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CH-8057 Zurich
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Year: 2008
A survey of the year 2006 literature on applications of isothermaltitration calorimetry
Okhrimenko, O; Jelesarov, I
Okhrimenko, O; Jelesarov, I (2008). A survey of the year 2006 literature on applications of isothermal titrationcalorimetry. Journal of Molecular Recognition, 21(1):1-19.Postprint available at:http://www.zora.uzh.ch
Posted at the Zurich Open Repository and Archive, University of Zurich.http://www.zora.uzh.ch
Originally published at:Journal of Molecular Recognition 2008, 21(1):1-19.
Okhrimenko, O; Jelesarov, I (2008). A survey of the year 2006 literature on applications of isothermal titrationcalorimetry. Journal of Molecular Recognition, 21(1):1-19.Postprint available at:http://www.zora.uzh.ch
Posted at the Zurich Open Repository and Archive, University of Zurich.http://www.zora.uzh.ch
Originally published at:Journal of Molecular Recognition 2008, 21(1):1-19.
A survey of the year 2006 literature on applications of isothermaltitration calorimetry
Abstract
Isothermal titration calorimetry (ITC) is a fast and robust method to determine the energetics ofassociation reactions in solution. The changes in enthalpy, entropy and heat capacity that accompanybinding provide unique insights into the balance of forces driving association of molecular entities. ITCis used nowadays on a day-to-day basis in hundreds of laboratories. The method aids projects both inbasic and practice-oriented research ranging from medicine and biochemistry to physical chemistry andmaterial sciences. Not surprisingly, the range of studies utilizing ITC data is steadily expanding. In thisreview, we discuss selected results and ideas that have accumulated in the course of the year 2006, thefocus being on biologically relevant systems. Theoretical developments, novel applications and studiesthat provide a deeper level of understanding of the energetic principles of biological function areprimarily considered. Following the appearance of a new generation of titration calorimeters, recentpapers provide instructive examples of the synergy between energetic and structural approaches inbiomedical and biotechnological research.
A survey of the year 2006 literature on applications of isothermal titration
calorimetry
Oksana Okhrimenko and Ilian Jelesarov*
Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich,
Switzerland
* Correspondence to: Ilian Jelesarov, Biochemisches Institut der Universität Zürich,
Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. E-mail: [email protected]
SUMMARY
Isothermal titration calorimetry (ITC) is a fast and robust method to determine the
energetics of association reactions in solution. The changes in enthalpy, entropy and heat
capacity that accompany binding provide unique insights into the balance of forces driving
association of molecular entities. ITC is used nowadays on a day-to-day basis in hundreds of
laboratories. The method aids projects both in basic and practice-oriented research ranging from
medicine and biochemistry to physical chemistry and material sciences. Not surprisingly, the
range of studies utilizing ITC data is steadily expanding. In this review we discuss selected
results and ideas that have accumulated in the course of the year 2006, the focus being on
biologically relevant systems. Theoretical developments, novel applications and studies that
provide a deeper level of understanding of the energetic principles of biological function are
primarily considered. Following the appearance of a new generation of titration calorimeters,
recent papers provide instructive examples of the synergy between energetic and structural
approaches in biomedical and biotechnological research.
Keywords: thermodynamics, calorimetry, molecular recognition, ligand binding, enthalpy,
entropy, heat capacity
INTRODUCTION
Recent achievements in structural biology and bioinformatics have deepened our
understanding of the molecular principles of biological function. Biological systems evolve and
are maintained in accord with the laws of chemistry and physics. Indeed, at the molecular level,
highly complex biological processes can be regarded as variations of non-covalent and covalent
interactions. Therefore, descriptive and qualitative information has to be supplemented by
quantitative approaches, both experimental and theoretical, in order to understand why biological
macromolecules function the way they do. Thermodynamics reveals the essential energetic
principles of biological phenomena. It provides a general formalism for describing a system in
terms of its energy. Thanks to the development of commercially available precision instruments,
we now witness a real revival of calorimetry in biological sciences.
