for 15 min, resulting in 99% of the
enzyme being bound inthe complex, and this mixture was
then diluted 1000-fold into 100 l
M
substrate. In both cases,
the dissociation ofthe complex was monitored in a
conventional fluorimeter by continuously recording the
fluorescence increase due to cleavage ofthe substrate by the
liberated cathepsin L. The fluorescence never exceeded that
corresponding to 5% substrate hydrolysis. k
diss
was deter-
mined by nonlinear least-squares regression analysis of the
progress curves [15].
Fluorescence emission spectroscopy
Fluorescence emission spectra of free papain and wild-type
or L73G-cystatin A, as well as ofcomplexesof papain with
either ofthe two cystatinA variants, were recorded in an
SLM 4800S spectrofluorimeter (SLM-Aminco, Urbana, IL,
USA) with an excitation wavelength of 280 nm, as
described previously [16,41]. Papain and cystatin concen-
trations were 1.0 and 1.2 l
M
, respectively, giving > 99%
saturation of enzyme with inhibitor in analyses of the
complexes. All spectra were corrected for inner-filter effects
and for the wavelength dependence ofthe instrumental
response [41] and were normalized to a fluorescence
intensity of 1.0 for free papain at the wavelength of the
emission maximum. Difference spectra between the com-
plexes and the free proteins were calculated as in [41].
Protein modeling
The structure of human cystatinAin complex with active
papain was modeled on to the X-ray structure of the
complex between human C3S-cystatin B and S-(carboxy-
methyl)papain (PDB entry 1STF) [13] withthe program
SWISS
-
PDB
Viewer (http://www.expasy.ch/spdbv/). The most
favorable rotamers ofthe side chains ofthe 46 residues
of cystatinA which differ from those ofcystatin B [1]
were initially selected bythe program [48], and the
5652 A. Pavlova et al.(Eur. J. Biochem. 269) Ó FEBS 2002
S-carboxymethyl group ofthe papain moiety of the
complex was removed inthe same manner. The model
was then corrected bythe program facility ÔQuick and Dirty
FixingÕ of all side chains inthe complex, followed by
ÔExhaustive Search FixingÕ ofthe side chains within the
Leu73–Asn77 segment inthesecondbindingloop of
cystatin A. After each of these steps, the conformation of
the secondbindingloopinthe complex was refined by
energy minimization ofthe Leu73–Asn77 segment and all
neighboring residues within 6 A
˚
. The possibility of other
residues replacing Gly75 inthe final model was evaluated by
ÔQuick and Dirty FixingÕ of all side chains inthe complex
after each replacement.
Miscellaneous procedures
For N-terminal sequencing and determination of molecular
masses, the mutants were first desalted into 0.1% (v/v)
trifluoroacetic acidby gel chromatographyon Fast-Desalting
PC 3.2/10 columns (Amersham Biosciences). N-Terminal
sequences were analyzed by Edman degradation in an
Applied Biosystems 477A Protein Sequencer. Molecular
masses were measured by MALDI MS ina Kratos Kompact
MALDI 4 instrument (Kratos, Manchester, UK) as in
[18]. SDS/PAGE under reducing and nonreducing condi-
tions was performed withthe Tricine buffer system [49].
Experimental conditions
All equilibrium and kinetic experiments were performed at
25.0 ± 0.2 °C. Theproteases were first activated by 1 m
M
dithiothreitol inthe reaction buffer for 10 min at 25 °C. The
inhibition of papain was studied in 50 m
M
Tris/HCl,
pH 7.4, containing 100 m
M
NaCl, 0.1 m
M
EDTA and,
except inthe displacement experiments, 1 m
M
dithiothreitol
and 0.01% (w/v) BrijÒ 35. The interaction with cathepsin L
wasanalyzedin100 m
M
sodium acetate, pH 5.5, containing
100 m
M
NaCl, 1 m
M
EDTA, 1 m
M
dithiothreitol, and
0.01% (w/v) BrijÒ 35, whereas the buffer for cathepsin B
was 50 m
M
Mes/NaOH, pH 6.0, containing 100 m
M
NaCl,
0.1 m
M
EDTA, 1 m
M
dithiothreitol, and 0.1% (w/v)
poly(ethylene glycol) 6000.
RESULTS
Preparation, homogeneity and activity ofcystatin A
mutants
Four variants ofcystatin A, each witha single amino-acid
residue, Leu73, Pro74, Gln76 or Asn77, substituted by Gly
were produced by recombinant DNA techniques. All these
mutations are inthe most exposed part ofthe second
protease-binding loopofthe inhibitor (Fig. 1A). Residue 75
was not substituted, as it is Gly inthe wild-type sequence.
The expression vectors were constructed by PCR-based site-
directed mutagenesis and contained the expected mutant
sequences inthe case ofthe L73G, P74G and N77G
mutants. However, all vectors for the Q76G mutant purified
from 18 individual clones had, in addition to the desired
mutation, a T fi C substitution inthe codon for Thr83.
