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ABSTRACT
calorimetry, outline some critical experimental and data analysis aspects, discuss
the latest developments, and give three recent examples of studies published with
respect to macromoleculeligand interactions that have utilized ITC technology.
INTRODUCTION
and was used by Galileo and Drebbel. They independently used a bulb with an
open-ended stem inverted over water to observe the expansion of air. The results
obtained with these so-called thermoscops were very inaccurate, confused with the
effects of barometric pressure and lacking scaling. The next crucial step to make
satisfactory thermometers was the use of (pure) liquids instead of air (water,
ethanol, mercury) in a closed compartment. By the end of the 17th century, a
reliable temperature scale was established by Fahrenheit and Celsius. It was
around this time when the nature of heat and its quantitative aspects became of
interest.
People had speculated on the nature of heat since ancient times. It was a
widespread belief that heat was a substance, some held the view that it was composed
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of atoms. During the 18th century the foundations of calorimetry were laid by
Joseph Black. He preferred an alternative explanation of heat being a fluid that can
be absorbed or squeezed out of bodies and can flow from one place to another. He
recognized that heat applied to melting ice did not change the temperature of the
mixture but was consumed for the solidliquid phase transition, for the first time
clearly discriminating between the strength and amount of heat. Black
introduced the concept of latent heat and showed that quantities of heat could be
estimated from the amount of melted ice. This view brought him to the first
calorimetric experiments with a simple phase-transition calorimeter. A warm probe
was placed in the cavity of an block of ice, covered with a plate of ice and brought to
thermal equilibrium. Furthermore, he adopted the idea of mixing water of different
temperatures (mixing calorimeter) from Brooke Tylor (1723) to determine a series of
latent heats of different substances.
At the same time, A. L. Lavoisier and P. S. Laplace became interested in the
theory of heat. They considered the widespread mixing calorimeters as unsuitable
because of several disadvantages: the need of delicate corrections for the heat
capacity of vessel and thermometer, heat loss by cooling, chemically reacting
substances, inmiscible liquids. Moreover, this method did not allow the
measurement of the heat produced during combustion and other chemical
reactions, and during respiration, topics in which they were mostly interested.
They developed the first convenient phase transition calorimeter that led to
reproducing results. It was a simple but ingenious ice calorimeter, a device for
measuring heat release due to respiration and combustion (Fig. 1). The instrument
consisted of a chamber surrounded by an ice-packed jacket, and the whole device
was further insulated with another ice-packed jacket to improve accuracy. The
amount of water collected from the melted ice of the inner jacket was used as a
measure of the heat evolved in the chamber. The handling was difficult and
experiments could only be performed on days when the outside temperature was a
few degrees above freezing. With this device, Lavoisier and Laplace determined the
specific heat of various substances and found fairly good results compared to
modern standards. The most famous experiments were conducted around 1780,
when Lavoisier and Laplace measured the heat generated by a guinea pig and
determined the amount of carbon dioxide in its exhaled air during the experiment.
They compared it to heat release and carbon dioxide formation when burning
charcoal. The results were accurate enough to conclude that respiration was a form
of combustion.
ORDER REPRINTS
Figure 1. The ice calorimeter of Lavoisier and Laplace (from Oeuvres de Lavoisier, Tome
Premier, Paris, Imprimerie Imperiale, 1862).
Principles of Measurement
The heat quantity is thus proportional to the area under the signal time curve.
The most common type of calorimeter in use is the isoperibol calorimeter, also
called constant temperature environment calorimeter. The vessel is separated by
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ITC Instrumentation
temperature changes in the sample solution of just a few millionths of a degree and
is comparable to the inevitable heat effects of dilution, mixing, and stirring. The
absolute detection limit of the latest generation VP-ITC calorimeter, expressed as
the minimum detectable heat quantity, is reported to be 0.1 mcal (20).
EXPERIMENTAL DESIGN
characteristics of the system of interest, i.e., the expected binding affinity and the
heat effect of the interaction. The appropriate concentration range for the
macromolecule placed in the cell depends on the binding constant of the reaction.
The shape of the binding curve is dependent on the product of the binding constant
KB (in M1) and the molar concentration of macromolecule [MT] being titrated (19):
C KB MT 3
The sensitivity of the shape of the binding isotherm to the dimensionless
parameter C is crucial for determination of the binding constant. At high values for
the so-called C-value (C > 500), the shape of the curve approaches a step function
and becomes increasingly insensitive to changes in KB (Fig. 2). Experience shows
that conditions should be chosen to have a C-value in the range of 10100 for an
accurate determination of KB. Therefore, to measure at these C-values, very strong
1
0
-1
-2
kcal/mol of injectant
-3
-4 C=1
-5
-6 C = KB[MT]
-7
-8
C=10 C=50
-9 C=1000
C=500
-10
-11
0 1 2
Molar Ratio
Figure 2. Simulated calorimetric binding curves illustrating the dependence of the shape of
the curve on the product of the association constant KB and the total macromolecule
concentration MT (C KB [MT]). The curves are simulated for several C-values (as indicated
in the plot) according to Eqs. (16) and (18) for H 10 kcal mol1. For high C-values the
binding isotherms approach a step function, becoming increasingly insensitive to changes
in KB. At low C-values, the binding curve becomes a horizontal trace that yields very little
information about KB, making it necessary to use high macromolecule concentrations to
obtain suitable binding isotherms.
ORDER REPRINTS
higher than that of the protein solution will result in an adequate binding isotherm. If
the ligand is poorly soluble, it is possible to place it in the sample cell and to inject the
macromolecule. As long as the binding stoichiometry is 1:1, either interacting
molecule can act as the titrant without adjusting the binding model. For more
complicated cases where this assumption does not hold, the model must be modified
accordingly (22).