Isothermal titration calorimetry (ITC) directly quantifies the heat effects accompanying
association between molecular entities. The principle is compellingly simple. Molecule M1 is
added in small aliquots to the calorimetric cell, which contains the binding partner, M2, and the
heat change associated with each addition is measured. The concentrations are selected so that
the theoretical saturation of the available binding sites varies from < 0.1 to > 2-3 (or more)
during the titration experiment. Equilibrium distribution between free M1, free M2 and their
complex M1:M2 is attained after each addition. The total heat change accumulated after each
addition is proportional to the amount of M1:M2, and, is therefore proportional to the degree of
saturation Y = [M1:M2]/[M 2]tot, very much like the change of a spectroscopic signal at partial
saturation is proportional to the fractional population of molecules in the bound state relative to
the fully (i. e. 100 %) associated state of the system. In contrast to spectroscopic signals,
however, at constant pressure and temperature the accumulated heat is also proportional to the
molar enthalpy of association, ∆HA. (Index “A” stands for “association”.) It follows that
deconvolution of the binding isotherm obtained by ITC allows the simultaneous determination of
the binding constant, ( )[ ]1DA MY1
YK1
K−
== , and of ∆HA. Hence, in a single experiment all
relevant thermodynamic parameters describing the association reaction can be determined, since
the free energy change, ∆GA, is related to KA by ∆GA = −RTlnKA and ∆SA = (∆HA − ∆GA)/T. If
the experiment is repeated at several temperatures, the heat capacity change, ∆Cp, can also be
calculated from ∆Cp = dHA/dT. However, the measured heat changes do not only describe the
binding event per se in terms of the energy accumulated in bonds between M1 and M2. While we
are interested to characterize the energetics of a given reaction (formation of a complex) the
heats measured in the ITC experiment also contain contributions from accompanying processes:
changes in hydration, changes in the number of ions bound to the free components and the
complex, proton uptake/release, conformational transitions, etc, all of which are manifested by
heat changes. The raw data have to be corrected for “unspecific heats” by performing blank
titrations of ligand into buffer and buffer into the macromolecule. Binding-induced changes of
protonation states are relatively frequent, yet cannot be inferred from structural data. pKa
changes are easily detected by ITC if ∆HA is measured as a function of the ionization enthalpy of
the buffer (∆Hbuf) and the data are plotted according to ∆HA = ∆Hbind + nH+∆Hbuf. The slope
yields the number of proton(s), nH+, being taken up or released, and the intercept, ∆Hbind, is the
protonation-independent binding enthalpy [1]. Still, it is important to keep in mind that ∆GA,
∆HA and ∆SA are apparent parameters, and any discussion of their magnitude and any
interpretations invoking details on the underlying physical process should be made with caution.
There are many in-depth reviews covering the theoretical foundation of ITC, the practical
aspects of the method, and the information content of the determined binding parameters [1-7].
Heat release or uptake is a universal property of chemical processes, so that the
experiment does not require introduction of artificial reporter groups or immobilization, and can
be performed under natural conditions. These simple features of the technique explain the
growing interest of the biologically oriented scientific community in using ITC for analyzing the
behaviour and function of biological macromolecules under conditions as close as possible to
their natural milieu. Less than 20 years after the appearance of a new generation of
microcalorimeters, ITC is now used on a day-to-day basis in hundreds of laboratories. The early
excitement of following a binding reaction by monitoring heat changes has been replaced by the
wish of many investigators to explore the method to its limits. ITC is a powerful tool for solving
problems in basic and practice-orientedapplied research. Not surprisingly, the number of
publications reporting ITC data is steadily growing, more complex systems are being explored,
and new applications are constantly being devised.
We have identified 400 papers published in the year 2006 that describe data from ITC
experiments. This number is higher than in the surveys of the years 2002-2005 [8-11] but this
does not necessarily mean that more research projects currently utilize ITC since it might only
reflect the use of new search strategies and increased maintenance of bibliographic databases.
We have searched the literature for “titration calorimetry” and “ITC” appearing as keywords, or
in the text. Records including the abbreviation ITC in a different context have been removed.
Also, papers reviewing or referring to previously published ITC studies have not been
considered, with a few exceptions which provide a deeper level of analysis or improved
understanding of data from a more general perspective [12-14]. However robust and meticulous
the search strategy, and however powerful the search engines, it is impossible to use a single
satisfactory criterion for the inclusion of papers. Our hope is that we have not missed too many
papers and we would like to apologize to colleagues who may be disappointed not to see their
work included in the references.
For the sake of clarity, and in the tradition of previous surveys, the reference list is
divided into subsections:
(i) General subjects and articles cited in the text [1-56].
(ii) Protein-protein. Association between folded proteins is considered [15, 19, 21, 23,
24, 27-33, 35-38, 57-129].
(iii) Protein-peptide. Papers reporting data on binding of unstructured peptides to proteins
are grouped in this section [39, 40, 130-159].
(iv) Protein/peptide-small ligand. The term “small ligands” lumps together various small-
molecular weight ligands, which form a heterogeneous group: nucleotides, sugars
(mono-or oligosaccharides), co-factors, fatty acids, detergents, drugs, etc [12, 16, 34,
41, 42, 51. 160-269].
(v) Protein/peptide-metal[270-300].