This substitution was inthe region specified bythe forward
mutagenic primer for this mutant and was probably due to
an erroneously synthesized primer. As this additional
mutation is silent, one ofthe isolated vectors was neverthe-
less used for expression of Q76G-cystatin A. The mutants
were expressed witha removable His-tag and witha signal
peptide directing the proteins to the periplasmic space of
E. coli, facilitating purification.
All purified mutants were > 99.5% homogeneous on
SDS/PAGE. N-Terminal sequencing ofthe first five
residues confirmed that the His-tag was cleaved off properly
by enterokinase for all mutants. The molecular masses,
determined by MS, corresponded within 4.5 Da to those
calculated from the expected amino-acid sequences, con-
firming the correct length ofthe mutants, as well as the
presence ofthe desired mutations. All mutants bound active
papain and S-(methylthio)papain with stoichiometries
between 0.95 and 1.0, i.e. they were essentially fully active
in inhibition ofcysteine proteases.
Binding affinity
All four cystatinA mutants bound so tightly to papain that
the affinity ofthebinding could not be determined by
equilibrium methods, because ofthe instability of the
enzyme at the low concentrations and the long reaction
times that would have been necessary. Therefore, K
d
for the
interaction with papain was calculated as k
diss
/k
ass
from
independently measured rate constants (see below and
Table 2), as was K
d
for wild-type cystatinAbinding to this
enzyme in previous work [18]. Only the L73G mutation
caused a pronounced, 300-fold, decrease inthe affinity for
papain, compared with that ofthe wild-type inhibitor
(Table 2). In contrast, the P74G, Q76G, and N77G muta-
tions resulted in minimal, less than twofold, changes in
affinity.
The high affinity of most mutants for cathepsin L also
precluded an accurate determination of K
i
from equilibrium
measurements. Such experiments gave only upper limits of
K
i
for the interaction of P74G, Q76G, and N77G cystatin A
with this protease (Table 2), similar to previous analyses of
K
i
for the wild-type inhibitor [35]. Moreover, as k
diss
for
these tight interactions could not be determined (see below),
K
d
could not be calculated from the rate constants. No
meaningful comparisons ofthe affinities ofthe three
mutants for cathepsin L with that of wild-type cystatin A
were therefore possible. However, a reliable K
i
for the
inhibition of cathepsin L by L73G-cystatin A was obtained
by equilibrium measurements and was > 10-fold higher
than that for wild-type cystatin A. The measured K
i
for this
mutant agreed well with K
d
calculated from k
ass
and k
diss
(see below and Table 2).
K
i
for the inhibition of cathepsin B by all cystatin A
forms was sufficiently high to be well determined by
equilibrium analyses. The L73G mutation caused a sub-
stantial, 4000-fold, increase in K
i
which was confirmed by
calculations of K
d
from k
ass
and k
diss
(Table 2). A smaller,
10-fold, increase in K
i
for cathepsin B was also observed
for the P74G mutant, whereas the affinities of both Q76G
and N77G cystatinA for the enzyme differed minimally,
about twofold, from that of wild-type cystatinA (Table 2).
Association rate constants
The kinetics of association ofthecystatinA mutants
with papain, cathepsin L and cathepsin B were analyzed
Ó FEBS 2002 Second protease-binding loopofcystatinA (Eur. J. Biochem. 269) 5653
by continuously monitoring the decrease in enzyme acti-
vity against a fluorogenic substrate. Most reactions were
studied by conventional fluorimetry, whereas the rapid
association of L73G-cystatin Awith cathepsin B required
the use of stopped-flow measurements. All progress
curves were well fitted to a single-exponential function.
Plots ofthe dependence of k
obs,app
, derived from these
fits, on inhibitor concentration were linear inthe concen-
tration range covered for all mutants. Values of k
ass
were determined from the slopes of these plots. All four
amino-acid substitutions inthesecondbindingloop of
cystatin A had a marginal effect on k
ass
for the binding
to papain, cathepsin L or cathepsin B (Table 2).
Dissociation rate constants
The low dissociation rate constants ofthe complexes
between thecystatinA mutants and papain were measured
by displacement ofthe mutants from thecomplexeswith an
excess ofa tighter-binding inhibitor, chicken cystatin, in
experiments monitored by ion-exchange chromatography.
Only the L73G mutation altered k
diss
to any appreciable
extent, increasing it by 170-fold over that for wild-type
cystatin A. k
diss
for all other mutants was essentially
unaffected, with at most a twofold increase being observed
for P74G-cystatin A.
k
diss
of the complex between L73G-cystatin A and
cathepsin L was measured by displacement experiments, in
which the enzyme dissociating from the complex was cap-
tured by an excess ofa tight-binding fluorogenic substrate.
