Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans containing more than one cytochrome.

Abstract

According to the model proposed in previous papers [Pettigrew, G. W., Prazeres, S., Costa, C., Palma, N., Krippahl, L., and Moura, J. J. (1999) The structure of an electron-transfer complex containing a cytochrome c and a peroxidase, J. Biol. Chem. 274, 11383-11389; Pettigrew, G. W., Goodhew, C. F., Cooper, A., Nutley, M., Jumel, K., and Harding, S. E. (2003) Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans, Biochemistry 42, 2046-2055], cytochrome c peroxidase of Paracoccus denitrificans can accommodate horse cytochrome c and Paracoccus cytochrome c(550) at different sites on its molecular surface. Here we use (1)H NMR spectroscopy, analytical ultracentrifugation, molecular docking simulation, and microcalorimetry to investigate whether these small cytochromes can be accommodated simultaneously in the formation of a ternary complex. The pattern of perturbation of heme methyl and methionine methyl resonances in binary and ternary solutions shows that a ternary complex can be formed, and this is confirmed by the increase in the sedimentation coefficient upon addition of horse cytochrome c to a solution in which cytochrome c(550) fully occupies its binding site on cytochrome c peroxidase. Docking experiments in which favored binary solutions of cytochrome c(550) bound to cytochrome c peroxidase act as targets for horse cytochrome c and the reciprocal experiments in which favored binary solutions of horse cytochrome c bound to cytochrome c peroxidase act as targets for cytochrome c(550) show that the enzyme can accommodate both cytochromes at the same time on adjacent sites. Microcalorimetric titrations are difficult to interpret but are consistent with a weakened binding of horse cytochrome c to a binary complex of cytochrome c peroxidase and cytochrome c(550) and binding of cytochrome c(550) to the cytochrome c peroxidase that is affected little by the presence of horse cytochrome c in the other site. The presence of a substantial capture surface for small cytochromes on the cytochrome c peroxidase has implications for rate enhancement mechanisms which ensure that the two electrons required for re-reduction of the enzyme after reaction with hydrogen peroxide are delivered efficiently.

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Electron Transfer Complexes of Cytochrome c Peroxidase from Paracoccus
denitrificans Containing More than One Cytochrome†
Graham W. Pettigrew,*,‡Sofia R. Pauleta,‡,§Celia F. Goodhew,‡Alan Cooper,|Margaret Nutley,|Kornelia Jumel,⊥
Stephen E. Harding,⊥Cristina Costa,§Ludwig Krippahl,§Isabel Moura,§and Jose Moura§
Preclinical Veterinary Sciences, Royal (Dick) School of Veterinary Studies, UniVersity of Edinburgh, Summerhall,
Edinburgh EH9 1QH, U.K., Department of Chemistry, UniVersity of Glasgow, Glasgow G12 8QQ, U.K.,
Centre for Macromolecular Hydrodynamics, UniVersity of Nottingham, Sutton Bonington, Nottingham LE12 5 RD, U.K., and
Departamento de Quimica, CQFB, UniVersidade NoVa de Lisboa, 2829-516 Monte de Caparica, Portugal
ReceiVed May 19, 2003; ReVised Manuscript ReceiVed August 21, 2003
ABSTRACT: According to the model proposed in previous papers [Pettigrew, G. W., Prazeres, S., Costa,
C., Palma, N., Krippahl, L., and Moura, J. J. (1999) The structure of an electron-transfer complex containing
a cytochrome c and a peroxidase, J. Biol. Chem. 274, 11383-11389; Pettigrew, G. W., Goodhew, C. F.,
Cooper, A., Nutley, M., Jumel, K., and Harding, S. E. (2003) Electron transfer complexes of cytochrome
c peroxidase from Paracoccus denitrificans, Biochemistry 42, 2046-2055], cytochrome c peroxidase of
Paracoccus denitrificans can accommodate horse cytochrome c and Paracoccus cytochrome c550at different
sites on its molecular surface. Here we use1H NMR spectroscopy, analytical ultracentrifugation, molecular
docking simulation, and microcalorimetry to investigate whether these small cytochromes can be
accommodated simultaneously in the formation of a ternary complex. The pattern of perturbation of heme
methyl and methionine methyl resonances in binary and ternary solutions shows that a ternary complex
can be formed, and this is confirmed by the increase in the sedimentation coefficient upon addition of
horse cytochrome c to a solution in which cytochrome c550fully occupies its binding site on cytochrome
c peroxidase. Docking experiments in which favored binary solutions of cytochrome c550 bound to
cytochrome c peroxidase act as targets for horse cytochrome c and the reciprocal experiments in which
favored binary solutions of horse cytochrome c bound to cytochrome c peroxidase act as targets for
cytochrome c550show that the enzyme can accommodate both cytochromes at the same time on adjacent
sites. Microcalorimetric titrations are difficult to interpret but are consistent with a weakened binding of
horse cytochrome c to a binary complex of cytochrome c peroxidase and cytochrome c550and binding of
cytochrome c550to the cytochrome c peroxidase that is affected little by the presence of horse cytochrome
c in the other site. The presence of a substantial capture surface for small cytochromes on the cytochrome
c peroxidase has implications for rate enhancement mechanisms which ensure that the two electrons required
for re-reduction of the enzyme after reaction with hydrogen peroxide are delivered efficiently.
The original concept of a lock-and-key relationship
between redox partners in an electron transfer complex has
given way to a more complex picture of a family of weakly
bound orientations of one protein against the other during
an encounter (1, 2). For one of the best studied electron
transfer systems, that of yeast cytochrome c peroxidase, a
crystallographic solution has been obtained for the enzyme
in association with a cytochrome c (3). It may be that this
solution is just one of several possible orientations during
encounter, and this underlines the problem of studying
systems that form weak complexes. The existence of
secondary sites on redox enzymes has been a recurring theme
in work on electron transfer complexes. An example is the
secondary site on yeast cytochrome c peroxidase which was
originally controversial but is now accepted as a structurally
distinct weaker binding site (4). It is often not clear whether
a secondary site is a functional electron transfer site or a
site which allows a second redox protein to be waiting ready
to switch position when the primary site is vacated. One can
see the potential advantages of multiple electron transfer sites
when the redox process catalyzed by the enzyme requires
more than one electron. Rapid synchronous delivery of
electrons may protect against the formation and release of
partly reduced chemical species which have toxic radical
character. A similar argument may apply to binding sites
which are not electron transfer sites. These may be part of
a general capture surface which facilitates rate enhancement
by reducing the dimensions of search. A second redox protein
may be held at such a site so that it can readily move into
the electron transfer site when it is vacated and ensure rapid
delivery of a second electron. In the case of yeast cytochrome
†G.W.P. acknowledges the support of BBSRC (Grant 15B/13005).
The microcalorimetry facility (University of Glasgow) and the analytical
ultracentrifugation facility (University of Nottingham) are funded jointly
by the BBSRC and EPSRC. S.R.P. thanks the Fundacao para a Ciencia
e Tecnologia (BD/18297/98) for its support.
* To whom correspondence should be addressed. Telephone: 0131
650 6135. Fax: 0131 650 6576.
‡University of Edinburgh.
§Universidade Nova de Lisboa.
|University of Glasgow.
⊥University of Nottingham.
11968
Biochemistry 2003, 42, 11968-11981
10.1021/bi034829c CCC: $25.00© 2003 American Chemical Society
Published on Web 09/26/2003

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c peroxidase, Mei et al. (5) have shown that the second site
is not functional in electron transfer and propose that it acts
to promote dissociation of the product cytochrome c from
the electron transfer site.
Our model system for studying such questions has been
the diheme cytochrome c peroxidase from Paracoccus
denitrificans and the complexes that this enzyme forms with
its redox partners. After reaction with hydrogen peroxide,
the oxidized enzyme requires two electrons to return it to
an active form in which one heme (the electron-transferring
or E heme) contains ferrous iron and the other heme (the
peroxidatic or P heme) contains ferric iron.
A small mono-heme class I cytochrome c called cyto-
chrome c550acts as a physiological donor to the cytochrome
c peroxidase. This cytochrome is a homologue of mitochon-
drial cytochromes c, and indeed, horse cytochrome c acts as
a nonphysiological electron donor that has kinetic activity
similar to that of cytochrome c550. We have used the
combination of the physiological and nonphysiological redox
partners to probe the nature of the complexes formed with
the cytochrome c peroxidase. This sort of approach has also
been a feature of studies of the monoheme yeast cytochrome
c peroxidase (6, 7).