(vi) Protein/peptide-nucleic acid [13, 26, 43, 55, 56, 301-316].
(vii) Protein/peptide-polymer [317-322].
(viii) Protein/peptide-lipid [323-334]
(ix) Nucleic acid-small ligands (drugs)[14, 25, 44, 335-353]
(x) Enzyme kinetics [48, 49, 354, 355].
(xi) Miscellaneous. The subjects of the papers in this section are very heterogeneous:
guest-host studies, chelation, complexation between inorganic molecules,
coordination chemistry, micellization, phase transitions, applications in material
sciences, pharmaceutics, etc [45, 356-420].
In the limited space of an annual review, it is impossible to discuss all the studies that have
used ITC data to gain new insights into a specific problem. In the following we will discuss
studies, that opened new paths for applying ITC to complex problems and which illustrate how
ITC can be used to relate energetic changes to the mechanism of underlying biological processes.
Chemists and physicists who deal with inorganic molecules will find relevant papers in the
“Miscellaneous” section. Although this review is focused on biologically oriented topics, many
of these “miscellaneous” studies may provide new ideas on how to apply ITC to the biological
realm.
NEW THEORETICAL DEVELOPMENTS AND NON-STANDARD APPLICATIONS
Analysis of cooperative ligand binding by ITC
Allosteric communication between binding sites is a widespread phenomenon in proteins
and underlies important biological phenomena such as signal transduction, regulation of catalytic
activities, formation of multifunctional assemblages, etc. Binding of one ligand can increase
(positive cooperativity) or decrease (negative cooperativity) the affinity for another ligand.
Velazques-Campoy et al. have presented an exact analysis of heterotropic binding for arbitrary
values of the cooperativity parameter α [15]. For binding of ligands A and B to protein P, the
change in free energy related to the cooperative interaction can be defined as ∆g = −RTlnα =
∆GAB − ∆GA − ∆GB, where ∆GAB, ∆GA and ∆GB are the Gibbs free energy change for formation
of the ternary complex PAB, and the bimolecular complexes PA and PB, respectively. The
cooperative parameter α must be understood as a genuine equilibrium constant which can have
values α = 0 (full negative cooperativity), 0 < α < 1 (negative cooperativity), α = 1 (no
cooperativity) or α > 1 (positive cooperativity). In addition to ∆G, the enthalpy and entropy can
be obtained from an ITC experiment. Therefore, the enthalpic (∆h = ∆HAB − ∆HA − ∆HB) and
entropic (∆s = ∆SAB − ∆SA − ∆SB) contributions to ∆g can be measured. Since ∆h and ∆s are
manifestations of the molecular origins of allostery, the potential of ITC in characterization of
heterotropic interactions has been recognized early and simplified formal approaches to data
analysis have been developed. Typically, binding of ligand A to the macromolecule in the
presence of ligand B in the cell is measured and the data are analyzed by the standard procedure
for single ligand binding to obtain apparent values for the equilibrium constant, Kapp, and for the
enthalpy, ∆Happ, characterizing binding of A in the presence of B. From a series of experiments
with varying concentration of B, the interaction parameters α and ∆h can be estimated by
analyzing the dependence of Kapp and ∆Happ on the concentration of B. Alternatively, α and ∆h
can be obtained by comparing Kapp and ∆Happ measured in the absence of B and in the presence
of saturating concentrations of B. The disadvantages of these approaches are that the free
concentration of B throughout the titration, is not precisely known, many experiments must be
performed and it is difficult to vary the concentration in B over a wide range, especially for
reaching saturation levels when binding of B is weak. Furthermore, depending on the ratio of the
binding constants, the molar enthalpies, and the concentrations used in the experiment, the
Wiseman-type isotherms can be asymmetrical around the inflection mid-point, and well defined
steps may appear, which make it impossible to use a standard analysis. Complicated isotherms
arising from cooperative interactions can be characterized by Bayesian analysis according to a
step-wise binding model to determine the macroscopic constants describing the step-wise
equilibria between stoichiometric states of a receptor [16]. Earlier, exact analytical treatment of
heterotropic binding equilibria have been developed only for the trivial case of α = 1 (no
cooperativity) and for α = 0 (displacement; full negative cooperativity; [17, 18]). Velazques-
Campoy et al. [15] discuss simulations and real experiments with ternary complexes formed
between ferredoxin-NADP+-reductase and the substrates NADP+, ferredoxin and flavodoxin.