The values of k
diss
obtained by two modifications of this
procedure agreed well with each other and with that
calculated from K
i
and k
ass
(Table 2). The L73G mutation
resulted ina greater than sevenfold increase in k
diss
,
compared withthe value for wild-type cystatin A. This
method could not be used to determine k
diss
for the
complexes ofthe P74G, Q76G, and N77G mutants with
cathepsin L, because ofthe high stabilities of these complexes
and, consequently, very long dissociation times. Moreover,
the limited amounts of cathepsin L available precluded
Table 2. Equilibrium and rate constants at 25 °C for thebindingofcystatinA variants with substitutions inthesecondbindingloop to papain,
cathepsin L and cathepsin B. Methods and experimental conditions are described in Materials and Methods. Values determined in this work are
given as means ± SEM withthe number of experiments in parentheses. Values for wild-type cystatin A, reported previously and shown for
comparison, as well as calculated values are given without errors. Numbers in square brackets indicate the ratio ofthe corresponding constant to
that for wild-type cystatin A.
Enzyme
Cystatin A
form
K
d
(
M
)
k
ass
(
M
)1
Æs
)1
)
k
diss
(s
)1
)
Papain Wild-type 1.8 · 10
)13 a
3.1 · 10
6a
5.5 · 10
)7a
[1] [1] [1]
L73G 5.8 · 10
)11 b
(1.58 ± 0.02) · 10
6
(9) (9.1 ± 0.9) · 10
)5
(3)
[320] [0.5] [170]
P74G 2.8 · 10
)13 b
(3.64 ± 0.06) · 10
6
(9) (10.2 ± 0.7) · 10
)7
(3)
[1.6] [1.2] [1.9]
Q76G 1.8 · 10
)13 b
(3.07 ± 0.02) · 10
6
(8) (5.6 ± 0.5) · 10
)7
(3)
[1] [1] [1]
N77G 0.95 · 10
)13 b
(3.58 ± 0.07) · 10
6
(9) (3.4 ± 0.3) · 10
)7
(3)
[0.5] [1.2] [0.6]
Cathepsin L Wild-type £ 1 · 10
)11 a
5.2 · 10
6a
£ 5 · 10
)5a
[1] [1] [1]
L73G (1.09 ± 0.08) · 10
)10
(10) (2.98 ± 0.04) · 10
6
(10) (3.4 ± 0.4) · 10
)4
(3)
[‡ 11] [0.6] [‡ 7]
1.1 · 10
)10 b
3.2 · 10
)4c
P74G £ 2.4 · 10
)11
(7) (4.6 ± 0.2) · 10
6
(10)
[0.9]
£ 1.1 · 10
)4c
Q76G £ 1.1 · 10
)11
(8) (6.3 ± 0.2) · 10
6
(9)
[1.2]
£ 6.9 · 10
)5c
N77G £ 1.1 · 10
)11
(8) (6.3 ± 0.2) · 10
6
(14)
[1.2]
£ 6.9 · 10
)5c
Cathepsin B Wild-type 9.1 · 10
)10 a
3.9 · 10
4a
3.5 · 10
)5a
[1] [1] [1]
L73G (3.6 ± 0.2) · 10
)6
(11) (8.5 ± 0.3) · 10
4
(8) 0.28 ± 0.05 (8)
[4000] [2.2] [8000]
3.3 · 10
)6b
0.31
c
P74G (9.7 ± 0.6) · 10
)9
(10) (5.5 ± 0.2) · 10
4
(11) 5.3 · 10
)4c
[11] [1.4] [15]
Q76G (1.4 ± 0.1) · 10
)9
(8) (3.95 ± 0.07) · 10
4
(8) 5.5 · 10
)5c
[1.5] [1] [1.6]
N77G (2.4 ± 0.2) · 10
)9
(9) (2.26 ± 0.08) · 10
4
(11) 5.4 · 10
)5c
[2.6] [0.6] [1.5]
a
From previous work [18,35].
b
Calculated from k
ass
and k
diss
.
c
Calculated from K
i
and k
ass
.
5654 A. Pavlova et al.(Eur. J. Biochem. 269) Ó FEBS 2002
determination of k
diss
by the method used for papain, in
which the displacement was monitored by chromatography.
Therefore, only upper limits of k
diss
for thebindingof these
mutants to cathepsin L could be estimated, as for wild-type
cystatin Ain previous work [35] (Table 2).
Values of k
diss
for thecomplexesofthe four cystatin A
mutants with cathepsin B were calculated from K
i
and k
ass
determined in separate experiments (Table 2). In addition,
k
diss
for the L73G-cystatin A–cathepsin B complex was
obtained from the analyses ofthe association kinetics (see
above) as the intercept on the ordinate ofthe plot of k
obs,app
vs. inhibitor concentration and was ina good agreement
with the calculated k
diss
(Table 2). The L73G mutation
markedly affected the rate of dissociation ofthe complex
with cathepsin B, increasing k
diss
by 8000-fold. The P74G
mutation resulted ina smaller, 15-fold, increase in k
diss
,
whereas the other mutations altered k
diss
minimally.