Using a combination of molecular docking simulation and
1H NMR spectroscopy, we have shown that horse cyto-
chrome c and cytochrome c550 bind to the cytochrome c
peroxidase at distinct surface sites (8). The cytochrome c550
is located above the exposed edge of the E heme, and the
horse cytochrome c is located on the surface roughly
equidistant between the E and P heme groups. The location
and orientation of cytochrome c550are exactly what might
have been predicted for an electron transfer complex. Its
heme edge is almost touching that of the E heme, and the
iron-iron distance is 16 Å. Whether the preferred “between
hemes” site for horse cytochrome is also an electron transfer
site is more debatable since the iron-iron distances are 22-
23 Å.
The binding of both cytochromes is endothermic and
driven by a large entropy change, consistent with a freeing
of water molecules from the interface (9). The enzyme binds
just one cytochrome c550 but can accommodate two horse
cytochrome c molecules in higher- and lower-affinity binding
sites. The binding to the higher-affinity site is weakened by
increasing the ionic strength in the range of 0.01-0.05 M,
and this is accompanied by an increase in the steady state
oxidation rates (9). If we accept that the high-affinity site
equates with the between hemes site observed for horse
cytochrome c in the molecular docking simulation, we can
propose that this represents a nonproductive orientation
which is released by increasing the ionic strength. According
to this model, the lower-affinity site for horse cytochrome c
may be equated with the E heme site, and indeed, if the top-
ranking binary complex of horse cytochrome c and cyto-
chrome c peroxidase is used as a target for ternary complex
formation with a second horse cytochrome c, the preferred
binding is at the E heme (9).
In this study, we investigate whether the cytochrome c
peroxidase can accommodate both cytochrome c550and horse
cytochrome c at the same time in a ternary complex.
Demonstration of such a complex would tend to support the
current model for how the two cytochromes bind, but it
would also raise the possibility of an electron transfer
mechanism which ensures the synchronous or rapid sequen-
tial delivery of two electrons.
MATERIALS AND METHODS
Source of Proteins. Cytochrome c peroxidase and cyto-
chrome c550 were purified from P. denitrificans [ATCC
19367, NCIB 8944, LMD 52.44) (now called Paracoccus
pantotrophus (10)] as described by Goodhew et al. (11) and
used in the oxidized state. Horse cytochrome c (C7752) was
obtained from Sigma and used in the oxidized state. Enzyme
and cytochrome concentrations were determined using
extinction coefficients of 250 mM-1cm-1(cytochrome c
peroxidase, 409 nm), 108 mM-1cm-1(cytochrome c550, 410
nm), and 109 mM-1cm-1(horse cytochrome c, 408 nm).
1H NMR Spectroscopy. High-resolution1H NMR spectra
were recorded in the Fourier transform mode on a Bruker
ARX-400 spectrometer (400 MHz). Data were recorded at
299 K, and 2000 transients were acquired for each spectrum.
To improve the signal-to-noise ratio, an exponential multi-
plication by 10 Hz line broadening of the free induction
decay was applied prior to Fourier transformation. All
chemical shifts are quoted in parts per million (ppm) from
internal 3-trimethylsilyl[2,2,3,3-2H4]propionate; positive val-
ues refer to low-field shifts. Protein samples were exchanged
several times with the appropriate buffer in D2O by
centrifugation above a Vivaspin membrane. (Note that the
spectra iii and iv of Figure 1 do not appear to reflect the
equimolar composition of horse cytochrome c and cyto-
chrome c550. In part, this is due to the dramatic broadening
effect on the heme methyls of the cytochrome c550 when
bound to the peroxidase, making integration unreliable. If
spectrum iv of Figure 1 is compared to Figure 6A of ref 8,
it is clear that in the presence of NaCl, the complex has not
fully dissociated and the heme methyls of cytochrome c550
remain quite broad. In addition, the heme methyls of horse
cytochrome c in spectrum iii of Figure 1 lie on top of broad
peroxidase resonances making their integration difficult.)
Microcalorimetry. Protein solutions were equilibrated with
the appropriate buffer by molecular exclusion chromatog-
raphy on Sephadex G25. The titrant solution was then
concentrated by centrifugation above a Vivaspin membrane
(Mrcutoff of 5000). Protein concentrations were determined
using the extinction coefficients noted above.
The target cytochrome c peroxidase was degassed and
placed in the sample chamber of the VP-ITC1microcalo-
rimeter (Microcal). The syringe was filled with a solution
of the protein used to form the binary complex, and
successive injections of 10 µL were delivered into the
chamber while its contents were stirred (310 rpm). The
duration of the additions was 20 s, and they were 180 s apart.
At a chosen point of particular proportions of probe protein
to target, the syringe was refilled with the other protein used
to form the ternary complex. Heat changes were analyzed
within Microcal Origin software which fits on the basis of
iteration within a Marquandt routine. Data were fitted using
models for one set of sites or for two independent sets of
sites. Dilution titrations of the probe protein into buffer alone
1Abbreviations: ccp, cytochrome c peroxidase; Mes, 2-(N-mor-
pholino)ethanesulfonic acid; ITC, isothermal titration calorimetry; D,
diffusion coefficient; s, sedimentation coefficient; ∆H°, standard
enthalpy change.
Ternary Electron Transfer Complexes of ccp
Biochemistry, Vol. 42, No. 41, 2003 11969

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were also performed and the results used to correct the
binding titrations.
Analytical Ultracentrifugation. Partial specific volumes of
the proteins were calculated from the amino acid composi-
tions and are 0.732 mL/g for cytochrome c peroxidase, 0.735
mL/g for cytochrome c550, and 0.744 mL/g for horse
cytochrome c. Protein solutions were equilibrated with the
appropriate buffer by molecular exclusion chromatography
on Sephadex G25 and were used at a concentration ranging
from 5 to 40 µM. Nonideality effects were assumed to be
negligible at the dilute concentrations that were studied.
The Beckman Optima XL-A or XL-I (Beckman, Palo
Alto) analytical ultracentrifuges, equipped with scanning
absorption optics, were used in all investigations. Sedimenta-
tion velocity experiments were carried out at 45 000 rpm
and 25 °C. Sedimentation coefficients were obtained by
scanning at 440 nm. The extinction coefficients of cyto-
chrome c peroxidase, horse cytochrome c, and cytochrome
c550at these wavelengths are 33, 17.8, and 15 mM-1cm-1,
respectively. The DCDT+ program of Philo (12) was used
to analyze groups of boundaries to derive sedimentation
coefficients. This method is based on the time-derivative
method developed by Stafford (13, 14) which fits Gaussian
functions to the so-called g(s*) distribution. For a given
component, the breadth of this distribution also facilitates
an estimate for the translational diffusion coefficient D*. The
asterisks indicate the inability to distinguish whether intensity
on either side of a peak really represents material sedimenting
with that s value or is merely broadening due to diffusion
of material sedimenting at the s value of the peak. Sedi-
mentation and diffusion coefficients were corrected to
standard solvent conditions (the viscosity, and the density
of water at 20 °C) using the SEDNTERP program (based
on ref 15). The derivation of a value of Mr from the
sedimentation velocity experiments is based on the s/D ratio
and is dependent on reliable estimates of both. In the case
of interacting systems such as those described here, a
boundary may contain more than one species in equilibrium,
and Mr values derived from such a boundary can only be
regarded as approximate estimates. In such a case, the
diffusion coefficient is likely to be an overestimate and the
Mran underestimate.
Individual sedimentation velocity scans were used to
calculate the binding of a cytochrome c to the peroxidase.
For a given total cytochrome c, the proportion bound to the
cytochrome c peroxidase could be calculated from the
increment in the absorbance of the leading boundary over
that due to the peroxidase itself. The proportion of free
cytochrome could be calculated from the absorbance at the
trailing boundary. When the separation between the leading
and trailing boundaries was difficult to resolve in a single
scan, the absorbance of the trailing boundary was obtained
from a later scan in which the leading boundary had already
sedimented. The absorbance values of boundaries were
corrected for the radial dilution effect of the sectored cell.