The time between successive injections is another important parameter. If
association is rapid, the instrument baseline will be equilibrated in a short time,
depending on the response time of the calorimeter. Under such conditions 34 min
are sufficient to reach baseline again after injection. In contrast, heat signals of slow
processes require much more time to reach thermal equilibrium. Several other issues
related to experimental design should be mentioned. It is crucial that solutions of
ligand and macromolecule are pure and exactly match with respect to pH, buffer
capacity, and salt concentration. This means that macromolecule and ligand are
preferably dissolved in the same buffer. To achieve this goal, it is good practice to
dialyze the protein prior to the experiment and dissolve the ligand in the dialysis
buffer. This procedure will prevent spurious heat effects resulting from mixing of
different buffers. Both interacting components, often purified from biological
source, must be free of contaminating enzymatic activity that could affect the
association event under investigation. Furthermore, the formation of air bubbles has
to be avoided. Thus it is very important to thoroughly degas all solutions prior to the
experiment. Any air in the syringe can cause variation in the injected volume or lead
to additional heat signals, and bubbles in the sample cell interfere with the thermal
contact of solution and cell wall. Finally, in most experiments the heat effect of the
first injection of a series of injections is obviously too small. This results from
diffusion while equilibrating the system. Even if care is taken to avoid this leakage,
the problem may persist. Therefore it is common practice to make a small first
injection of 1 mL and then to remove the first data point before data analysis.
Control Experiments
Isothermal titration calorimetry not only measures the heat released or absorbed
during binding reactions, but it detects the total heat effect in the calorimetric cell
upon addition of ligand. Thus, the experimental heat effect contains contributions
arising from nonspecific effects, such as dilution of ligand in the buffer, dilution of
ORDER REPRINTS
11
the protein sample, heat of mixing, temperature differences between the cell and the
syringe, and mixing of buffers of slightly different composition. These contributions
need to be determined by performing control experiments in order to extract the heat
of complex formation. This would need at least a further three titrations to measure
these effects (ligand into buffer solution, buffer into protein solution, buffer into
buffer solution). In practice however, the latter contributions are found to be small
and frequently negligible, whereas the heat of ligand dilution may be significant and
needs to be corrected for. Alternatively, if the titration experiment is designed to
ensure complete saturation of the enzyme before the final injection, and if the blank
experiments mentioned above show the heat of ligand dilution to be concentration-
independent, then the nonspecific heat effects can be estimated very well by
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DATA ANALYSIS
The signal monitored by ITC is the differential power applied to the sample cell.
The total heat released or absorbed upon an injection of ligand into the cell
ORDER REPRINTS
Time (min)
-10 0 10 20 30 40 50 60 70 80 90 100
0
A
cal/sec -2
-4
-6
-8
kcal/mole of injectant
0
-2
B
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-4 Ribonuclease A
-6 Single site binding model
-8 KB(105M1) 2.51 0.029
-10 H (kcal/mol) 12.98 0.02
-12 n 0.953 0.001
-14
0.0 0.5 1.0 1.5 2.0 2.5
Molar Ratio [2CMP]/[RNASE A]
Figure 3. Calorimetric data for the exothermic binding of cytidine 20 -monophosphate
(20 CMP) to ribonuclease A (RNase A) at pH 5.5 (0.2 M K-acetate, 0.2 M KCl) and 28 C
(figure kindly provided by Dr. I. Jelesarov). A: raw data obtained for 25 automatic injections
of 5 mL. Concentrations of RNase A and 20 CMP are 0.145 mM and 3.72 mM respectively. The
area of each peak represents the total heat evolved upon addition of a single aliquot of 20 CMP.
B: titration plot derived from the integrated heats of binding, corrected for heats of dilution.
The solid line represents the nonlinear best fit to the data assuming a single-site binding model.
corresponds to the area under the signal vs. time curve (Fig. 3, panel A). The
instrumental baseline and other unspecific heat effects must be carefully subtracted
from the raw data. Experimental data can be presented as a sigmoid plot (differential
mode) or as a hyperbolic saturation curve (integral mode). The differential
mode treats each injection as an independent point and is plotted as heat evolved
per injection vs. total ligand concentration or the ratio of the total ligand
concentration to the concentration of macromolecule (Fig. 3, panel B). In the
integral mode, the total cumulative heat is plotted against the total ligand
concentration. Fitting a binding model to the calorimetric data plotted in either
mode yields equivalent results. Generally, random errors tend to cancel out in the
integral mode, whereas systematic errors tend to be amplified. Comparative
statistical analysis of both modes can give information about the accumulation of
systematic errors (27,28).
13
yield concentrations for the macromolecule [M], ligand [L], or complex [ML]
to calculate KB. Spectroscopic methods are more indirect by detecting an observable
p, the change of which is proportional to the degree of saturation (18,2830).
ITC is the most direct method to measure the heat change on complex formation.
In general, a simple reversible association between a macromolecule M and a
ligand L,
M L $ ML 7
is characterized by its binding constant KB:
ML
KB 8
ML
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where [ML]i is the total concentration of complex after the ith injection.
Evaluation of microcalorimetric data requires the consideration of the
observable response in terms of total ligand added or the total ligand concentration.
Therefore, the binding equations must be expressed as a function of total ligand and
macromolecule concentration:
MT ML M 11
LT ML L 12
where [MT] and [LT] are total macromolecule and ligand concentrations,
respectively, and [M] and [L] are free concentrations of macromolecule and ligand,
respectively. [ML] is the concentration of the formed complex.