Fluorescence emission difference spectra
The fluorescence difference spectra between complexes of
wild-type or L73G-cystatin Awith papain and the free
proteins had minima at different wavelengths, 360 and
368 nm, respectively (Fig. 2). Moreover, the spectrum for
the L73G mutant had an appreciably lower amplitude than
that for wild-type cystatin A, reflecting a smaller fluores-
cence change on interaction ofthe mutant than ofthe wild-
type inhibitor with papain. These fluorescence changes must
reflect different changes inthe environment of one or more
Trp side chains in papain on formation ofthe two enzyme–
inhibitor complexes, as cystatinA does not contain Trp [1].
DISCUSSION
The X-ray structure ofthe complex between human C3S-
cystatin B and S-(carboxymethyl)papain reveals a number
of predominantly hydrophobic but also solvent-mediated
interactions between thesecondbindingloopof the
inhibitor and papain [13]. In particular, Leu73 and His75
in this loop are seen to make four and seven intermolecular
contacts withthe enzyme, respectively, that are < 4 A
˚
in
length. In agreement with this structural evidence, site-
directed mutagenesis has shown that the two residues
contribute substantial free energy to the interaction of
cystatin B withcysteineproteases [37]. The sequence of the
second bindingloopofthe related family 1 cystatin,
cystatin A, differs appreciably from that ofcystatin B.
Most notably, cystatinA lacks the essential His75 and
instead has a Gly in this position [1]. This substitution would
be expected to lead to loss ofa number of interactions with
the enzyme and therefore to considerably decrease the
contribution ofthesecondbindingloopofcystatinA to the
inhibition oftarget proteases. However, the flexibility of
the secondbindingloopofcystatinA demonstrated by
NMR [20] may allow other amino acids oftheloop to make
additional favorable contacts withthe protease, thereby
compensating for the absence of this residue. Alternatively,
this flexibility may instead destabilize the interactions of the
loop withthetarget protease, resulting ina lower binding
energy. To clarify the functional roleofthesecond binding
loop ofcystatin A, we have studied the contribution by the
residues within the most exposed segment of this loop to the
inhibition ofcysteine proteases. The L73G, P74G, Q76G,
and N77G mutants ofcystatinA were constructed by site-
directed mutagenesis, and their inhibition of papain,
cathepsin L and cathepsin B was characterized.
Our results show that thesecondbindingloop of
cystatin Ais essential for the formation of tight complexes
between the inhibitor and thecysteineproteases studied.
However, in contrast withcystatin B, this roleis exerted
predominantly by only one residue, Leu73, which is highly
conserved in family I cystatins. The major roleofLeu73 in
the interactions isinstabilizingthecomplexes once they are
formed. This conclusion is indicated bythe L73G mutation
appreciably decreasing the affinity ofcystatinA for the
proteases by increasing the rate constants for dissociation
of thecomplexes but negligibly affecting the association
rate constants. This contribution ofLeu73 to the inhibitory
ability ofcystatinA varies for different target proteases,
being most pronounced for the inhibition of cathepsin B.
The Leu73 side chain thus contributes about )15 and
)21 kJÆmol
)1
to the unitary free energy change [50,51]
accompanying the formation ofthe complex ofcystatin A
with papain and cathepsin B, respectively. These changes
correspond to 18 and 34%, respectively, ofthe total
unitary free energy ofbindingofcystatinA to the two
enzymes [18]. The contribution ofLeu73ofcystatinA to
binding of papain, which has an open active-site cleft, is
comparable to that ofLeu73inthesecondbindingloop of
cystatin B and to that ofthe essential Trp106 residue in this
loop ofthe family 2 cystatin, cystatin C [37,52]. However,
the contribution ofLeu73ofcystatinA to binding of
cathepsin B, in which the occluding loop partially blocks the
active site, is substantially higher than that ofthe corres-
ponding residue ofcystatin C [52].
The results further show that one additional residue in
the secondbindingloopofcystatin A, Pro74, aids in
stabilizing the complex ofthe inhibitor with cathepsin B by
decreasing the dissociation rate constant. However, this
Fig. 2. Fluorescence emission difference spectra between complexes of
human wild-type cystatinA or the L73G cystatinA variant with papain
andthefreeproteins.Solid line, Wild-type cystatin A; dotted line,
L73G-cystatin A. Fluorescence emission spectra were measured as
describedinMaterialsandmethodswithpapainandcystatincon-
centrations of 1.0 and 1.2 l
M
, respectively. The difference spectra were
calculated from separately measured and corrected emission spectra
that were normalized to a fluorescence intensity of 1.0 for 1 l
M
papain
at the wavelength ofthe emission maximum [41].