Molecular Docking. Docking was performed as described
in ref 8 using the algorithm BiGGER developed by
Palma et al. (16). The original algorithm performs a com-
plete and systematic search of the rotational space of one
protein relative to the other, generating a large number of
docking geometries based solely on the complementarity of
the molecular surfaces. The 1000 best solutions thus gener-
ated were finally evaluated and ranked according to a
combination of additional interaction criteria that include the
electrostatic energy of interaction, the relative solvation
energy, and the relative propensity of adjacent side chains
to interact. For each solution, this combination process
produces a “global score”. This original algorithm has
evolved through several optimizing stages (see http://
www.dq.fct.unl.pt/bioin/chemera) to allow “softer” docking
in which side chains are truncated. This allows greater
overlap between the structures by ignoring steric clashes of
the more flexible side chains. As a consequence, correct
solutions are more reliably captured in some model cases,
but a higher level of “noise” is introduced due to the retention
of spurious incorrect solutions. To partly counteract that,
there is a second filtering involving evaluation of the
likelihood of side chain contacts. This evaluation is based
on a set of 87 structures used to train the neural network
classifier.
“Soft” and “hard” docking give different results. If the
conformations of the docking partners do not change
significantly, the hard docking algorithm (being more
FIGURE 1:
horse cytochrome c, cytochrome c550, and cytochrome c peroxidase.
Shown is the downfield heme methyl region. To a solution (0.75
mM) of horse cytochrome c in 10 mM Mes, 25 mM NaCl (pH
6.0), and D2O (i) was added equimolar cytochrome c peroxidase
from a 3.34 mM stock solution in the same buffer (ii) (final
concentration of 612 µM). Then equimolar cytochrome c550from
a 4.18 mM stock solution in the same buffer was added (iii) (final
concentration of 536 µM). Finally, the solution in the NMR tube
containing all three proteins was taken to 700 mM NaCl from a 3
M stock solution in the same buffer (iv) (final concentration of
411 µM). The dashed line indicates the free position of heme methyl
8 of the horse cytochrome c. The arrows in spectra iii and iv denote
the heme methyl peaks of the cytochrome c550. In the free state,
these methyls have chemical shifts of 29.1 and 28.7 ppm (not
shown). The former shifts to 31.20 ppm and the latter to 28.08 on
binding the peroxidase (iii). They return to near their free positions
in the presence of 700 mM NaCl (iv).
1H NMR spectroscopy of the complex formed between
11970 Biochemistry, Vol. 42, No. 41, 2003
Pettigrew et al.

Page 4

stringent) is better at filtering out “incorrect” models at the
stage of the surface complementarity calculations. However,
if there are critical changes in the side chain conformation,
the hard docking may reject correct models due to excessive
overlap and only the soft docking has a chance of retaining
these. In the general case, with no additional information
available, the use of soft docking is preferred to improve
the probability of retaining at least one “correct” model at
the stage of the surface complementarity filter. But if
additional information (such as electron-transfer constraints)
is available, one can confront the results of soft and hard
docking and ask whether the former retains “likely” models
that the latter fails to do. If that is not the case, then the
hard docking results can be preferred.
RESULTS
Detection of Ternary Complex Formation by1H NMR
Spectroscopy. Both cytochrome c550and horse cytochrome
c have two strongly downfield shifted heme methyl groups
which are further shifted on binding cytochrome c peroxidase
(8). The progressive shift in the resonances during these
titrations suggests a fast exchange, and the observed sub-
stantial broadening is probably due to the much higher
molecular weight of the complexes (an addition of an Mrof
75 000 for the peroxidase dimer) relative to the cytochromes
(Mr) 12000-15000). This broadening and the shift effect
are seen for horse cytochrome c in spectrum ii of Figure 1
and involve a 0.4 ppm upfield shift in a heme methyl from
35.20 to 34.80 ppm. Addition of equimolar cytochrome c550
to the horse cytochrome c-peroxidase complex results in a
small shift back (0.1 ppm) toward the 35.20 ppm position
(spectrum iii of Figure 1), and the “free” position can be
almost fully restored by addition of a high NaCl concentra-
tion (spectrum iv of Figure 1). The magnitudes of the shifts
suggest that perhaps 25% of the horse cytochrome c is
displaced by the addition of the cytochrome c550. The second
heme methyl of the horse cytochrome c (32.18 ppm) is also
shifted (this time further downfield to 32.76 ppm) by the
binding to the peroxidase (spectrum ii of Figure 1), and again
this shift survives addition of the cytochrome c550(spectrum
iii of Figure 1). In this case, however, the original free peak
position is not restored by addition of a high concentration
of NaCl (spectrum iv of Figure 1). This is due to an effect
of the NaCl on the position of this methyl in the absence of
binding cytochromes (data not shown).
At the same time, it is clear that the cytochrome c550itself
is bound. The chemical shifts of the two heme methyls of
free cytochrome c550are at 29.1 and 28.7 ppm (8). The former
methyl shifts to 31.2 ppm and the latter to 28.1 on binding
the peroxidase (8). These shifts are clearly seen in spectrum
iii of Figure 1. Again the association with cytochrome c550
can be broken by a high NaCl concentration with the two
heme methyls coming together near 28.63 ppm (spectrum
iv of Figure 1).
Support for the existence of a ternary complex also comes
from an examination of the upfield region populated by the
resonances associated with the methionine ligands of the
cytochrome hemes. The methionine methyl of free cyto-
chrome c550has a chemical shift of -17.87 ppm (spectrum
i of Figure 2A), and this is shifted downfield by 0.8 ppm in
the presence of cytochrome c peroxidase (8). The same shift
is observed when an equimolar complex of horse cytochrome
c and cytochrome c peroxidase is added to cytochrome c550
(spectrum iii of Figure 2A), and the cytochrome c550 is
released by addition of NaCl (spectrum iv of Figure 2A).
This effect is also seen in the inverse experiment when
cytochrome c550is added to the equimolar complex of horse
cytochrome c and cytochrome c peroxidase (spectrum iii of
Figure 2B). Again, the cytochrome c550 is released on
addition of a high NaCl concentration (spectrum iv of Figure
2B). The methionine methyl of horse cytochrome c at -25.13
ppm is scarcely shifted upon binding to the cytochrome c
peroxidase, but it does broaden due to the increase in the
associated particle size (spectrum ii of Figure 2B). This
broadened state is maintained in the presence of cytochrome
c550(spectrum iii of Figure 2A and spectrum iii of Figure
2B), and the peak sharpens again on addition of NaCl
(spectrum iv of Figure 2A and spectrum iv of Figure 2B).
Thus, in spectrum iii of Figure 2A and spectrum iii of Figure
2B, we have evidence that a ternary complex between
FIGURE 2:
horse cytochrome c, cytochrome c550, and cytochrome c peroxidase.
Shown is the upfield methionine methyl region. Panel A contains
spectra from an experiment in which the NMR tube initially
contained 0.75 mM cytochrome c550in 10 mM Mes, 25 mM NaCl
(pH 6.0), and D2O (i) to which was added an equimolar amount of
a horse cytochrome c/cytochrome c peroxidase solution from a stock
in which each protein is at 1.2 mM (iii) (final concentration of 462
µM). Then the solution in the NMR tube containing all three
proteins was taken to 700 mM NaCl from a 3 M stock solution in
the same buffer (iv) (final concentration of 362 µM). Spectrum ii
was obtained after addition of a half-molar amount of the binary
complex of horse cytochrome c and cytochrome c peroxidase. The
dashed line at -25.15 ppm denotes the virtually constant position
of the methionine methyl of horse cytochrome c. The dashed line
at -17.87 ppm denotes the free position of the methionine methyl
of cytochrome c550. Panel B shows spectra obtained during the same
experiment as shown in Figure 1. Final concentrations are like those
for Figure 1. To a solution (0.75 mM) of horse cytochrome c in 10
mM Mes, 25 mM NaCl (pH 6.0), and D2O (i) was added an
equimolar amount of cytochrome c peroxidase from a 3.34 mM
stock solution in the same buffer (ii) and then an equimolar amount
of cytochrome c550from a 4.18 mM stock solution in the same
buffer (iii). Finally, the solution in the NMR tube containing all
three proteins was taken to 700 mM NaCl from a 3 M stock solution
in the same buffer (iv). The dashed line at -25.13 ppm denotes
the virtually constant position of the methionine methyl of horse
cytochrome c. The dashed line at -17.82 ppm denotes the free
position of the methionine methyl of cytochrome c550in the presence
of added NaCl. In both panels A and B, the initial spectrum (i) is
unmagnified and the others are magnified 2-fold.
1H NMR spectroscopy of the complex formed between
Ternary Electron Transfer Complexes of ccp
Biochemistry, Vol. 42, No. 41, 2003 11971

Page 5

cytochrome c peroxidase, cytochrome c550, and horse cyto-
chrome c has been formed.