They demonstrate that, although mathematically more complex, the analysis provides a
thermodynamically rigorous description of the coupled equilibria. Only three experiments have
to be performed: (i) Binding of A to determine KA and ∆HA, (ii) Binding of B to determine KB
and ∆HB, and (iii) Binding of A in the presence of an arbitrarily chosen concentration of B to
determine α and ∆h. The paper hints at rules for designing experiments and discusses the
conditions which must hold in order to obtain interaction parameters with a high level of
confidence. This work increases the arsenal of tools available to calorimetrists for analyzing the
energetics of ternary interactions. By avoiding the uncertainties that characterize traditional
approaches, it provides a sound foundation for investigating the structural and energetic
mechanisms of allostery.
Velasquez-Campoy [19] has also published a formal description of another complicated
equilibrium phenomenon; namely multiple ligand binding to one-dimensional lattice-like
macromolecule bearing N/l potential binding sites, N and l being the number of homogeneously
distributed lattice points (structural units), and the number of lattice points occupied by the
ligand, respectively. In biology, this situation is not uncommon, since DNA, polysaccharides and
some proteins can be regarded as a one-dimensional lattice. However, the biophysical
characterization of binding equilibria of this type has been attempted only occasionally. The
McGhee-von Hippel general closed form of the Scatchard equation describes the dependence of
the degree of saturation on the free ligand concentration, N, l, the microscopic binding constant,
k, and in the case of cooperative binding, the cooperativity parameter ω [20]. The McGhee-von
Hippel formalism has been used previously to solve specific problems, including analysis of ITC
data. The paper of Velazques-Campoy [19], however, represents a systematic effort to explore
the potential of the derived analytical expression. Next to k, ω and the ligand binding enthalpy,
ITC experiments reveal also the interaction enthalpy associated with the interactions between
neighboring ligands on the lattice, thus providing a deeper level of understanding of the
cooperative process. Numerous simulations are presented in order to illustrate the influence of
different combinations of binding parameters on the shape of the binding isotherms. As some of
the examples show and as the author pointed out, there are situations where analysis is difficult
or uncertain when the data are not very precise, or if additional information on the properties of
the system is not available. It remains to be seen whether this method will find applications in
near future. The systems devised within the framework of the McGhee-von Hippel theory and
the presented extension are very challenging, bearing in mind their size, their largely unspecific
character (implying low affinity and enthalpy), and possibly slow kinetics which are all limiting
factors in ITC experiments.
Conformational transitions in macromolecules
Although ITC is typically used to characterize ligand binding, the method has also been
applied in studies of conformational transitions of macromolecules. Examples are protein
fragment complementation [21], protein folding or peptide coil-to-helix transitions triggered by
pH [22], salts, metals, and ligands, formation of oligomeric proteins by association of subunits
[23, 24], etc. Nucleic acid duplex formation from the isolated strands also represents large scale
conformational transitions amenable to ITC studies. [25]. Some studies published in 2006 are
worth mentioning. Protein fragment complementation studies provide a unique possibility to
investigate the energetic principles governing the hierarchical/modular organization of proteins
in terms of inter-domain versus intra-domain interactions. A good example of the approach can
be found in the paper by Shuman et al [21]. Calmodulin (CaM) is built up from four EF-hand
motifs, which are individually stabilized by Ca2+ and are arranged sequentially in two globular
domains. The reconstitution of the domains from the isolated EF-hand motifs was studied by
ITC. The pair of C-terminal EF-hands (EF3 and EF4) assembles with higher affinity than the N-
terminal pair (EF1 and EF2) but the difference is relatively small (a factor of 15). More
intriguing is the fact that the similar free energy changes are the result of very different enthalpy-
entropy balance. Both complexes are driven by enthalpy changes (at the selected conditions) but
the enthalpy of formation of EF3:EF4 is four times higher than that of EF1:EF2. In contrast,
formation of EF1:EF2 is entropically favored as well, while the total entropy changes oppose
association of FF3 and EF4. The pronounced energetic differences cannot be readily explained
by structural data, since the packing interaction at the interface of the EF-hand motifs within
each CaM domain is essentially identical. The likely explanation is structural differences in the
isolated EF-hand motifs, which are only partly folded, as judged by CD spectroscopy. Even so,
the picture is not totally clear since EF1 and EF2 experience more pronounced refolding within
the EF1:EF2 complex. Intuitively, association-coupled folding is expected to make the reaction
more exothermic and decrease the entropy, but the experiment shows the opposite.
Unfortunately, the paper does not state whether the tabulated parameters have been corrected for
possible contribution from proton uptake or release.