In the simplest case of ligand binding, each macromolecule consists of only one
type of binding sites with a finite number of identical noninteracting binding sites,
ORDER REPRINTS
all of which exhibiting the same intrinsic affinity for the ligand. For such a system,
the binding constant KB is given by
KB 13
1 L
where is the fractional saturation and [L] is the concentration of free ligand. It is
related to the total ligand [LT] and macromolecule concentration [MT], by mass
conservation:
L LT nMT 14
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where V0 is the cell volume and H is the molar heat of ligand binding. The
differential heat of the ith injection is
A nonlinear fit based on Eq. (17) to the hyperbolic saturation curve in the
integral mode (Q vs. [LT]) yields the parameters KB, H, and n from a single
experiment. Based on Eq. (18), the titration data can be fitted to the sigmoid
saturation curve in the differential heat mode (qi vs. [LT], or vs. [LT]/[MT]). The same
parameters are obtained.
Similar relationships as described above exist for other models, i.e., a model for
multiple sets of independent binding sites, single set of interacting sites (cooperative
sites), multiple sets of interacting binding sites. By use of statistical thermodynamic
treatment it is possible to deconvolute a binding isotherm of such complex systems
(3133). Instructive examples from the literature demonstrate the strength of this
approach (3438). However, the success strongly depends on the quality and
reliability of the experimental data.
ORDER REPRINTS
15
Often molecular interactions are very tight (>109 M1), and are not accurately
measurable even with the most sensitive calorimeters available. Generally, molecular
interactions occur to some degree in dependence of pH, reflecting the linkage
between the association of a ligand and the binding of protons (proton linkage). The
molecular basis of the linkage is the result of alterations of pKa values of ionizable
amino acid groups concomitant with binding.
If ligand binding is coupled with uptake of a single proton (Fig. 4), the observed
ligand binding constant Kobs is given as
1 KPc 10pH
Kobs Kint 25
1 KPf 10pH
where Kint is the intrinsic binding constant, KPc and KPf are the proton binding
constants for the complex and free form of the protein and are equal to 10 pKa,c and
10 pKa, f, respectively, of the ionizing group (40,41). According to Eq. (25) proton
linkage can be viewed as change in proton affinity, thus protons will either be
released or absorbed due to ligand binding.
If proton transfer occurs during binding, the Hobs is determined by the
ionization enthalpy of the buffer and the enthalpy of binding corrected for
buffer effects see according to Eq. (6), and both the number of protons (nH) and
Kint
M M:L
Kpf Kpc
M+ M:L+
17
the intrinsic binding enthalpy (Hbind) will vary as a function of pH. Thus nH is
given by
nH f c f f 26
c f
where f and f are the fractional saturation of protons at a given pH of the bound
and free protein. In case of a single protonation event, f c and f f can be expressed as
KPc 10pH
fc 27
1 KPc 10pH
and
KPf 10pH
ff 28
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1 KPf 10pH
The change in the number of protons bound by the protein upon binding of the
ligand is the difference between Eqs. (27) and (28):
KPc 10pH KPf 10pH
nH f c f f 29
1 KPc 10pH 1 KPf 10pH
Equation (29) clearly shows that at a minimum of two pH values pKa,c of the
complexed (KPc 10pKa,c) and pKa,f of free protein (KPf 10pKa,f ) can be calculated
by simultaneously solving Eq. (29) for nH determined at the corresponding pH
values, even when the ligand affinity is too tight to be measured (40). In practice, nH
is determined in a series of buffers of different ionization enthalpies as a function of
pH. Equation (29) is used to determine the pKa of the protein in the free and
complexed state. With these values KB at the tight binding conditions can be
calculated by Eq. (25) (40,41). In general this treatment can be applied to more
complicated systems that involve two protons linked with binding (31,41). A similar
approach based on free energy of binding linked to the number of protons
transferred as a function of pH has been developed (39).
The power of the calorimetric approach in evaluating proton linkage lies in the
fact that H can be determined with high precision under conditions where KB is
not measurable, and thus the contributions of the linkage.
The fundamental Eqs. (19) and (20) demonstrate that the equilibrium constant
for a process is related to the standard entropy and enthalpy changes, and to the
absolute temperature. The temperature dependence of the changes in free energy
(G) of the Gibbs-Helmholtz equation for a thermodynamic system is described as
G=T H
2 30
T T
where T is the absolute temperature and H is the reaction enthalpy. Substitution of
Eq. (30) with Eq. (19) yields the familiar vant Hoff equation:
lnKB H
31
1=T R
ORDER REPRINTS
Displacement Experiments
19
Thus, from knowledge of H2obs and K2obs the affinity K2 and binding heat H2
for the tight binding ligand B can be deduced using Eqs. (34) and (35). Both
equations assume that the concentration of B does not change during the
measurment. This can be achieved when B is also present in the syringe solution.
However, it is also possible to include dilution effects into the fitting procedure. An
exact mathematical treatment for the analysis of competition ligand binding using
displacement ITC has recently been published (47).
A restriction to the displacement method occurs when both ligands bind with
exothermic H, as the tight binder will be reduced by the endothermic contribution
of the dissociation of the first ligand. Therefore, it is necessary that the interaction
enthalpies for both ligands differ significantly.
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In several recent publications it has been proposed to dissect binding free energy
into several contributing terms. The total binding free energy contains a contribution
typically associated with the formation of secondary and tertiary structure (van der
Waals interactions, hydrogen bonding, hydration, conformational entropy),
electrostatic and ionization effects, contributions due to conformational transitions,
loss of translational and rotational degrees of freedom, and others that must
be accounted for on an individual basis (4855). For example, an observed G can
be the same for, an interaction with positive S and H (binding dominated by
hydrophobic effect) and an interaction with negative S and H (when specific
interactions dominate). Moreover, interacting systems tend to compensate enthalpic
and entropic contributions to G, making binding free energy relative insensitive to
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Binding Enthalpy
The observed heat effect of a binding reaction is a global property of the whole
system under investigation, reflecting the total heat change in the calorimetric cell
upon addition of ligand. On the one hand, the measured heat contains contribution
from unspecific heat effects, on the other hand, there might be protonation effects
coupled to binding. Therefore it is of outmost importance to determine possible
contributions to the intrinsic binding enthalpy and to correct for them. But even
corrected heat changes are composed of different contributions, which is the reason
why the enthalpy is an apparent or observed (Hobs) quantity (29).