For cytochrome c550, the shifts in heme methyls and the
methionine methyl associated with ternary complex forma-
tion are the same as those observed for saturation of binding
during binary complex formation (8), indicating that the
binding site is also fully occupied in the ternary complex.
A control experiment was performed in which cytochrome
c550is titrated into a horse cytochrome c solution. When this
is done in 10 mM Mes (pH 6.0) and D2O, some very small
chemical shifts are observed, consistent with weak nonspe-
cific binding (results not shown). One of the reasons for
conducting the above experiments in the additional presence
of 25 mM NaCl (see the legend of Figure 1) is that these
small shifts disappear under these conditions.
Analytical Centrifugation of the Binary and Ternary
Complexes. The leading boundaries in Figure 3 represent
cytochrome c peroxidase (i) or cytochrome c peroxidase
complexed to cytochromes (ii and iii). The trailing boundaries
represent free cytochrome. In the presence of cytochrome
c550, the sedimentation coefficient of the leading boundary
is increased (absorbance profile ii of Figure 3), indicating
binding of the cytochrome c550 and the peroxidase. The
proportion of cytochrome c550bound is given by a - b (after
correction for the radial dilution of the sectored cell), and
the proportion that is free is given by the absorbance of the
trailing boundary. From these figures and the total amount
of cytochrome c550added, the cytochrome c550binding site
is 97% occupied under these conditions.
The leading boundary has a sedimentation coefficient
(s20,w) of 5.43 S for the experiment in which the proportions
of cytochrome c550and cytochrome c peroxidase are 2:1 (part
ii of Figure 4), and an indication of the fits for different
proportions of cytochrome c550and cytochrome c peroxidase
is given by a (0.5:1), b (1:1), c (2:1), and d (4:1). The s20,w
value of 5.43 S together with an estimate of D from the
spread of the leading boundary can be used to derive an Mr
value of 96 000. The binding of two cytochrome c550
molecules (each with an Mrof 14 815) to a cytochrome c
peroxidase dimer (Mrof 75 026) should yield a particle with
an Mr of 104 656. Given that the analysis of boundary
absorbances suggests virtually complete occupancy of the
cytochrome c550site under these experimental conditions, the
underestimate of the molecular weight can be attributed to
the problems in analyzing a complex boundary mentioned
in Materials and Methods. We can be confident, however,
that the s value of 5.55 S (Figure 4d and ref 9) for the
solution proportions of four cytochrome c550molecules per
cytochrome c peroxidase is close to the value for the
saturated complex.
In the additional presence of horse cytochrome c in
proportions of 1:1 with the cytochrome c peroxidase (ab-
sorbance profile iii of Figure 3), there is a further increase
in the sedimentation coefficient of the leading boundary.
Using the same method of boundary absorbance analysis
outlined above, we can estimate that 63% of the horse
cytochrome c is bound (assuming that the distribution of
cytochrome c550between bound and free remains unaltered).
This indicates that the horse cytochrome c is binding to a
site distinct from the cytochrome c550site.
The s20,wvalue of this ternary complex boundary is 5.81
S, higher than the value of 5.55 S obtained for a 4:1 solution
of cytochrome c550and cytochrome c peroxidase (Figure 4d
and ref 9). This effect of the horse cytochrome c cannot
simply be due to competitive displacement because this
cytochrome has a lower molecular weight than the cyto-
chrome c550. The s20,w value of 5.81 S together with an
estimate of D can be used to derive a molecular weight for
a 1:1:1 ternary complex of the three proteins of 107 000.
The theoretical molecular weight for such a complex is
129 378. The shortfall will be in part due to the problems
associated with analysis of the complex boundary and partly
due to the incomplete occupancy of the horse cytochrome c
site.
FIGURE 3:
cytochrome c peroxidase alone and in the presence of binding
cytochromes. Solutions of cytochrome c peroxidase alone (10 µM)
(i) or in the presence of 20 µM cytochrome c550(ii) or 20 µM
cytochrome c550 and 10 µM horse cytochrome c (iii) were
centrifuged at 45 000 rpm in 10 mM Mes, 10 mM NaCl, and 2
mM CaCl2at pH 6 and 25 °C. Absorbance scans of the centrifuge
cells were carried out at 440 nm. The scans shown here are taken
at equivalent time points for the three experiments. The arrows
indicate the midpoints of the leading boundary. a is the absorbance
of the leading boundary containing cytochrome c550and cytochrome
c peroxidase; b is the absorbance due to the cytochrome c
peroxidase alone.
Sedimentation velocity boundaries of Paracoccus
FIGURE 4: Effect of cytochrome c binding on the sedimentation
coefficient of the Paracoccus cytochrome c peroxidase. Sedimenta-
tion velocity experiments were performed in 10 mM Mes, 10 mM
NaCl, and 2 mM CaCl2at pH 6.0, 25 °C, and 45 000 rpm. Paired
scans within a set of 10 sequential scans were used to produce a
distribution of sedimentation coefficients using the DCDT+ method
of Philo (12) and refs 13 and 14. For experiments in which two
boundaries were evident, both were analyzed: (i) 10 µM cyto-
chrome c peroxidase, (ii) 10 µM cytochrome c peroxidase and 20
µM cytochrome c550, and (iii) 10 µM cytochrome c peroxidase, 20
µM cytochrome c550, and 10 µM horse cytochrome c. Curves a-d
are portions of the theoretical fits to experiments in which the
proportions of cytochrome c550to cytochrome c peroxidase were
0.5:1, 1:1, 2:1, and 4:1, respectively. The vertical axis is in
absorbance units per svedberg.
11972 Biochemistry, Vol. 42, No. 41, 2003
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Isothermal Titration Microcalorimetry. (i) Binding of
Horse Cytochrome c to a Binary Complex of Cytochrome
c550and Cytochrome c Peroxidase. As previously reported
(9), the binding of horse cytochrome c to cytochrome c
peroxidase is endothermic under these conditions, with an
ITC differential binding curve inconsistent with simple 1:1
complexation. The data do, however, fit consistently well
to a two-site binding model. The results in Table 1 for the
binding of horse cytochrome c to cytochrome c peroxidase
alone (repeated here with the same batch of protein used for
the mixed ternary complexation studies) again show a higher-
affinity site and a lower-affinity site with binding parameters
very similar to those published (9) (Kd1) 0.9 µM, ∆H )
19.8 kJ/mol; Kd2) 5.9 µM, ∆H ) 10.4 kJ/mol). However,
when Paracoccus cytochrome c550 is also present prior to
the titration with horse cytochrome c, a much smaller
endothermic heat change is seen (part ii of Figure 5A and
part ii of Figure 5B). Unambiguous analysis of this ITC curve
is not feasible because of the small heat effects and the
apparent weak binding, but if we assume N ) 1, the data
are consistent with an apparent Kdof 88 µM (Table 1).
(ii) Binding of Cytochrome c550to a Binary Complex of
Horse Cytochrome c and Cytochrome c Peroxidase. The
results of Table 1 for the binding of cytochrome c550 to
cytochrome c peroxidase alone show binding parameters very
similar to those published (9) (Kd ) 3.7 µM, ∆H ) 10.4
kJ/mol). There is an exothermic effect for the dilution of
cytochrome c550into buffer alone (part iv of Figure 6A and
part iv of Figure 6B). Cytochrome c550is known to be in a
monomer-dimer equilibrium under these conditions, and the
dilution effect is consistent with a monomerization as the
titrant is diluted into the target buffer. That heat change
would be expected to decrease as the titration progresses,
and the concentration of cytochrome c550in the target solution
increases. This effect is apparent from the results of part iv
of Figure 6A and part iv of Figure 6B.
Two experiments were performed with target solutions of
one horse cytochrome c per peroxidase and 3.8 horse
cytochrome c molecules per peroxidase. On the basis of the
Kdvalues obtained from the binding of horse cytochrome c
to the peroxidase alone and taking into account the concen-
tration conditions of the experiment, we determine the
predicted occupancy of the two sites on the peroxidase for
horse cytochrome c, shown in Table 2.
When horse cytochrome c is present in proportions of 3.8:1
to the peroxidase prior to the titration with cytochrome c550,
the observed heat changes (part iii of Figure 6A and part iii
of Figure 6B) are not greatly different from those of dilution
into buffer alone (part iv of Figure 6A and part iv of Figure
6B). Competitive displacement of the horse cytochrome c
as the cytochrome c550concentration increases may account
for what difference there is [although there is little enthalpy
difference in the binding of the two proteins (Table 1)]. In
contrast, with horse cytochrome c in the proportion of 1:1
with the peroxidase prior to the titration, an endothermic
binding can be observed (part ii of Figure 6B). After allowing
for the dilution effect into buffer, we can fit the corrected
heat change data to 0.35 site with a binding constant of 4.6
µM (Table 1), not too different from the binding constant
for binding of cytochrome c550to the peroxidase alone.