Ó FEBS 2002 Second protease-binding loopofcystatinA (Eur. J. Biochem. 269) 5655
residue negligibly participates inthe inhibition of papain
and most likely also of cathepsin L. The side chains of
Leu73 and Pro74 jointly contribute 45% ofthe total
unitary free energy ofbindingofcystatinA to cathepsin B,
demonstrating a major roleofthesecondbindingloop of
cystatin Ainthe inhibition of this enzyme. Pro74 may be
directly involved inthe interaction with cathepsin B by
providing hydrophobic interactions withthe protease.
Alternatively, theroleof Pro74 might be to maintain an
appropriate orientation ofLeu73 for its specific interaction
with cathepsin B. In contrast withLeu73 and Pro74, the
two other residues ofthesecondbindingloopofcystatin A
studied, Gln76 and Asn77, are of minimal importance for
the affinity ofthe inhibitor for thecysteineproteases and
therefore presumably do not interact directly with the
enzymes. The remaining residue ofthe loop, Gly75, may
conceivably provide backbone interactions witha target
protease, but such a contribution cannot be investigated by
the approach taken in this work.
The conclusions drawn above from the results of this
work are in general agreement with modeling of the
cystatin A–papain complex. Although no X-ray structure of
cystatin Ais available, the NMR structure ofthe inhibitor is
similar to the X-ray structure of human C3S-cystatin B in
complex with S-(carboxymethyl)papain [13,20,53]. More-
over, human cystatins A and B are homologous, having
identical amino acids in 52 out of 98 positions [1].
Cystatin B inthe complex with papain can therefore be
used as an appropriate template for modeling of the
corresponding complex between cystatinA and this prote-
ase with reasonable accuracy [48,54]. The model generated
for the complex indicates that only two residues within the
second bindingloopofcystatin A, Leu73 and Pro74, are
involved in interactions with papain (Fig. 1B). Leu73 makes
six hydrophobic interactions of 3.4–4.0 A
˚
with Trp177 of
papain inthe model, in agreement withthe demonstration
that Leu73is essential for strong inhibition of cysteine
proteases bycystatin A. The involvement of Trp177 of
papain inthe interaction withLeu73is supported by the
changes caused bythe L73G mutation ofthe fluorescence
difference spectrum characterizing thecystatin A–papain
interaction. These changes indicate that one or more
tryptophans of papain, probably primarily Trp177 on the
surface ofthe active-site cleft, are exposed to a less
hydrophobic environment inthe complex with L73G-
cystatin A [55]. Inthe model, the side chain of Pro74 of
cystatin A also makes two hydrophobic contacts of 4A
˚
with Gln142 and Leu143 of papain (Fig. 1B). This obser-
vation isin apparent contrast withthe demonstration that
Pro74 is unimportant for papain binding and participates
only inthe inhibition of cathepsin B. This discrepancy with
the experimental data thus indicates that the model is
somewhat uncertain with regard to the putative interactions
involving Pro74. However, in agreement withthe experi-
mental results, the model accurately predicts that neither
Gln76 nor Asn77 ofthesecondbindingloopofcystatin A
interact with papain inthe complex. Moreover, although
the roleof Gly75 was not investigated experimentally, the
model suggests that Gly is not the only residue in this
position compatible with high-affinity interaction with
papain. The phi and psi angles of Gly75 deduced from the
model are thus within the Ramachandran plot region
sterically allowed for other types of residues. Most residues
other than Gly could also be modeled into this position
without observably interfering sterically withthe interac-
tion.
In conclusion, this study shows the importance of the
second bindingloopofcystatinA for thebinding of
cysteine proteases, in particular cathepsin B. Theroleof this
loop is comparable to that ofthe corresponding loops of
cystatin B and family 2 cystatins, to stabilize the cystatin–
protease complex by decreasing the dissociation rate. How-
ever, in contrast withthe latter inhibitors, this roleis exerted
almost exclusively by one residue ofthe loop, Leu73,
although Pro74 is also of some importance for cathepsin B
binding.
ACKNOWLEDGEMENTS
We are grateful to Dr A
˚
ke Engstro
¨
m (Department of Medical
Biochemistry and Microbiology, Uppsala University) for molecular
mass determinations and amino-acid sequencing. This project was
supported bythe Swedish Medical Research Council (Project No. 4212).
REFERENCES
1. Barrett, A.J., Rawlings, N.D., Davies, M.E., Machleidt, W.,
Salvesen, G. & Turk, V. (1986) Cysteine proteinase inhibitors of
the cystatin superfamily. In Proteinase Inhibitors (Barrett, A.J. &
Salvesen, G., eds), pp. 515–569. Elsevier, Amsterdam.
2. Turk, V. & Bode, W. (1991) The cystatins: protein inhibitors of
cysteine proteinases. FEBS Lett. 285, 213–219.