At first appearance, the physical meaning of H seems to be simple: it
represents the changes in noncovalent bond energy occurring during the interaction.
This interpretation is too simple to describe observed H values. The measured
enthalpy must be the result of the formation and breaking of many individual bonds,
since it is barely conceivable to form bonds without breaking any others, especially
in aqueous medium. The enthalpy change of binding reflects the loss of protein
solvent hydrogen bonds and van der Waals interactions, formation of proteinligand
bonds, salt bridges and van der Waals contacts, and solvent reorganization near
protein surfaces. These individual components may produce either favorable or
unfavorable contributions, and the resultant is likely to be smaller than the specific
interactions (30).
From calorimetric studies carried out in water and D2O it was concluded that a
large part of the observed enthalpy change is due to bulk hydration effect (58,59).
Often, water molecules are placed in the complex interface, improving the
complementarity of the complex surfaces and extending H-bond networks. This
can make enthalpies more favorable, but is often counterbalanced by an entropic
penalty (6062). The role of interfacial water was directly examined by lowering
water activity by means of glycerol or other osmolytes. Complexes with a low degree
of surface complementarity and no change in hydration are tolerant to osmotic
pressure (25,6366).
ORDER REPRINTS
21
Besides the unspecific hydration effects, all direct noncovalent bonds at the
binding interface contribute to H, actually reflecting the binding enthalpy in a
strict sense. The dissection of each noncovalent interaction is very difficult since the
net heat effect of a particular bond is the balance between the reaction enthalpy of
the ligand to the macromolecule and to the solvent. Moreover, structural alterations
at the binding site due to the binding event may contribute to the binding enthalpy.
Several mutational approaches have been applied to investigate the energetics of
individual bonds: alanine scanning mutagenesis (67), removal of particular H-bonds
at the active site (68), construction of double mutant cycles (69). However, all these
approaches suffer from the problem that a direct relation between the change in H
and the removal of the corresponding specific contact in the active site cannot be
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Binding Entropy
the contact with solvent results in a large negative Cp. The basis of this observation
is the different behavior of solvent on the surface of a macromolecule and to that in
the bulk, particularly with respect to water molecules interacting with hydrophobic
surfaces. This means that for any process, in which water is released from the
surface, Cp will be substantial and would be proportional to the amount of surface
involved. Through this correlation of Cp and burial of surface area, the heat
capacity provides a link between thermodynamic data and structural information of
macromolecules. Therefore in the last years, there has been considerable progress
in the parameterization of all thermodynamic parameters and the predictions
thereof (82,83).
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EnthalpyEntropy Compensation
Binding Stoichiometry
23
protein quality (unfolded, missfolded). If these systematic errors can be ruled out
and the fitted values for n still deviate significantly from expected values known from
additional independent information, they should be reexamined. It has been
proposed to fit the data to the hyperbolic equation and then to reanalyze them by
means of a double reciprocal plot (30). However, it is recommended to corroborate
stoichiometric data obtained by microcalorimetry with additional independent
information.
Once the model is verified, ITC can be used as an excellent quality control tool
for the analysis of the fractional binding activity of different lots of protein (e.g.,
antibodies), for stability testing (freeze-thaw) and many more (86).
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According to Lee and Richards (95), the solvent-accessible surface area (ASA) is
defined as the surface traced out by the center of a solvent probe (frequently taken as
a sphere with a radius of 1.4 A) as it moves over the surface of the protein. There are
a number of implementations described and used to determine ASA (95,96), and it is
very important to recognize that each implementation yields slightly different results.
The original description of the predicting parameters is based on the Lee and
Richards algorithm as implemented in the program ACCESS, using a probe radius
of 1.4 A and a slice width of 0.25 A, but there exist reparameterized values for other
implementations (82). When performing calculations, it must be assured that the
appropriate parameters are used, because they are dependent on the algorithm used.
ORDER REPRINTS
In the ideal case, structural information will be available for the complex and for
both interacting species, i.e., the free macromolecule and the ligand. This will
account for any structurally defined conformational differences that occur on
binding. If there are no conformational changes linked with the association (rigid
body binding), it is good practice to extract the free state of the protein by removing
the coordinates of the ligand from the complex. However, the assumption of rigid
body binding must be verified by other independent methods because any structural
rearrangement will contribute to the energetics. For the case where binding is linked
to order/disorder of particular regions which are not defined in the coordinate file of
the macromolecule, it may be necessary to add a model of the region. This is
especially found in protein peptide interactions, for which it is necessary to define
a solution structure of the free peptide (73,79).
Calculation of DCp
The largest contribution to the Cp for a binding process arises from
dehydration of protein and ligand surface with negative contributions due to
burial of apolar surfaces (ASAnp) and positive contributions due to burial of polar
surfaces (ASAp). From studies of the dissolution of solid model compounds,
the following relationship has been proposed (77,80):
Cp cnp ASAnp cp ASAp 36
The parameters cnp and cp that are suitable for calculations based on ASAs
determined by different programs are given in Table 1. Equation (36) is used to
predict the Cp for ligand binding.