Docking of Cytochromes to Paracoccus Cytochrome c
Peroxidase. (i) Binary Complex with Cytochrome c550. For
the binary complex formed between cytochrome c550 and
cytochrome c peroxidase, Pettigrew et al. (8) found that six
of the top 10 ranking docks showed cytochrome c550binding
above the E heme of the peroxidase. Five of the six had
Table 1: Thermodynamic Parameters for the Binding of Horse Cytochrome c with Cytochrome c Peroxidase and with the Binary Complex of
Cytochrome c Peroxidase and Cytochrome c550
titranttarget analysis
horse cyt c
ccp alone two sets of sites
NKa(×10-5M-1)
10.2 ( 1.8
1.6 ( 0.1
0.11 ( 0.005
2.8 ( 0.15
2.2 ( 0.6
Kd(µM)
0.98
6.2
88
3.6
4.6
∆H° (kJ/mol)
19.7 ( 0.7
10.3 ( 0.7
(37.0 ( 1.1)a
11.5 ( 0.17
3.6 ( 0.57
(1)
(1)
(1)
1.0 ( 0.01b
0.35 ( 0.05
ccp and cyt c550
ccp alone
ccp and horse cyt c (1:1)
one set of sites
one set of sites
one set of sites
Paracoccus c550
aThis ∆H° is reported for information only and should not be considered reliable in such weak affinity situations.bThe goodness of fit is
indicated by the standard deviations for the independent variables.
FIGURE 5: Isothermal titration calorimetry of the binding of horse
cytochrome c to Paracoccus cytochrome c peroxidase in the
presence and absence of cytochrome c550. (A) Horse cytochrome
c, Paracoccus cytochrome c550, and Paracoccus cytochrome c
peroxidase were equilibrated in 10 mM cacodylate (pH 6.0), 10
mM NaCl, and 2 mM CaCl2by being passed down a Sephadex
G25 molecular exclusion column. The microcalorimetry chamber
at 25 °C contained degassed cytochrome c peroxidase at 23 µM (i)
or 20.6 µM (ii), and in the case of part ii, 58 µM cytochrome c550
was also present. The syringe contained degassed horse ferricyto-
chrome c at 441 µM. Each delivery of titrant was set to take 20 s
with 180 s between additions. (B) Heat changes for results obtained
in panel A. (i) Titration of Paracoccus cytochrome c peroxidase
with horse cytochrome c (b). The best fit of the results is with a
two-sets-of-sites model in which N is constrained to 1 for each
site. Thermodynamic parameters are given in Table 1. (ii) Titration
of a solution of Paracoccus cytochrome c peroxidase and cyto-
chrome c550with horse cytochrome c (O). The best fit of the results
is with a one-set-of-sites model in which N is constrained to 1.
Thermodynamic parameters are given in Table 1.
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very similar orientations (we will call these type I), and this
is represented by the top-ranking solution shown in Figure
8G. In one of the six, the orientation was rotated 180° around
the region of contact with the peroxidase (Figure 8A). We
will call this type II. These orientations can be distinguished
in Figure 8 by examining the position of the C-terminus
(indicated by an arrow) and a loop of chain (indicated with
an asterisk). These docks were done with an early version
of BiGGER which has subsequently been refined.
In the more recent version of BiGGER, docking can be
performed either by considering the molecules as rigid bodies
(hard docking) or by allowing for side chain mobility and
uncertainty in surface structure (soft docking). In the case
of cytochrome c550, it is the soft docking mode that produces
very clear-cut results, comparable to those already published
using the original version of BiGGER. Again six of the top
10 ranking solutions showed cytochrome c550bound above
the E heme site (Figure 7A). [Notice that this dock involves
the peroxidase monomer and four docking solutions are
excluded from the top 10 list because the cytochrome c550is
bound at the dimer interface, a structural impossibility in
solution where the active enzyme is dimeric (17). These
interface solutions are on the right side of Figure 7B.] Again
there are two types of solution which match the types I and
II seen with the original BiGGER program, and these two
types are related by a rotation of 180° around the region of
contact with the peroxidase. This time only two of the six
are in the type I orientation (Figure 8H,I), and the other four
are in the type II orientation (Figure 8B-E). It is noticeable
that the type I orientation seems to allow a slightly closer
approach of the iron of the cytochrome c550to the heme iron
of the E heme of the cytochrome c peroxidase (distances in
the figure are in angstroms).
Within the top 500 docking solutions, there is a large
cluster that is situated above the E heme (Figure 7A). In the
vast majority of these and in all of the group in the top 10
ranked solutions, the orientation of the heme of the cyto-
chrome c550 is toward the surface of the cytochrome c
peroxidase, thus minimizing the iron-iron distance and
achieving a close approach of the edges of the cytochrome
heme and the peroxidase E heme. Only a few solutions have
the opposite orientation with the heme of the cytochrome
c550turned outward. These outliers are visible in Figure 7B
(indicated by the arrow). In the hard docking mode, there
is a much smaller cluster of solutions situated above the E
heme (Figure 7C), and of these, only three are ranked in the
top 10.
(ii) Binary Complex with Horse Cytochrome c. For the
binary complex formed between horse cytochrome c and
cytochrome c peroxidase, six of the top 10 ranking docks
showed horse cytochrome c binding between the two hemes
of the peroxidase (8). Using the refined version of BiGGER,
it is the hard docking mode that, in this case, produces a
pattern (Figure 9A) similar to the published pattern in ref 8.
Again six of the top 10 ranking solutions were located
between the two peroxidase hemes (the between hemes
cluster of Figure 9A) rather than at the E heme location that
is observed with the cytochrome c550. [Notice that in the
views presented in Figure 9, the hemes of these docking
solutions appear to be closer to the P heme of the peroxidase
rather than between the two hemes. However, the P heme is
buried and the iron-iron distances from the cytochrome to
the two heme groups are very similar (see, for example,
Figure 10A,B).] The top-ranking solution from the original
published dock is shown in Figure 10A, and a top-ranking
solution from the current hard docking is shown in Figure
10B.
FIGURE 6: Isothermal titration calorimetry of the binding of cytochrome c550to Paracoccus cytochrome c peroxidase in the presence and
absence of horse cytochrome c. (A) Horse cytochrome c, Paracoccus cytochrome c550, and Paracoccus cytochrome c peroxidase were
equilibrated in 10 mM cacodylate (pH 6.0), 10 mM NaCl, and 2 mM CaCl2by being passed down a Sephadex G25 molecular exclusion
column. The microcalorimetry chamber at 25 °C contained degassed cytochrome c peroxidase at 23 (i), 21.9 (ii), or 19.2 µM (iii) or buffer
only (iv). In the case of part ii, 21.8 µM horse cytochrome c was also present, and in the case of part iii, 73.5 µM horse cytochrome c was
also present. The syringe contained 565 µM degassed cytochrome c550. Each delivery of titrant was set to take 20 s with 180 s between
additions. (B) Heat changes for results obtained in panel A. (i) Titration of Paracoccus cytochrome c peroxidase with cytochrome c550(b).
(ii) Titration of a 1:1 solution of Paracoccus cytochrome c peroxidase and horse cytochrome with Paracoccus cytochrome c550(O). (iii)
Titration of a 1:3.8 solution of Paracoccus cytochrome c peroxidase and horse cytochrome with Paracoccus cytochrome c550(2). (iv)
Titration of Paracoccus cytochrome c550into buffer alone (4). (C) Best fit of results obtained for parts i and ii of panel B after correction
for the dilution effect and using a single-set-of-sites model. The thermodynamic parameters are given in Table 1.
Table 2: Occupancy of the Two Sites on Cytochrome c Peroxidase
that Bind Horse Cytochrome c
occupancy (%)a
Kd(µM)
0.98
6.2
1:1 horse cyt c:ccp
67
25
3.8:1 horse cyt c:ccp
98
87
site 1
site 2
aUnder the conditions of the isothermal microcalorimetry experiment.