The strength and energetic signature of interactions between the non-covalently
associated subunits of a protein may give clues about the physical-chemical mechanisms that
have led to the appearance and diversification of oligomeric proteins in the face of the
evolutionary pressure. ITC provides a useful alternative to study the energetics of
homooligomers by performing a dilution experiment [2]. The assembled oligomer at high
concentration is injected into the cell containing buffer. Initially, the protein concentration in the
cell is low and the monomeric state is populated predominantly. After additional injections, the
monomer concentration increases and the equilibrium shifts towards the oligomeric state. The
resulting titration curve can be deconvoluted to extract the equilibrium constant and the enthalpy
of oligomerization. This approach has been used by Luke et al. to characterize the assembly of
the heptameric GroES protein from the constituting monomers [23]. As for other proteins in the
family, both the entropy and enthalpy of association are positive, indicating that dehydration of
the inter-subunit interface is the major thermodynamic factor driving the assembly of the
heptamer.
Scolnik et al. have compared the energetics of coil-to-helix transition of poly (L-Glu)24
and poly (D-Glu)24 peptides [22]. Hydrochloric acid was titrated into the calorimetric cell to
lower pH from neutral to acidic. The shift of equilibrium of the peptides from the coil state (at
neutral pH) to the α-helical state (at low pH) was monitored by the associated heat changes. The
onset of the coil-to-helix transition was ~0.3 pH units higher, and proceeded with considerably
higher cooperativity and molar enthalpy in the case of poly (D-Glu)24. This means that poly (D-
Glu)24 helices are more stable than their chiral isomers and are more populated at lower degree of
deprotonation of Glu side chains. The most intriguing observation, however, was that the
differences disappear when the experiment is performed in D2O-H2O (4:1 v/v) mixtures. These
results represent one of the first experimental confirmations that L-amino acids are slightly more
hydrated (i.e. more hydrophilic) than the corresponding D mirror images. Further investigations
are needed to clarify whether the hypothesized minor structural and energetic differences
between peptides (and other compounds) composed of L and D enantiomers could have
represented a thermodynamic advantage in the chiral selection at the early stages of evolution of
organic matter.
Almost all ITC studies of conformational transitions in macromolecules have
concentrated on extracting thermodynamic parameters. Recently, Fanghänel et al. have
investigated more systematically the potential of ITC to yield data on protein folding kinetics
[27]. As a model system they have selected RNase A, one of the best kinetically characterized
proteins to date. The idea of the experiment is to monitor the time-dependent changes of the
differential power signal after folding of the protein has been initiated at the desired buffer
conditions and temperature. For that purpose, after thermal equilibration, the injection syringe is
removed, the protein is injected manually into the cell, the system is reassembled and rotation is
started again. These manipulations disturb the thermal equilibrium, and meaningful data can be
collected after re-equilibration, which in these author’s hands takes 200 to 400 s. In a blank
experiment, the same manipulations are repeated but plain buffer is injected into the cell. The
difference of the two differential power-versus-time traces reflects the time-dependent heat
changes associated with the folding process. At conditions where the native state of RNAse is
marginally stabilized and folding is a simple mono-exponential process, a very reasonable
agreement was obtained between the time constants extracted from ITC data and spectroscopic
data. However, at strongly stabilizing conditions the time constants estimated by ITC for the bi-
phasic folding trace considerably overestimated the spectroscopic data. Further results with
RNAse and short proline-containing peptides demonstrate the potential feasibility of the method
in studies of processes involving proline cis-trans isomerization. There is an additional benefit
from studying folding by ITC. Knowing the time constant(s) from kinetic analysis, the
differential power-versus-time trace can be extrapolated to time zero and the molar enthalpy of
folding can be obtained by integration. Hence, the energetics of protein folding can be
characterized in the temperature range where the native state dominates, without the need of long
extrapolation of thermal melting data. In principle, folding intermediates populated at low
temperatures could be detected in this way. Altogether the paper is intriguing in that it introduces
new tools to study protein folding. However, some notes of caution are in order. First, as in other
kinetic experiments, meaningful time constants can be calculated only when the half time of the
studied process is substantially larger than the dead time of the measurement, which is on the
order of several minutes in this case. Second, a thorough thermal baseline equilibration and
negligible baseline drift should be warranted within the “productive” data collection interval,
both in the genuine and in the control experiments.
Another publication presenting kinetic data acquired by ITC deals with reconstitution of
the heterodimeric protein monellin from its constituent monomeric polypeptide chains [24]. The
experiment for such a system is straightforward: One component is titrated into the cell
containing the counterpart and the heat flow is followed after the system has re-equilibrated. The
reported ITC traces yield data which agree well with spectroscopic data. Unfortunately, little
experimental details are given in the paper, making it difficult to assess the general applicability
of the experimental setup.