Calculation of DH
25
Table 1. Empirical parameters for calculation of Cp and H for three different
implementations (units for c in cal K1 (molA2)1; for h in cal (molA2)1; probe radius
1.4 A; slice width 0.25 A).a
a
Values from Ref. (82)
b
Ref. (141)
c
Ref. (95)
d
Ref. (96)
e
Ref. (97).
where ASAp is the change in polar accessible surface area and is negative for a
binding reaction.
Above dissection contains a linear extrapolation of protein unfolding enthalpies
as a function of polar and apolar surface area (77,80,91). A regression analysis at the
medium unfolding temperature of proteins (60 C) minimizes the extrapolation
error and yields the elementary contributions per A2 of apolar (hap) and polar
(hp) surface to the enthalpy function at the reference temperature of 60 C
(Hbind(60 C)):
Hbind 60 C hap ASA hp ASAp 39
Values for hap and hp are given in Table 1. At any other temperature T,
H(T) is given by the standard equation
Hbind T Hbind 60 C CpT 333:15 40
Above calculations were shown to hold reasonably well at predicting the binding
enthalpy for proteinprotein and proteinpeptide interactions, but correlation of
structure and enthalpy has yielded inconsistent results for interactions of small
molecules (MW < 800) with biological macromolecules. A first attempt for empirical
parameterization of H for small ligands has been published recently (97). As a first
ORDER REPRINTS
The intrinsic enthalpy (Hint) reflects the interaction of the ligand with the
protein and corresponds to the situation when ligand and protein adopt the same
conformation in the free and the bound state. These contributions to the enthalpy
are assumed to scale with changes in accessible surface area that can be param-
eterized. Contributions from conformational changes (Hconf) cannot be easily
described in terms of ASA. Hprot contains binding enthalpy that is due to
protonation effects that can and need to be dissected experimentally by performing
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The intrinsic enthalpy is now described in terms of ASA with hap(25) and
hp(25) as the scaling coefficients that yield the elementary contributions per A2
of apolar and polar surface, respectively. The values for hap(25) and hp(25) are
given in Table 1.
In practice, a system under investigation will be analyzed using the scaling
parameters, ASA and leaving Hconf as the only adjustable parameter that needs
to be determined for each protein separately from a training set of known protein
ligand structures. This new approach is based on a HIV-1 protease database and
has been validated by six different datasets for which structural data of complexed
and free protein was available (97).
Calculation of DS
where Ssolv describes the change in entropy resulting from solvent release upon
binding, Sconf is a configurational term reflecting the reduction of rotational
degrees of freedom around torsion angles of protein and ligand. Sr/t entails the loss
of translational and rotational degrees of freedom when a complex is formed from
two molecules free in solution.
The most important contribution to the entropy change arises from the
solvation term (Ssolv), primarily due to burial of apolar surface area and is
approximated for any temperature (T ) by following equation:
Ssolv Cp ln T=TS 44
ORDER REPRINTS
27
where ASAsc,i is the change in ASA of side chain i on binding, and ASAAXA,i is
the ASA of the side chain in an extended Ala-X-Ala tripeptide (82). The summation
is carried out over all side chains participating in the interface. Values for ASAsc,i
are determined from structural data, estimates for ASAAXA,i and Sbu!ex,i (111)
are available, and they have been adapted for different implementations (82).
These data are presented in Table 2.
For interaction processes involving transitions, two additional terms associated
with the backbone entropy (Sbb) and with the entropy of the transition from
ORDER REPRINTS
29
To date, Eq. (48) has not yet been widely applied, and in fact it has only been
tested for the analysis of HIV-1 protease inhibitors. However, for these interactions
k1 was found to be 1.76 cal K1 mol1, whereas k2 equals 0.414 cal K1 mol1
(83,112).
Linkage Effects
Above calculations apply for systems that do not involve linked equilibria. If
binding of a second ligand is coupled to binding of a first one, the contributions
of the second equilibrium must be considered. Protonation linkage is a common
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thermodynamic data has been established. The situation has changed with the
realization that changes in solvent-accessible surface area (ASA) are related to the
thermodynamic parameters. The semi-empirically derived set of structural
energetic parameters (summarized in Table 1), based on the parameterization of
G, H, S, and Cp in terms of ASA, is a promising thermodynamic approach
to drug design.
It is possible now to predict the energetics of folding of a globular protein
(77,80,81,87,89,91) with an accuracy within 912% (82). The parameterization has
reached the state in which accurate predictions of binding energetics is possible as
well, as shown for peptideprotein and proteinprotein association (73,79,93,94),
and also for nonpeptide ligandprotein interactions (112). However, the thermo-
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31
Introduction
Herpes viruses encode their own thymidine kinases, which differ considerably from
the enzyme of the human cellular host (hTK1). While the human enzyme is highly
specific, HSV1 TK is a multifunctional enzyme of broad substrate specificity and
requires low stereo-chemical specificity. Therapeutic applications involving
HSV1 TK make use of the broad substrate diversity of the viral enzyme in the
background of strict substrate selectivity of the host cell enzyme. Therefore, a
detailed thermodynamic analysis of substrate binding to the viral kinase is a
prerequisite for the successful design of new therapeutically useful compounds. ITC
has been used to investigate the thermodynamic parameters of the binding
of thymidine (dT) and adenosine triphosphate (ATP) to wild type and mutated
HSV1 TK (118,119).
In the ternary complex TK:dT:ATP, the substrate dT and the cofactor ATP are
located in separate and well defined binding pockets of the enzyme. Formation of the
ternary enzymesubstrate complex may either proceed through an obligatory
sequential pathway or by a random mechanism. Two sequential pathways are
possible: TK!TK:dT!TK:dT:ATP (reactions (i) and (ii) of Fig. 5), or TK! TK:
ATP!TK:dT:ATP (reactions (iii) and (iv) of Fig. 5). In a random mechanism,
TK TK:dT
(i)
(iii) (ii)
(iv)
TK:ATP TK:dT:ATP
Figure 5. Formation of the ternary enzymesubstrate complex TK:dT:ATP. The two ordered
sequential pathways are (i), plus (ii) and (iii), plus (iv), respectively. In a random binding
mechanism, all four reactions will take place.