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The results for the soft docking mode are quite differ-
ent (Figure 9B,C). Although the between hemes location
is still populated, a large proportion of the top 500
solutions and six of the top 10 solutions are located
above the E heme. However, the problem with these
solutions can be seen by comparing Figure 9C with Figure
7B. Both show strong clusters above the E heme, but in
the case of this soft dock for horse cytochrome c, almost
all the heme iron locations for the horse cytochrome c are
further from the molecular surface and reflect heme orienta-
tions turned outward. An example of this is shown in
Figure 10C.
FIGURE 7: Docking of cytochrome c550to cytochrome c peroxidase of P. denitrificans. The side of the peroxidase monomer at which the
E heme edge is exposed (A and C-E) or the front of the monomer (B) is shown as faint gray empty cicles with the P and E hemes in red
and partially visible. The two views are related by a 90° rotation about a vertical axis. The E heme is the more exposed and is in the lower
half of the peroxidase structure; the P heme is mostly buried, and portions of it can be seen in the upper half of the peroxidase molecule
unless concealed by docking clusters. In panels D and E, the docked horse cytochrome c molecule is shown in green. In all simulations,
the 500 most favorable solutions are shown as small yellow circles marking the heme iron of the probe protein, cytochrome c550. The top
10 docking solutions are shown as larger circles filled with dark gray. The E heme cluster is circled in panels A and B. (A) Side view of
the soft docking of cytochrome c550to the peroxidase monomer. (B) Front view of the soft docking of cytochrome c550to the peroxidase
monomer. The arrow denotes outlying heme iron positions which reflect cytochrome c550orientations facing away from the molecular
surface of the peroxidase. The solutions at the right side are situated at what would be the dimer interface of the peroxidase and can be
ignored. (C) Side view of the hard docking of cytochrome c550to the peroxidase monomer. (D) Side view of the soft docking of cytochrome
c550to a binary complex of the cytochrome c peroxidase and horse cytochrome c. The top-ranking solution of this dock is shown in Figure
8F. The binary complex that was used was the third-ranking solution (Figure 10B) of the hard dock shown in Figure 9A. (E) Side view of
the hard docking of cytochrome c550to a binary complex of the cytochrome c peroxidase and horse cytochrome c. The binary complex that
was used was the top-ranking solution of the published dock using the original version of BiGGER and is shown in Figure 10A.
Ternary Electron Transfer Complexes of ccp
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Page 9

(iii) Ternary Complexes. If the top type I orientation of
the cytochrome c550against the peroxidase from ref 1 (Figure
8G) is used as a target for the ternary docking of horse
cytochrome c, nine of the top 10 ternary complexes have
the horse cytochrome c positioned between the two peroxi-
dase heme groups (Figure 9D). An example of one of these
high-ranking ternary docks in which the orientation of the
horse cytochrome c is similar to the binary dock of Figure
10B is shown in Figure 10D. If the top type II orientation
of the cytochrome c550against the peroxidase (Figure 8B) is
used as a target, there is again a good cluster of docks situated
between hemes with eight of the top 10 docks in this position
(Figure 9F). An example from this cluster that again
resembles the orientation of horse cytochrome c in Figure
10B is shown in Figure 10E. (The horse cytochrome c in
panel D is rotated in the plane of the page relative to panel
B so that the N-terminal helix is closer to the peroxidase.
This is also the case in panel E but with an additional rotation
of the “bottom” of the molecule given by the position of the
protruding propionate groups of the heme.) It therefore seems
that either the type I or the type II orientation observed in
the binary docks with cytochrome c550 and cytochrome c
peroxidase is permissive as a binding target for horse
cytochrome c. However, interestingly, the type I relative
shown in Figure 8H in which the cytochrome c550heme is
rotated about 30° relative to its position in Figure 8G shows
a quite different docking pattern with horse cytochrome c
(Figure 9E) because the cytochrome c550interferes with the
between hemes surface.
The critical importance of the orientation of the bound
cytochrome in the target for ternary docking is also seen
with the docking of cytochrome c550to a horse cytochrome
FIGURE 8: Top-ranking solutions for cytochrome c550docking to cytochrome c peroxidase of P. denitrificans. The backbone of the cytochrome
c peroxidase monomer is shown from the front enclosing the E heme (lower) and the P heme (upper) filled in red. This view is equivalent
to that of Figure 7B. The probe cytochrome c550heme is shown in red enclosed by a blue polypeptide backbone. The iron-iron distances
between the cytochrome c550heme and the E heme iron of the cytochrome c peroxidase are indicated (angstroms). Panels A-F are described
as type II solutions as explained in the accompanying text. Panels G-I are type I solutions. These cytochrome c550orientations are related
by a rotation of approximately 180°, and this rotational relationship between type I and type II solutions is indicated by the arrows pointing
to the C-terminus of the cytochrome c550backbone and is also evident in most cases in the position of the polypeptide loop marked with
an asterisk which is below and above the heme group, respectively. (A) Top-ranking type II solution from the top 10 docks obtained using
the original version of BiGGER (8). (B-E) Four type II solutions from the six top-ranking solutions above the E heme in the soft docking
shown in panels A and B of Figure 7. (F) Top-ranking solution from the soft dock of cytochrome c550to a binary complex of horse
cytochrome c (shown in green) and cytochrome c peroxidase. The overall docking results are shown in Figure 7D, and the binary complex
that was used is shown in Figure 10B and was the third-ranking solution of the hard dock shown in Figure 9A. (G) Top-ranking type I
solution from the top 10 docks obtained using the original version of BiGGER (8). (H and I) Two type I solutions from the six top-ranking
solutions above the E heme in the soft docking shown in panels A and B of Figure 7.
11976 Biochemistry, Vol. 42, No. 41, 2003
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c-cytochrome c peroxidase target. If the binary solution
shown in Figure 10A is used a target, there are no high-
ranking solutions found that are positioned above the E heme
(Figure 7E). However, if the binary solution shown in Figure
10B is used as a target, then cytochrome c550can bind above
the E heme (Figure 7D) in eight of the top 10 ranking
solutions. The top-ranking example of this which has an
orientation of the cytochrome c550close to type II is shown
in Figure 8F.
(iV) The Top 10 Ranking Solutions. In Figures 7 and 9,
we have emphasized the top 10 solutions in dark gray and
with larger circles. To some extent, how many of the top-
ranking solutions are emphasized is arbitrary. However,
Figure 11 shows (at least for the case of the soft docking of
cytochrome c550 to the peroxidase) that there is some
justification for emphasizing the top 10 solutions as they are
characterized by a step change in the global score. Figure
11 also shows the clustering of top-ranking solutions (boxed)
with close approach of the cytochrome heme group to the E
heme of the peroxidase.
DISCUSSION
Ternary Complex of Horse Cytochrome c, Cytochrome
c550, and Cytochrome c Peroxidase. We are interested in
using a variety of methods to study the transient complexes
formed by electron transfer proteins, partly because such
complexes are harder to demonstrate than tight complexes
and partly because the different methods cast different lights
FIGURE 9: Docking of horse cytochrome c to cytochrome c peroxidase of P. denitrificans. The side of the peroxidase monomer at which
the E heme edge is exposed (A, B, and D-F) or the front of the monomer (C) is shown in faint gray empty circles with the P and E hemes
in red and partially visible. The two views are related by a 90° rotation about a vertical axis. The E heme is more exposed and is in the
lower half of the peroxidase structure; the P heme is mostly buried, and portions of it can be seen in the upper half of the peroxidase
molecule. In panels D-F, the docked cytochrome c550molecule is shown in cyan. In all simulations, the 500 most favorable solutions are
shown as small yellow circles marking the heme iron of the probe protein, horse cytochrome c. The top 10 docking solutions are shown
as larger circles filled with gray. The between hemes cluster is circled in panel A. (A) Side view of the hard docking of horse cytochrome
c to the peroxidase monomer. (B) Side view of the soft docking of horse cytochrome c to the peroxidase monomer. (C) Front view of the
soft docking of horse cytochrome c to the peroxidase monomer. The arrow indicates outlying heme iron positions which reflect horse
cytochrome c orientations facing away from the molecular surface of the peroxidase. The solutions at the right side are situated at what
would be the dimer interface of the peroxidase and can be ignored. (D) Side view of the hard docking of horse cytochrome c to a binary
complex of the cytochrome c peroxidase and cytochrome c550. An example of a top 10 ranking solution of this dock is shown in Figure
10D. The binary complex that was used was the highest-ranking type I dock from the top 10 docks obtained using the original version of
BiGGER (8). This binary complex is shown in Figure 8G. (E) Side view of the hard docking of horse cytochrome c to a binary complex
of the cytochrome c peroxidase and cytochrome c550. The binary complex that was used was a type I dock with an orientation slightly
different from that in Figure 8G taken from the top 10 solutions of Figure 7A. This binary complex is shown in Figure 8H. (F) Side view
of the hard docking of horse cytochrome c to a binary complex of the cytochrome c peroxidase and cytochrome c550. An example of a top
10 ranking solution of this dock is shown in Figure 10E. The binary complex that was used was the highest-ranking type II dock taken from
the top 10 solutions of Figure 7A. This binary complex is shown in Figure 8B.