DIVERSE APPLICATIONS UTILIZING STANDARD PROTOCOLS
Protein-ligand binding
By far most of the published papers are devoted to characterization of protein-ligand
interactions. Two general types of studies can be distinguished. First, in-depth thermodynamic
description of a particular complex, or of closely related complexes is attempted [for example
see refs. 28-34]. Second, ITC is used to map binding sites and clarify binding modes by
determining the dissociation constants of wild type complexes and designed variants thereof [for
example see refs. 35-42]. An illustration of the latter type of study is the paper by Honnappa et
al. [37]. The interaction between the carboxy-terminal domain of EB1 (EB1c) and the N-
terminal CAP-Gly domain of the dynactin large subunit p150glued (p150n) was studied. The X-ray
structure of the EB1c-p150n complex was solved from a crystal form that proved to be identical
to the one analyzed previously by others. In the asymmetric unit, two p150n molecules contact
the EB1c dimer, thus defining two major contacts between EB1c and p150n, referred to as A and
B. Contact A has been described extensively by Hayashi et al. and put forward as the
biologically relevant contact [37]. On the basis of sequence alignments and earlier biochemical
data, Honnappa et al. hypothesized that contact B is more likely to be the relevant binding spot
in solution. ITC experiments revealed that mutations removing intermolecular interactions within
contact B greatly diminish or abolish binding. The result was confirmed by “positive design”
experiments. An alanine side chain on p150n points to a conserved hydrophobic cavity on EB1c
within contact B and the designed Ala-to-Met replacement caused a 20 fold increase of binding
affinity. In the X-ray structure of the mutant complex the methionine side chain fits into the
EB1c hydrophobic cavity, thereby expelling the four water molecules that are present in the wild
type structure.
Although the described approach is no doubt valid, two potential problems must be
considered. First, straightforward interpretation of the results of mutational studies is only
possible if extensive controls are undertaken to establish that the mutant proteins are correctly
folded. Second, KD changes induced by mutations are often listed and discussed in terms of
corresponding enthalpy and entropy changes, although controls for possible changes in
protonation and other nonspecific effects have not been carried out or are not mentioned. The
absence of such controls may jeopardize conclusions that are drawn regarding the contribution of
individual binding spots to the stability of a complex.
Nucleic acid recognition
Protein-DNA binding is an enigmatic case of macromolecular recognition: The DNA
duplex is structurally monotonous, yet DNA-binding proteins utilize a variety of structural and
thermodynamic strategies for binding. Association is structurally promoted by α-helices, the face
or edges of β-sheets, and loops. Both the major and minor DNA grooves can accommodate
proteins. A protein-DNA complex can be enthalpically or entropically driven at physiological
temperatures, the magnitude of ∆H and ∆S varying in a broad range. Certain classes of proteins
use N-terminal or C-terminal, unstructured extensions to contact DNA. In 2006 a “Tale of tails”
has been narrated by Crane-Robinson et al. [13] who reviewed results from Peter Privalov’s
laboratory [see also ref. 305]. The DNA binding properties of homeodomains, HMG boxes, and
members of the HMGA family, all containing DNA-contacting tails, have been characterized.
The strategy is the following. First, ITC is used in combination with differential scanning
calorimetry to obtain the binding parameters “free” of contributions from temperature-induced
and binding-induced partial refolding. Second, the binding parameters in 1 M NaCl are
determined to separate the electrostatic and non-electrostatic contributions to the energy terms.
Third, the contribution of the DNA-contacting tails is filtered out by comparing the energetic
signatures of complexes formed by proteins containing the extension or truncated domains. The
analysis led to the conclusion that there was no unifying principle. Homeodomain arms
contribute mostly non-electrostatic binding free energy. The purely electrostatic interactions
involving the HMG-box tails confer not only stabilization but neutralize asymmetrically the
phosphate charges in the major groove and promote bending of the DNA duplex. The so-called
AT hooks bind in the minor groove driven in part by electrostatics, yet the main driving force is
the favorable entropy change, i.e. the hydrophobic effect.
Two interesting papers on protein-DNA association are discussed below in the
“Structural parameterization” section.
In view of the ever-growing interest in the development of DNA-binding drugs in
anticancer research, we would like to draw attention to the paper by Jonathan Chairs [14]. This
author compiled a large amount of calorimetric data on binding of small molecules to DNA. The
analysis reveals a very different energetic signature for intercalating and groove-binding
compounds. The binding of intercalators is enthalpically driven, while groove-binding is
entropically driven. Possible molecular origins of the distinctive energetic patterns are discussed.
Furthermore, the author contrasts the enthalpy-entropy fingerprints of small molecules and
DNA-binding proteins.