ORDER REPRINTS
binding of one substrate is not a prerequisite for binding of the other, and all four
reactions of Fig. 5 can take place. To distinguish between ordered and random
binding, HSV1 TK was titrated with dT and with ATP, respectively. The titration
with dT was characterized by a significant exothermic heat effect. The nonlinear least
squares fit for a single-site binding model gave a KB of 1.9 105 M1 and Hbind
of 19.1kcal mol1 (Table 3). Under identical conditions ATP did not bind to empty
HSV1 TK. An ordered binding mechanism was confirmed by titrating the preformed
TK:dT binary complex with ATP (reaction ii of Fig. 5). The reaction was again
exothermic and yielded a KB of 3.9 106 M1 and Hbind 13.8 kcal mol1.
Moreover, titration of TK with a 1:1 mixture of dT and ATP yielded within error a
heat change corresponding to the sum of the heat changes for reactions (i) and (ii) of
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Fig. 5. The ITC experiment provides the binding constant KB for a single-site
reaction, and G of reactions (i) and (ii) were calculated from Eq. (19). S was
obtained from Eq. (20). Reactions (i) and (ii) were driven by favorable negative
changes in binding enthalpy and strongly opposed by unfavorable entropic
contributions. Although the reaction with the 1:1 mixture of dT and ATP was
more complex, it could still be treated as a single-site reaction if one considered
dT ATP as one ligand. ITC measurements performed in the temperature range of
1025 C showed strong dependence of H and TS on temperature while G was
almost insensitive due to enthalpyentropy compensation. Values of Cp were
calculated from the slopes of the regression lines of Hbind vs. temperature. Binding
of dT to the free enzyme was characterized by Cp of 360 cal K1 mol1. For ATP
binding to the TK:dT complex, Cp of 140 cal K1 mol1 was determined,
and for the titration of the enzyme with a 1:1 mixture of dT and ATP, a Cp
Table 3. Thermodynamic parameters for the binding of thymidine and ATP to HSV1 TK
at pH 7.5 and 25 C.ab Values of H are corrected for protonation effects by Eq. (6).
33
of 510 kcal K1 mol1 was measured. The latter value was very close to the sum
of Cps of reactions (i) and (ii).
The stoichiometry of binding obtained from all experiments was in the range
0.70.8 mol ligand per mol of HSV1 TK monomer. Deviation from a value of 1 was
due to the presence of inactive protein (118).
Protonation Effects
The results for the decomposition of Stot for substrate binding to HSV1 TK are
summarized in Table 4. It is evident that the favorable solvent contribution Ssolv is
overcompensated by the large unfavorable conformational entropy change Sconf.
The contribution by Sr/t is unfavorable but small. In accordance with a
thermodynamic cycle, the decomposed entropy changes of reactions (i) and (ii)
add up to the changes calculated for the titration of the enzyme with the 1:1 mixture
of dT and ATP.
Solvent reorganization provided a substantial gain in binding entropy due to
water release, about 90 cal K1mol1 for dT binding and about 35 cal K1mol1
for ATP binding. This considerable Ssolv is in agreement with fact that
phosphorylation of an acceptor OH-group must occur in the absence of
competing water molecules. After subtracting from Stot the favorable Ssolv
Table 4. Decomposition of entropy changes for substrate binding to HSV1 TK at 25 C.a
term and the small unfavorable cratic Sr/t, a large unfavorable entropic
contribution Sconf remained. Sconf may have two main origins, the first being
freezing of bond rotations, i.e., amino acid side chains which are in direct
contact with the bound substrate or involved in building a closed or more
compact conformation, become less mobile. The other contribution to Sconf is
partial folding or tightening of domains, particularly in the area of substrate
binding. Interdomain movements within the enzyme dimer also can contribute to
Sconf if the HSV1 TK dimer becomes more closed in the substrate-bound form.
An estimation of these contributions according to Eq. (47) showed that
approximately 95% of Sconf may be due to conformational domain movements
and partial folding, or refolding, of domains, in line with the general concept that
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Table 5. Changes of solvent accessible surface area (ASA) caused by substrate binding to
HSV1 TK.a
35
Mutational Studies
The mechanism of the broad substrate diversity observed with HSV TK1 was
investigated by a thorough mutational study, kinetic measurements and ITC. The
residue triad H58/M128/Y172 was identified to confer distinctive binding of an
exceptionally large variety of substrates to HSV TK1 and to guide catalytic
properties. Mutations in this triad (H58L, M128F, Y172F) have been prepared
and were analyzed by ITC (Table 6).
The mutation M128F with a phenylalanine in this position resulted in a
completely inactive enzyme when examined by kinetic measurements and an HPLC
assay. It was shown that the lack of activity for the M128F mutant was not due to
hydrophobic collapse initiated by the mutation, but was the result of disturbed dT
binding (200-fold reduced affinity compared to the wild-type enzyme) that yielded an
unproductive orientation of the substrate. This view is corroborated by the strongly
reduced binding enthalpy, in combination with the more than seven-fold reduction
of unfavorable entropy. It is evident that the major structural changes needed for
catalytic competence, which are induced by dT in wild-type HSV1 TK, could not
take place.
Similar results were found with the double mutant M128F/Y172F. In this
mutant the dT binding site is formed by a double-F sandwich, a particular
Table 6. Thermodynamic data for dT binding in presence of ATP of wild type HSV1 TK and
triad H58/M128/Y172 mutants.