Ternary Electron Transfer Complexes of ccp
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on the nature of electron transfer complexes. Of the methods
used here, we have strong evidence from1H NMR spec-
troscopy and sedimentation velocity centrifugation that a
ternary complex can be formed between cytochrome c
peroxidase, horse cytochrome c, and cytochrome c550.
In the case of
proteins present in equimolar proportions, it is clear that the
cytochrome c550is fully bound and horse cytochrome c is
∼75% bound. The essentially complete binding of the
cytochrome c550under these conditions is reasonably con-
sistent with a 91% occupancy calculated from the Kdvalue
(4.3 µM) obtained by microcalorimetry under the higher-
ionic strength conditions of this NMR experiment (9). Horse
cytochrome c alone with the cytochrome c peroxidase would
be expected to partition between the higher- and lower-
affinity binding sites according to the Kdvalues of 11.6 and
1H NMR spectroscopy, with the three
25.9 µM obtained by microcalorimetry under comparable
conditions (9). Using these values, site occupancies for horse
cytochrome c under the conditions in the NMR experiment
are predicted to be 59 and 39%, respectively. We propose
that, when all three proteins are present, cytochrome c550
preferentially occupies the lower-affinity binding site for
horse cytochrome c and some displacement of horse cyto-
chrome c is therefore observed. But the important point is
that a ternary complex is detected in which the cytochrome
c550site is fully occupied and the remaining horse cytochrome
c site is mostly occupied.
The existence of such a complex is confirmed by
sedimentation velocity ultracentrifugation. Analysis of the
leading and trailing boundaries suggests that the cytochrome
c550 site is almost fully occupied under the conditions of
absorbance profile ii of Figure 3, and yet when the smaller
FIGURE 10: Top-ranking solutions for horse cytochrome c docking to cytochrome c peroxidase of P. denitrificans. The backbone of the
cytochrome c peroxidase monomer is shown from the front enclosing the E heme (lower) and the P heme (upper) in red. The probe horse
cytochrome c heme is shown in red enclosed by a green polypeptide backbone. The iron-iron distances between the horse cytochrome c
heme and the two heme irons of the cytochrome c peroxidase are indicated (angstroms). The upper number in each case is the horse
cytochrome c heme iron-P heme iron distance; the lower number is the horse cytochrome c heme iron-E heme iron distance. In some of
the frames, the N- and C-terminal R-helices of the horse cytochrome c molecule are indicated. (A) Top-ranking solution from the top 10
docks obtained using the original version of BiGGER (8). This was used as the target for the ternary docking shown in Figure 7E. (B)
Example of a top 10 solution from the hard docking shown in Figure 9A. This was used as the target for the ternary docking shown in
Figure 7D. (C) Top-ranking solution from the soft dock of horse cytochrome c to cytochrome c peroxidase shown in panels B and C of
Figure 9. (D) One of the top 10 ranking solutions of the ternary dock (Figure 9D) of horse cytochrome c to the type I binary target shown
in Figure 8G. (E) One of the top 10 ranking solutions of the ternary dock (Figure 9F) of horse cytochrome c to the type II binary target
shown in Figure 8B.
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horse cytochrome c is also present, a further increase in the
s value is observed (absorbance profile iii of Figure 3). This
can only be explained by horse cytochrome c occupying a
distinct vacant site on the cytochrome c peroxidase surface.
Under these conditions, higher-affinity horse cytochrome c
binding is associated with a Kdvalue of 0.98 µM obtained
by microcalorimetry (9) (Table 1). Using this value, the
occupancy of the higher-affinity horse cytochrome c site in
the ultracentrifugation experiment is predicted to be 76%
which is comparable to the value of 63% obtained by
calculation from the boundary absorbances. This level of
occupancy partially explains the shortfall in the estimate of
Mrfor the ternary complex.
Thus, on the basis of the results of NMR and ultracen-
trifugation and with reference to the binding model proposed
in ref 8, we propose that a ternary complex can be formed
by cytochrome c550binding to a single site at the E heme
and horse cytochrome c binding to a second site between
the two hemes. Horse cytochrome c alone can form a
complex containing two molecules of horse cytochrome c
and one of the peroxidase monomer (9). We propose that
this second site for horse cytochrome c is the E heme site at
which cytochrome c550also binds.
Molecular Docking Simulations. (i) Binary Docks. We
should not believe the molecular docking simulations provide
definitive independent answers; we should view them in the
context of the results obtained by1H NMR spectroscopy and
ultracentrifugation which demonstrate that ternary complexes
can exist and can be interpreted in terms of a peroxidase
surface with two distinct binding sites. As shown previously
(8) and confirmed here in the new hard docking simulation
of Figure 9A, the favored binding surface for the binding of
horse cytochrome c is between hemes, and we propose that
this represents the higher-affinity site observed by micro-
calorimetry. Previously published work had shown that the
favored binding surface for the cytochrome c550 is at the
exposed edge of the E heme (8), and this is confirmed by
the new soft docking experiment depicted in panels A and
B of Figure 7. We propose that this represents the single
site for cytochrome c550 observed by microcalorimetry.
According to the molecular docking simulation, a cytochrome
c550occupying that site can adopt one of two main orienta-
tions (called type I and type II) which are related by a rotation
of 180° about a perpendicular to the molecular surface of
the peroxidase (Figure 8). These may represent real alterna-
tive binding modes.
It is the different geometric relationships between the
cytochrome c550and the horse cytochrome c bound at these
two sites and the E heme of the cytochrome c peroxidase
that give rise to the different patterns of chemical shift
perturbation observed in the downfield-shifted methyl reso-
nances of this heme (8). It was this observation that originally
gave rise to the proposal that two distinct binding sites on
the molecular surface were present.
We have chosen to emphasize the results of the hard
docking for horse cytochrome c and the soft docking for the
cytochrome c550. In the case of the horse cytochrome c, the
same sort of high-ranking between hemes solution is retained
in both the hard and soft docking (Figure 9A,B), but the
soft docking algorithm also retains a very large number of
solutions at the E heme position, none of which have a heme
orientation compatible with electron transfer at the exposed
heme edge (Figure 9C). Thus, in this case, hard docking
retains relevant solutions without the need for the more
permissive procedure of soft docking (which simply intro-
duces a higher level of noise). In the case of the cytochrome
c550, the soft docking also retains a very large number of
solutions at the E heme (Figure 7A), but in this case, a high
proportion of these, including high-ranking solutions, have
heme orientations compatible with electron transfer (Figure
7B). The hemes of the donor cytochromes and the E heme
of the peroxidase have edges exposed at the protein surface
at which we assume electron transfer occurs. A productive
complex will therefore have a juxtaposition of these heme
edges as shown in Figure 8, while Figure 10C, for example,
would not be expected to be productive. Such solutions are
retained in the hard docking (Figure 7C) but to a much
smaller degree. In this case, we would argue that the more
permissive docking is required for a good proportion of these
relevant solutions to be retained. It may be that the different
docking requirements of the two cytochromes reflect the real
difference in their relationship with the peroxidase. One can
argue that the physiological donor, cytochrome c550, has
evolved to form specific salt bridges with the peroxidase
surface and these can only be accommodated in a docking
procedure if flexibility in the position of side chains is
permitted. On the other hand, the nonphysiological donor,
horse cytochrome c, may interact on a more global electro-
static basis, and this can be accommodated by the rigid body
approach of the hard docking algorithm.
FIGURE 11: Analysis of the high-ranking solutions from the soft
docking simulation of cytochrome c550to the peroxidase monomer
(Figure 7A,B). (A) The distance between the iron of the cytochrome
c550and the iron of the electron-transferring heme is shown for the
top 50 ranked solutions. The boxed solutions are those that have
both a high global score and a close approach of the two heme
groups. (B) The global score is shown for the top 50 solutions
expressed relative to that of the top solution (100%). This is a
number derived from the combination of the interaction criteria
described in Materials and Methods.