3. Abrahamson, M. (1994) Cystatins. Methods Enzymol. 244,685–
700.
4. Turk,B.,Turk,V.&Turk,D.(1997)Structuralandfunctional
aspects of papain-like cysteine proteinases and their protein
inhibitors. Biol. Chem. 378, 141–150.
5. Henskens, Y.M.C., Veerman, E.C.I. & Nieuw Amerongen, A.V.
(1996) Cystatins in health and disease. Biol. Chem. Hoppe-Seyler
377, 71–86.
6. Blankenvoorde, M.F., Van’t Hof, W., Walgreen-Weterings, E.,
van Steenbergen, T.J., Brand, H.S., Veerman, E.C. & Nieuw
Amerongen, A.V. (1998) Cystatin and cystatin-derived peptides
have antibacterial activity against the pathogen Porphyromonas
gingivalis. Biol. Chem. 379, 1371–1375.
7. Collins, A.R. & Grubb, A. (1998) Cystatin D, a natural salivary
cysteine proteaseinhibitor, inhibits coronavirus replication at its
physiologic concentration. Oral Microbiol. Immunol. 13, 59–61.
8. Kos, J. & Lah, T.T. (1998) Cysteine proteinases and their
endogenous inhibitors: target proteins for prognosis, diagnosis
and therapy in cancer. Oncol. Rep. 5, 1349–1361.
9. Das, L., Datta, N., Bandyopadhyay, S. & Das, P.K. (2001) Suc-
cessful therapy of lethal murine visceral leishmaniasis with cystatin
involves up-regulation of nitric oxide and a favorable T cell
response. J. Immunol. 166, 4020–4028.
10. Ruzindana-Umunyana, A. & Weber, J.M. (2001) Interactions of
human lacrimal and salivary cystatins with adenovirus endo-
peptidase. Antiviral Res. 51, 203–214.
11. Turk,V.,Turk,B.&Turk,D.(2001)Lysosomalcysteinepro-
teases: facts and opportunities. EMBO J. 20, 4629–4633.
12. Bode, W., Engh, R., Musil, D., Thiele, U., Huber, R., Karshikov,
A.,Brzin,J.,Kos,J.&Turk,V.(1988)The2.0A
˚
X-ray crystal
structure of chicken egg white cystatin and its possible mode of
interaction withcysteine proteinases. EMBO J. 7, 2593–2599.
13.Stubbs,M.T.,Laber,B.,Bode,W.,Huber,R.,Jerala,R.,
Lenarcic, B. & Turk, V. (1990) The refined 2.4 A
˚
X-ray crystal
structure of recombinant human stefin B in complex with the
cysteine proteinase papain: a novel type of proteinase inhibitor
interaction. EMBO J. 9, 1939–1947.
5656 A. Pavlova et al.(Eur. J. Biochem. 269) Ó FEBS 2002
14. Bjo
¨
rk, I., Alriksson, E. & Ylinenja
¨
rvi, K. (1989) Kinetics of
binding of chicken cystatin to papain. Biochemistry 28, 1568–1573.
15. Bjo
¨
rk, I. & Ylinenja
¨
rvi, K. (1990) Interaction between chicken
cystatin and thecysteine proteinases actinidin, chymopapain A,
and ficin. Biochemistry 29, 1770–1776.
16. Lindahl, P., Abrahamson, M. & Bjo
¨
rk, I. (1992) Interaction of
recombinant human cystatin C withthecysteine proteinases
papain and actinidin. Biochem. J. 281, 49–55.
17. Turk, B., Colic, A., Stoka, V. & Turk, V. (1994) Kinetics of
inhibition of bovine cathepsin S by bovine stefin B. FEBS Lett.
339, 155–159.
18. Pol,E.,Olsson,S.L.,Estrada,S.,Prasthofer,T.W.&Bjo
¨
rk, I.
(1995) Characterization by spectroscopic, kinetic and equilibrium
methods ofthe interaction between recombinant human cystatin
A (stefin A) and cysteine proteinases. Biochem. J. 311, 275–282.
19. Dieckmann,T.,Mitschang,L.,Hofmann,M.,Kos,J.,Turk,V.,
Auerswald, E.A., Jaenicke, R. & Oschkinat, H. (1993) The
structures of native phosphorylated chicken cystatin and of a
recombinant unphosphorylated variant in solution. J. Mol. Biol.
234, 1048–1059.
20. Martin, J.R., Craven, C.J., Jerala, R., Kroon-Zitko, L., Zerovnik,
E., Turk, V. & Waltho, J.P. (1995) The three-dimensional solution
structure of human stefin A. J. Mol. Biol. 246, 331–343.
21. Ekiel, I., Abrahamson, M., Fulton, D.B., Lindahl, P., Storer,
A.C., Levadoux, W., Lafrance, M., Labelle, S., Pomerleau, Y.,
Groleau, D., LeSauteur, L. & Gehring, K. (1997) NMR structural
studies of human cystatin C dimers and monomers. J. Mol. Biol.