While dozens of studies address the energetics of protein-DNA recognition, much less is
known about protein binding to RNA. This may change since several reports in 2006 describe
the thermodynamics of RNA binding by proteins and small molecular weight compounds [for
example see references 43 and 44]. Following the increase of structural data accumulated in
recent years, it seems likely that the number of biophysical and calorimetric studies of RNA
binding reactions will also increase.
Lipid/membrane systems
As in other fields of biomolecular research, the applications of ITC in studies of lipid
phases, membranes and mixed protein-lipid/membrane systems also increase steadily. Given the
ongoing multidisciplinary efforts toward a better structural and functional characterization of
membrane proteins, there is no doubt that more ITC studies will be done in the future. A good
example is the work published by Keller et al. [45]. These authors derived a function that can
be used to assess membrane translocation of charged substances. The function is general in the
sense that it unifies ITC release and uptake titrations and makes possible the implementation of
different membrane partitioning models. Electrostatic effects are modeled within the framework
of the Guoy-Chapman theory. The merits of the method have been tested by characterizing the
flip-flop of SDS across the membrane of unilamellar POPC vesicles. Membrane translocation of
charged substances is a ubiquitous phenomenon in biology and the proposed methodology
widens the number of systems that can be analyzed without the need of introducing reporter
groups.
ENZYME KINETICS
The potential of calorimetry to study enzymatic reactions is well established [46]. The
rate of enzymatic reactions is proportional to the heat flow associated with formation or breakage
of chemical bonds. Therefore, the measurement is independent of the existence and properties of
spectroscopically active groups, or of the availability of substrate analogues bearing artificial
spectroscopic tags. The principle, data acquisition and data analysis of kinetic experiments using
ITC to extract Km and kcat of enzymatic reactions have been reviewed [47]. D’Amico et al. have
presented an extension of the standard methodology [48]. While studying the activity of α-
amylases, the authors injected enzyme aliquots into the cell containing the substrate at varying
concentrations instead of making serial additions of substrate to the enzyme solution. Using
enzyme-to-substrate molar ratios sufficiently low to avoid substrate depletion, the steady state
regime is reached. The differential power signal deflects from the thermal baseline (Pi) and
rapidly reaches a plateau (Pr). The reaction rate is proportional to the heat exchange of the
reaction, i.e. to Pr − Pi. Consecutive enzyme additions in the steady state regime cause equally
sized “steps” in the differential power signal, allowing a straightforward check of the linear
dependence of the reaction rate on the enzyme concentration (which should be maintained in the
absence of product inhibition). Decreasing concentrations of substrate lead to a decrease of the Pr
− Pi differences. From the hyperbolic saturation plots of (Pr − Pi) versus [S], Km and Vmax can be
calculated in the usual way by regression analysis using the Michaelis-Menten equation.
Whether this experimental setup is superior to the “standard” protocol remains to be seen, but it
appears that it facilitates easy monitoring of product inhibition and requires less a priori
knowledge or educated guesses to design meaningful experiments, a clear advantage when
studying enzymatic reactions for the first time.
Søren Olsen has published the results of an interesting investigation dealing with the
capability of ITC to measure enzyme kinetics and activity in solutions which cannot be classified
as “ideal”, in the usual way this adjective is used in the biochemical literature [49]. Since
enzyme specificity tends to be very high, the heat flow observed in an ITC experiment conducted
in a complex solution should directly reflect the enzyme activity at fixed pH, temperature,
pressure and salt concentration. Yet the influence of additives that interfere either with the
enzymatic action per se (inhibitors, allosteric regulators, etc), or with the enzyme structure has
never been rigorously tested. The problem is important since enzymes work in a “crowded”
environment in the cell, and many biotechnological processes require addition of highly
concentrated supplements. Using a model system, Olsen studied the activity of hexokinase in
solutions containing very high concentrations of BSA as the crowding agent (up to 300 mg ml–1).
It is noteworthy that the sensitivity of the method was not influenced by the crowded
environment. However, Km, kcat and the enthalpy (∆Hreact) of glucose phosphorylation decreased
as the concentration of BSA increased. This could be interpreted by assuming that the kcat
decrease is probably due to a slower diffusion rate of the product away from the enzyme-product
complex. Considering the decrease of Km, the author discussed the decrease of the activity
coefficient of the enzyme-substrate complex relative to the activity coefficient of the free
enzyme caused by the volume/surface reduction of the former relative to the latter. In view of the
reduction of ∆Hreact, the high BSA concentration might have changed the relative hydration
properties of the substrate and product. Although the paper reaches no definitive conclusion
regarding the molecular origins of the observed effects, the results point to the importance of
hydration effects in modulating the kinetic and thermodynamic parameters of enzymatic
reactions in crowded environments. It is worth noting that the specificity constant of hexokinase
(kcat/Km) is not influenced by the presence of high BSA concentrations. It is not clear whether
this study encountered another case of “compensation behavior”.