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Biochemistry, Vol. 42, No. 41, 2003 11979

Page 13

(ii) Ternary Docks. It is clear from the ternary docking
experiments that a binary complex of cytochrome c550and
cytochrome c peroxidase can physically accommodate a
horse cytochrome c in the between hemes site (Figure 9D,F)
and with an orientation (Figure 10D) that resembles high-
ranking solutions of the binary docking of horse cytochrome
c with the enzyme (Figure 10B). It is also clear from the
ternary docking simulations that a binary complex of horse
cytochrome c and cytochrome c peroxidase can physically
accommodate a cytochrome c550in the E heme site (Figure
7D) and with an orientation (Figure 8F) that resembles high-
ranking solutions of the binary docking of cytochrome c550
with the enzyme (Figure 8A-E).
We should emphasize that there are uncertainties in the
process of ternary docking in addition to those encountered
in binary docking simulations. One is that the training of
the program was done using binary complexes. A second is
that it is likely that an incoming ternary partner would
influence the binding of the binary partner. And finally and
probably most importantly, we can see from the results in
panel E of Figures 7 and 9 that the choice of the particular
binary complex as a target can have a dramatic effect on
the results of the ternary docking experiment.
Isothermal Microcalorimetry. The most difficult data to
interpret are those of the microcalorimetry experiments.
Previous ITC experiments (9), also reproduced here, have
shown that horse cytochrome c can bind simultaneously at
two sites on cytochrome c peroxidase, albeit with different
affinities, thus demonstrating the existence of a ternary
complex comprising one cytochrome c peroxidase with two
horse cytochrome c molecules. The question we wish to
address here is whether it is feasible to form a mixed ternary
complex comprising cytochrome c peroxidase, horse cyto-
chrome c, and cytochrome c550. Unfortunately, the ITC data
do not give a clear answer. This is partly because of the
complicated mixture of heat changes that will be occurring
due to probable competition effects and partly because one
cannot design an experiment in which one horse cytochrome
c site is occupied while the other is empty.
In the experiment whose results are depicted in part ii of
Figure 5, in which horse cytochrome c is added to a solution
containing cytochrome c550 and cytochrome c peroxidase,
there are two possible origins for the observed heat changes.
They may represent horse cytochrome c binding to one of
the two sites seen in the absence of cytochrome c550but with
a weakened affinity (Kd) 88 µM) due to the presence of
the latter. The second alternative is that there is competition
between the horse cytochrome c and the cytochrome c550.
These possibilities are now discussed.
If we assume a Kd value of 3.6 µM for the binding of
cytochrome c550(Table 1), we can calculate that, under the
conditions of the experiment whose results are depicted in
part ii of Figure 5, the single cytochrome c550site is 92%
occupied. If horse cytochrome c binding was in competition
with that of cytochrome c550, the binding constant would be
predicted to be altered by a factor of 1 + [I]/KI, where [I] is
the concentration of cytochrome c550and KIis the dissociation
constant for cytochrome c550. Thus, competition at the high-
affinity horse cytochrome c site would be expected to yield
an apparent binding constant of 16.8 µM and competition at
the low-affinity site a binding constant of 106 µM. Since
the actual fit of part ii of Figure 5B is 88 µM, competition
at the lower-affinity site seems to be, at first sight, a feasible
scenario. However, we must remember that the overall heat
change observed would be a composite of the change due
to the binding of horse cytochrome c and the change due to
the dissociation of cytochrome c550. Since the binding of both
is endothermic with similar ∆H values (10.3 and 11.5 kJ/
mol, respectively), the binding of one, coupled to the
dissociation of the other, should be essentially athermic.
Thus, the more likely of the two possibilities would appear
to be that the horse cytochrome c is binding to a second site
on the cytochrome c550-cytochrome c peroxidase binary
complex. However, one surprising feature of this binding is
the weakened affinity, something not suggested by the other
methodologies employed here. A second surprising feature
is the much higher ∆H° value (Table 1) (although this may
be a consequence of the long extrapolation required for fitting
the weaker binding).
Experiments were also performed in the reciprocal mode
with horse cytochrome c already bound to the cytochrome c
peroxidase and cytochrome c550as the titrant. These experi-
ments are more difficult to design satisfactorily because,
unlike the binding of cytochrome c550 to the enzyme,
conditions cannot be created whereby one of the two horse
cytochrome c sites is mostly filled while the other is mostly
empty. With a horse cytochrome to peroxidase ratio of 3.8:1
prior to titration with cytochrome c550, there is no sign of
the endothermic changes associated with binding of cyto-
chrome c550, and this is consistent with the high occupancy
of both its sites by horse cytochrome c under these conditions
(Table 2). This implies the cytochrome c550shares a site with
horse cytochrome c. In contrast, with horse cytochrome c in
the proportion of 1:1 with the peroxidase prior to the titration,
an endothermic binding to 0.35 site with a binding constant
of 4.6 µM is observed, not too different from the Kd for
binding of cytochrome c550 to the peroxidase alone. If
cytochrome c550 is binding to the lower-affinity horse
cytochrome c site, at least part of the heat change that is
observed may, in fact, be due to the horse cytochrome c that
is displaced from this weaker binding site, and then binding
endothermically to the partially occupied higher-affinity site.
It may be that this complexity in the heat changes that are
occurring leads to the observed anomalous molar ratio.
Thus, the evidence for formation of a ternary complex
from these two experiments alone is not strong. Only with
the input of the other methodologies can we be sure that a
ternary complex is present.
Binding Sites and Electron Transfer Sites. What this work
does not address is whether the ternary complexes that are
formed are active in electron transport. When the mixed-
valence enzyme is oxidized by hydrogen peroxide, two
electrons are lost, and these must be replaced by electron
transfer. The presence of distinct binding sites for horse
cytochrome c and cytochrome c550raises the possibility that
the required electrons might be delivered synchronously. In
the case of cytochrome c550, docking at the E heme yields
complexes in which the distance between the iron atoms is
around 16 Å and the heme edges of the two proteins are
virtually touching (Figure 8), an arrangement that is certainly
compatible with the expected geometric constraints of
electron transfer. It is less certain whether the docking of
horse cytochrome c between the two heme groups of the
peroxidase also represents an electron-transferring complex
11980 Biochemistry, Vol. 42, No. 41, 2003
Pettigrew et al.

Page 14

since the iron-iron distances are somewhat larger (Figure
10). Pettigrew et al. (9) addressed the question of whether
the high-affinity binding of horse cytochrome c was produc-
tive in electron transfer and noted that the looser binding to
the site as the ionic strength was increased was associated
with a marked increase in steady state kinetic activity. They
concluded that the higher-affinity binding was, in fact,
nonproductive and that only when that attachment was
loosened could the horse cytochrome c migrate to the true
electron transfer site. If we relate these conclusions to the
docking simulations, we can propose that the between hemes
site is the high-affinity site for horse cytochrome c and is
not an electron transfer site, while the E heme site is the
low-affinity site and is functional in electron transfer. Thus,
the possibility of synchronous delivery of two electrons
appears to be ruled out.
Of course, horse cytochrome c is a nonphysiological redox
partner for Paracoccus cytochrome c peroxidase, but we are
working on the assumption that it may be probing a real
capture surface on the enzyme. The capture of an “active
and waiting” cytochrome c on the molecular surface of the
cytochrome c peroxidase represents a potential mechanism
for physiological rate enhancement. Such a mechanism
whereby a second cytochrome induces a substrate-assisted
dissociation of the first is proposed in the case of the yeast
cytochrome c peroxidase (5). But if that is the case, then it
clearly cannot involve the nonphysiological horse cytochrome
c. Nor can it involve two molecules of the cytochrome c550
since there is no indication from any of the methods used
that two cytochrome c550molecules could be accommodated
on the enzyme at the same time. However, P. denitrificans
does contain pseudoazurin, a second redox protein that is
active as an electron donor to cytochrome c peroxidase (S.
R. Pauleta, unpublished observations). It is possible that a
physiological ternary complex might contain both cyto-
chrome c550 and pseudoazurin with implications for the
mechanism and rate of electron transfer. Current work is
addressing this question. The ready replaceability of the
copper in pseudoazurin with non-redox active metals such
as cadmium opens up the possibility of studying the influence
of the binding of one redox partner on the electron transfer
activity of the other. This is difficult with horse cytochrome
c and cytochrome c550because of the possibility of electron
transfer between the two as well as with the peroxidase itself.
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Ternary Electron Transfer Complexes of ccp
Biochemistry, Vol. 42, No. 41, 2003 11981