271, 266–277.
22. Rawlings, N.D. & Barrett, A.J. (1994) Families ofcysteine pep-
tidases. Methods Enzymol. 244, 461–486.
23. Turk, D., Guncar, G., Podobnik, M. & Turk, B. (1998) Revised
definition of substrate binding sites of papain-like cysteine pro-
teases. Biol. Chem. 379, 137–147.
24. Turk, B., Turk, D. & Turk, V. (2000) Lysosomal cysteine proteases:
more than scavengers. Biochim. Biophys. Acta 1477, 98–111.
25. Musil, D., Zucic, D., Turk, D., Engh, R.A., Mayr, I., Huber, R.,
Popovic,T.,Turk,V.,Towatari,T.,Katunuma,N.&Bode,W.
(1991) The refined 2.15 A
˚
X-ray crystal structure of human liver
cathepsin B: the structural basis for its specificity. EMBO J. 10,
2321–2330.
26. Nycander,M.,Estrada,S.,Mort,J.S.,Abrahamson,M.&Bjo
¨
rk,
I. (1998) Two-step mechanism of inhibition of cathepsin B by
cystatin C due to displacement ofthe proteinase occluding loop.
FEBS Lett. 422, 61–64.
27. Pavlova,A.,Krupa,J.C.,Mort,J.S.,Abrahamson,M.&Bjo
¨
rk, I.
(2000) Cystatin inhibition of cathepsin B requires dislocation of
the proteinase occluding loop. Demonstration by release of loop
anchoring through mutation of His110. FEBS Lett. 487, 156–160.
28. Bjo
¨
rk,I.,Pol,E.,Raub-Segall,E.,Abrahamson,M.,Rowan,
A.D. & Mort, J.S. (1994) Differential changes inthe association
and dissociation rate constants for bindingof cystatins to target
proteinases occurring on N-terminal truncation ofthe inhibitors
indicate that the interaction mechanism varies with different
enzymes. Biochem. J. 299, 219–225.
29. Machleidt, W., Thiele, U., Laber, B., Assfalg-Machleidt, I., Esterl,
A., Wiegand, G., Kos, J., Turk, V. & Bode, W. (1989) Mechanism
of inhibition of papain by chicken egg white cystatin. Inhibition
constants of N-terminally truncated forms and cyanogen bromide
fragments ofthe inhibitor. FEBS Lett. 243, 234–238.
30. Machleidt, W., Thiele, U., Assfalg-Machleidt, I., Forger, D. &
Auerswald, E.A. (1991) Molecular mechanism of inhibition of
cysteine proteinases by their protein inhibitors: kinetic studies with
natural and recombinant variants of cystatins and stefins. Biomed.
Biochim. Acta 50, 613–620.
31. Abrahamson, M., Mason, R.W., Hansson, H., Buttle, D.J.,
Grubb, A. & Ohlsson, K. (1991) Human cystatin C. Role of
the N-terminal segment inthe inhibition of human cysteine
proteinases and in its inactivation by leucocyte elastase. Biochem.
J. 273, 621–626.
32. Lindahl, P., Nycander, M., Ylinenja
¨
rvi,K.,Pol,E.&Bjo
¨
rk, I.
(1992) Characterization by rapid-kinetic and equilibrium methods
of the interaction between N-terminally truncated forms of
chicken cystatin and thecysteine proteinases papain and actinidin.
Biochem. J. 286, 165–171.
33. Hall, A., Ha
˚
kansson, K., Mason, R.W., Grubb, A. & Abra-
hamson, M. (1995) Structural basis for the biological specificity of
cystatin C. Identification of leucine 9 inthe N-terminal binding
region as a selectivity-conferring residue inthe inhibition of
mammalian cysteine peptidases. J. Biol. Chem. 270, 5115–5121.
34. Auerswald, E.A., Na
¨
gler, D.K., Assfalg-Machleidt, I., Stubbs,
M.T., Machleidt, W. & Fritz, H. (1995) Hairpin loop mutations of
chicken cystatin have different effects on the inhibition of cathe-
psin B, cathepsin L and papain. FEBS Lett. 361, 179–184.
35. Estrada, S., Pavlova, A. & Bjo
¨
rk, I. (1999) The contribution of
N-terminal region residues ofcystatinA(stefin A) to the affinity
and kinetics of inhibition of papain, cathepsin B, and cathepsin
L. Biochemistry 38, 7339–7345.
36. Pol, E. & Bjo
¨
rk, I. (2001) Roleofthe single cysteine residue, Cys 3,
of human and bovine cystatin B (stefin B) inthe inhibition of
cysteine proteinases. Protein Sci. 10, 1729–1738.