HSV1 TK H (kcal mol1) KB (105 M1) G (kcal mol1) TS (kcal mol1)
Wild type 26.35 0.47 229 146 9.95 0.40 16.4 0.85
M128F 8.14 0.20 1.04 0.10 6.84 0.08 1.30 0.20
M128F/Y172F 3.71 0.08 0.34 0.19 6.14 0.34 2.43 0.42
H58L/M128F/Y172F 19.82 0.13 2.61 0.06 7.38 0.01 12.44 0.14
ORDER REPRINTS
combination that also occurs in various thymidine kinases. In this case even the sign
for the entropy changed, giving evidence for a favorable preformed binding pocket
with a subsequent reduced induced fit movement. However, the hydrogen bonding
network seems to be impaired as deduced from the almost 700-fold reduced dT
affinity as compared to wild-type HSV1 TK.
Sequence alignments show that this double-F combination never occurs with a
histidine at position 58 (HSV1 TK numbering). Subsequently H58 was replaced by
leucine, giving the triple mutant H58L/M128F/Y172F. With this third mutation
enzymatic activity was regained, but the broad substrate diversity was lost since
activity and kinetic studies as well as HPLC assays did not show any activity of the
triple mutant against non-natural substrates. Although the binding affinity is almost
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90-fold reduced, binding enthalpy and entropy adopt similar values as for wild-type
HSV1 TK, indicating restored flexibility of the enzyme.
Conclusion
37
Introduction
Therefore it was concluded that both isocitrate and tricarballylate do not bind to the
citrate binding site.
Depending on the pH, citrate exists in four different species, i.e., H3-citrate,
H2-citrate, H-citrate2, and citrate3 with pK1 3.13, pK2 4.76, and pK3
6.40 (126). In order to determine the preferred ligand species, the pH-dependency of
the citrate binding constant to CitAPHis was determined in the range of pH 4.09.0
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(Table 7). The curve obtained from a plot of log KB vs. pH showed a maximum at
about pH 5.7 and decreased above and below this value, indicating that citrate
binding is linked to ionization events (41). The Hobs and S values were negative
over the pH range studied, showing that binding of citrate to CitAPHis was driven by
the enthalpy change, whereas the entropy change was opposite.
It is very likely that this result can be explained by the assumption that
H-citrate2 is the citrate species responsible for the interaction, as the affinity of
citrate to CitAPHis at different pH values closely reflects the appearance of the
H-citrate2 form at the corresponding pH. As deduced from Table 7, the maximal
affinity was found at pH 5.7 and it decreased above and below this value, similar to
the occurrence of the divalent citrate form. An obvious explanation of this result
is that CitAPHis binds the H-citrate2 species specifically and therefore proton
release has to occur at pH values below pH 5.7 (where the H2-citrate species
becomes dominant) and proton uptake must take place at pH values above
pH 5.7 (where the citrate3 form becomes prevalent). Assuming that the H-citrate2
species is recognized by CitAPHis, four functional groups are available for binding
interactions, i.e., one uncharged and two charged carboxyl groups and the hydroxyl
group. Current crystallographic data of macromolecules involved in binding of
uncomplexed citrate clearly indicate that citrate binding is preferred in the extended
conformation with important interactions of all four functional groups (127130).
KB KD Hobs G TS
pH n (104 M1) (mM) (kcal mol1) (kcal mol1) (kcal mol1)
4.0 0.98 0.01 6.26 1.33 16.7 3.6 24.71 0.04 6.53 0.13 18.18 0.17
5.0 0.85 0.01 38.55 1.25 2.6 0.1 23.37 0.40 7.62 0.02 15.75 0.41
6.0 0.80 0.01 51.65 2.95 1.9 0.1 20.60 0.19 7.79 0.03 12.81 0.15
7.0 0.89 0.01 18.25 0.75 5.5 0.2 18.26 0.05 7.17 0.02 11.08 0.02
8.0 0.85 0.01 9.05 0.09 11.1 0.1 17.52 0.18 6.76 0.01 10.76 0.17
9.0 0.83 0.01 6.47 0.02 15.5 0.1 17.89 0.04 6.56 0.01 11.33 0.04
a
The data represent the mean of two independent experiments. Errors are quoted as standard
deviations for the two repeats of each titration.
ORDER REPRINTS
39
quoted for n, KB, and H are those for the least-squares fit to the binding isotherms in the
individual titrations.
The fact that neither isocitrate nor tricarballylate did bind to CitAPHis showed the
essential role of the hydroxyl group at position C3 in the citrate molecule.
The inhibitory influence of Mg2 ions on citrate binding observed before could
be confirmed by ITC. As shown by the titration experiments presented in Table 8,
increasing Mg2 concentrations resulted in an exponential decrease of the binding
affinity. At 20 mM Mg2, 10-fold reduction of KB was measured. In the context with
the above discussion of the four citrate species at different pH, it became clear that
the reduced binding affinity of citrate in the presence of Mg2 ions was due to Mg2
complexation by citrate3. Using a stability constant of 1585 M1(126) for the
Mgcitrate complex, the preferred Hcitrate2 species is reduced in the presence of
20 mM Mg2 at pH 7.0 to less than 0.01%, and nearly all of the citrate (96.2%) is
complexed as Mgcitrate. Crystallographic data of metal citrate complexes
generally show the hydroxyl group and either one or two of the carboxyl groups
being involved in metal binding (131). This means that the Mgcitrate complex has
to dissociate before the functional groups can interact with CitAPHis. This behavior
is reflected by the occurrence of additional binding enthalpy in the presence of Mg2.