37. Pol, E. & Bjo
¨
rk, I. (1999) Importance ofthesecondbinding loop
and the C-terminal end ofcystatin B (stefin B) for inhibition of
cysteine proteinases. Biochemistry 38, 10519–10526.
38. Estrada, S., Nycander, M., Hill, N.J., Craven, C.J., Waltho, J.P. &
Bjo
¨
rk, I. (1998) Theroleof Gly-4 of human cystatinA(stefin A) in
the bindingoftarget proteinases. Characterization by kinetic and
equilibrium methods ofthe interactions ofcystatinA Gly-4
mutants with papain, cathepsin B, and cathepsin L. Biochemistry
37, 7551–7560.
39. Higuchi, R., Krummel, B. & Saiki, R.K. (1988) A general method
of in vitro preparation and specific mutagenesis of DNA frag-
ments: study of protein and DNA interactions. Nucleic Acids Res.
16, 7351–7367.
40. Cohen, S.N., Chang, A.C.Y. & Hsu, L. (1972) Nonchromosomal
antibiotic resistance in bacteria: genetic transformation of
Escherichia coli by R factor DNA. Proc. Natl. Acad. Sci. USA 69,
2110–2114.
41. Lindahl, P., Alriksson, E., Jo
¨
rnvall, H. & Bjo
¨
rk, I. (1988) Inter-
action ofthecysteine proteinase inhibitor chicken cystatin with
papain. Biochemistry 27, 5074–5082.
42. Laber, B., Krieglstein, K., Henschen, A., Kos, J., Turk, V., Huber,
R. & Bode, W. (1989) Thecysteine proteinase inhibitor chicken
cystatin isa phosphoprotein. FEBS Lett. 248, 162–168.
43. Ellman, G.L. (1959) Tissue sulfhydryl groups. Arch. Biochem.
Biophys. 82, 70–77.
44. Barrett, A.J. & Kirschke, H. (1981) Cathepsin B, cathepsin H, and
cathepsin L. Methods Enzymol. 80, 535–561.
45. Mason, R.W. (1986) Species variants of cathepsin L and their
immunological identification. Biochem. J. 240, 285–288.
46. Dalet-Fumeron, V., Guinec, N. & Pagano, M. (1991) High-
performance liquid chromatographic method for the simulta-
neous purification of cathepsins B, H and L from human liver.
J. Chromatogr. 568, 55–68.
47. Hall, A., Abrahamson, M., Grubb, A., Trojnar, J., Kania, P.,
Kasprzykowska, R. & Kasprzykowski, F. (1992) Cystatin C based
peptidyl diazomethanes as cysteine proteinase inhibitors: influence
of the peptidyl chain length. J. Enzyme Inhibition 6, 113–123.
48. Guex, N. & Peitsch, M.C. (1997) Swiss-Model and Swiss-Pdb
Viewer: an environment for comparative protein modeling.
Electrophoresis 18, 2714–2723.
49. Scha
¨
gger, H. & von Jagow, G. (1987) Tricine-sodium dodecyl
sulfate-polyacrylamide gel electrophoresis for the separation
of proteins inthe range from 1 to 100 kDa. Anal. Biochem. 166,
368–379.
Ó FEBS 2002 Second protease-binding loopofcystatinA (Eur. J. Biochem. 269) 5657
50. Gurney, R.W. (1953) Ionic Processes in Solution, pp. 90–105.
McGraw-Hill, New York.
51. Karush, F. (1962) Immunologic specificity and molecular struc-
ture. Adv. Immunol. 2, 1–40.
52. Bjo
¨
rk, I., Brieditis, I., Raub-Segall, E., Pol, E., Ha
˚
kansson, K. &
Abrahamson, M. (1996) The importance ofthesecond hairpin
loop ofcystatin C for proteinase binding. Characterization of the
interaction of Trp-106 variants ofthe inhibitor with cysteine
proteinases. Biochemistry 35, 10720–10726.
53. Craven, C.J., Baxter, N.J., Murray, E.H., Hill, N.J., Martin, J.R.,
Ylinenja
¨
rvi, K., Bjo
¨
rk, I., Waltho, J.P. & Murray, I.A. (2000)
Wild-type and Met-65 fi Leu variants of human cystatinA are
functionally and structurally identical. Biochemistry 39, 15783–
15790.
54. Guex, N., Diemand, A. & Peitsch, M.C. (1999) Protein modelling
for all. Trends Biochem. Sci. 24, 364–367.
55. Lakowicz, J.R. (1983) Principles of Fluorescence Spectroscopy,pp.
187–214. Plenum Press, New York.
5658 A. Pavlova et al.(Eur. J. Biochem. 269) Ó FEBS 2002
. The role of the second binding loop of the cysteine protease inhibitor,
cystatin A (stefin A) , in stabilizing complexes with target proteases
is exerted. total
unitary free energy of binding of cystatin A to cathepsin B,
demonstrating a major role of the second binding loop of
cystatin A in the inhibition of this