In control experiments the additional amount of binding enthalpy (Hobs) and
entropy (S) corresponded very well to the dissociation heat and entropy of the
Mgcitrate complex. In summary, the pH and Mg2 dependency of citrate binding
to CitAPHis indicated that Hcitrate2 was the preferred binding species in a non-
restricted, extended conformation and that the inhibitory effect of Mg2 was not due
to an interaction with CitAPHis, but only due to complex formation with citrate.
Binding Stoichiometry
All data fitted excellently to a single-site binding model. Analysis of all ITC
experiments for the binding stoichiometry revealed values that varied between
ORDER REPRINTS
0.85 and 0.95 (mean value 0.87 0.06), which was in agreement with independent
binding assays using [14C]-citrate that typically gave values between 0.6 and 0.8
(122). These data clearly show that one molecule of citrate binds per CitAPHis
molecule. Thus deviations from the integer value are most likely due to inaccurate
protein determination and/or to missfolded protein.
Conclusion
In this study the direct thermodynamic approach turned out to be very powerful.
For the first time it was possible to describe the sensory characteristics of the
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periplasmic domain of the sensor kinase CitA, and it could be shown that it
functions as a highly specific citrate receptor that binds citrate in a nonrestricted,
extended conformation with a 1:1 stoichiometry. Measurements at different pH
values shed light on the responsible and preferred ligand species for the receptor. The
displacement studies using the citrate analogs isocitrate and tricarballylate gave
important hints to the essential role of the hydroxyl group at C3. In addition the
inhibitory effect of Mg2 could be very well observed in the ITC experiments, and
the interpretation of the results clearly indicated that CitAPHis is not inhibited due to
a separate receptor-Mg2 interaction, but only due to complex formation with
citrate. ITC was also used to localize important amino acids involved in citrate
binding by studying the influence of point mutations in CitAPHis(132). Just recently,
the crystal structure of CitAPHis in complex with citrate has been solved (133), and
it shows that the findings learned from the thermodynamic data fit very well to
the structural data.
In this part of the review we would like to focus on biological systems that are
difficult to address: membrane bound receptors. In general, the direct thermo-
dynamic approach is also applicable to such systems as long as ligand binding is
accompanied by a significant heat change. The most severe problems to address are
the quantities of receptor that are needed, and the stability and preparation of
concentrated receptor solutions. Membrane associated proteins are intrinsically
difficult to treat and usually need special purification protocols that include
detergents, vesicles and/or liposome containing preparations. At this point it must be
emphasized that ITC instrumentation does not at all exclude the use of such
complicated or even turbid systems. As the preparation of membrane bound
receptor can be solved in a lot of cases, it remains to provide sufficient amounts of
protein. With the latest advances in recombinant DNA technology and procaryotic
as well as eucaryotic expression systems, it has become possible to prepare significant
(i.e., mg) quantities of pure receptors. This means that in the near future more
membrane receptor systems will become amenable to the direct thermodynamic
approach.
To our knowledge the first system to which ITC was applied for investigating
membrane bound proteinligand interaction, was the serine receptor of Escherichia
ORDER REPRINTS
41
coli chemotaxis (134). Two years later followed the thermodynamic work on colicin-
N binding to the trimeric membrane bound porins OmpF, OmpC, and Phoe (135).
Later in 2003 ITC was used to shed light onto human apo- and holo-transferrin
binding to the Neisseria meningitidis transferrin receptor (136). The next section is
dedicated to the most recent example published, in which the interaction
characteristics for the sensory rhodopsin II of Natronobacterium pharaonis with its
cognate transducer are examined using ITC (137). It is a particularly interesting
example for the case of lateral membrane bound receptor interaction. Some
methodological aspects will be discussed since they may serve as starting point for
the development of new projects in this field.
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Introduction
Methodological Aspects
in the syringe; 0.1% DDM in the cell chamber). Titrations were carried out at
22 and 45 C in order to improve signal-to-noise ratios.
KB KD Hobs G S
NpHtrII T (K) (106 M1) (nM) (kcal mol1) (kcal mol1) (cal K1 mol1)
43
Conclusion
functional complex. Such lateral complex formation has only been elucidated in a
few examples. To date there is only rare data available that were primarily gained by
using sedimentation equilibrium and/or analytical ultracentrifugation (140). Of
general interest are those experiments that provide information about the
thermodynamics and kinetics of the transducer binding. This can be accomplished
by using a direct thermodynamic approach. As these data are difficult to determine
for membrane proteins, the present results provide a new approach to study these
interactions using a direct thermodynamic approach by means of ITC. This method
is rarely used so far for the study of membrane protein assembly due to the difficult
nature of the membrane protein family.
To our knowledge this work presents the first calorimetric approach to gain
information about the strength and energetics of lateral binding processes. This is of
general interest because it could be shown that ITC is a suitable method to study
directly membrane protein/protein interactions (137). It will contribute to our
understanding about this class of proteins, although the experiments need to be
performed in a micelle environment.
FUTURE DEVELOPMENTS
As outlined in the text and also shown with the examples, the ITC is a powerful
tool with high informational content that is applicable to various biological and non-
biological systems. A major drawback of first generation instrumentation has been
overcome by markedly increasing the sensitivity in a way that it has now reached a
physical limit. Significant further improvements with respect to sensitivity do not
seem possible in the near future (MicroCal, personal communication). Another
potential approach to decrease sample size may be miniaturization. Integrated
circuit microcalorimeters are being built and may allow the application of ITC to
micro-titre plate formats in the future.
Modern screening processes for drug candidates would profit from development
of high-throughput instruments. This would be a major breakthrough in the
detection of compounds in pharmaceutical chemistry. The current throughput only
allows measuring a limited number of promising candidates from a series which
could lead to missing candidates with unusual and unexpected binding character-
istics worth being further investigated. New calorimetric methods using such
technology are now being developed, and with this new methodology the
ORDER REPRINTS
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