DRUG DESIGN
A prime example for the potential of ITC for understanding the principles of molecular
recognition is the field of drug design and optimization [50]. The retroviral protease is a major
target for development of therapeutic strategies against retrovirus-caused syndromes. One of the
hurdles in AIDS therapy is the fast rate of appearance of strains that are drug-resistant to
protease inhibitors (PI). The viral protease is subjected to mutations which compromise severely
its affinity for artificial substrates (i.e. PI) with viable catalytic activity. Most of these mutations
affect non-polar side chains and re-shape the binding pocket without altering the polarity and
charge distribution. As the consequence, inhibitors designed for structural complementarity to
the wild-type binding site are incapable to bind with high affinity, either because enthalpically-
rich interactions become sub-optimal, or because the entropy gain stemming from dehydration of
the binding interface is low within the geometrically altered binding pocket. Ernesto Freire has
published an insightful review on current attempts at overcoming the HIV-1 resistance to
protease inhibitors [12]. His description of the thermodynamic evolution of PI illustrates the
conceptual complementarity between structural information and thermodynamic data. There are
two general energetic mechanisms of preservation of drug potency (in terms of binding affinity)
in the face of the most frequently occurring active site mutations in the HIV-1 protease. First,
small losses in binding enthalpy and binding entropy may still preserve a reasonable affinity.
Second, large enthalpic losses must be compensated by entropy gain, or alternatively,
pronounced enthalpic optimization must over-compensate the entropic expenditure. Cihlar et al.
have reported an interesting illustration of this phenomenon [51]. They have modified two of the
closely related high-affinity HIV-1 protease drugs, amprenavir and TMC-126, by attaching a
phosphonic acid moiety to the drug scaffold in a position that is not buried in the protease-drug
complex. The modified drugs are less affected by common resistance-inducing protease
mutations in antiviral activity assays. ITC experiments revealed that the modification does not
alleviate the enthalpic losses experienced by amrenavir and TMC-126 in the mutated binding
pocket, yet leads to entropic gains. On the basis of structural analysis the authors suggest a
“solvent anchoring” thermodynamic mechanism: The solvent-exposed and favorably hydrated
phosphonate group stabilizes the protease-inhibitor complex, since the inhibitor, being “solvent
anchored” (i.e. being “fixed” in an approximately favorable orientation), can explore a wider
conformational space within the binding pocket. The result is a favorable increase of the binding
entropy. This paper illustrates how an investigation that was conceived to answer certain
questions, may lead to totally new ideas when applied in different context.
The identification of binding sites and the mapping of hot spots within a binding pocket
are key steps in the development of drugs. A study by Ciulli et al. presents a very clear example
of a useful experimental approach [41]. They have used the E. coli ketopantoate reductase as a
model system to probe for the energetically important structural elements that confer affinity and
specificity in binding of the cofactor NADPH. The binding of NADPH-derived fragments to the
wild type protein and binding site mutants thereof was characterized by ITC. Two hot spots were
identified at the opposite ends of the binding cavity. The paper demonstrates the potential of
binding studies using small fragments for exploring the hierarchical structural organization that
determines ligand efficiency and to chemical scaffolds as targets of optimization.
STRUCTURE-ENERGY CORRELATIONS
The advantage of the calorimetric method over other techniques is that it provides a direct
decomposition of the binding free energy into temperature-dependent enthalpic and entropic
components. But even if measured with very high precision, the “generic” ∆HA, ∆SA and ∆Cp,A
(after corrections for (de)protonation and other non-specific effects) are still numbers that
contain no "molecular" information. Real progress in understanding the mechanisms of
macromolecular association can be achieved only if an intimate link is to be established between
energy and structure. Since non-polar and polar contacts exhibit different thermodynamic
signatures, the intuitive and relatively simple approach which has been pursued is to
parameterize the observed quantities in terms of the amount and type of surface buried in a
complex [52, 53]. The idea has been adopted from studies of protein energetics; namely that ∆H,
∆S, and ∆Cp of protein unfolding could be predicted with relatively good precision from the
increase in surface exposure upon disruption of the compact native state [ref. 54 and references
therein]. It is debatable whether the surface-energy correlations found for proteins really take
into account the physics of the underlying process, or whether they simply represent a useful
empirical observation. If such correlations could be established for binding reactions, a deeper
understanding of the forces holding the binding partners together would result and predictions of
the binding profile may become possible, which would be of considerable value in the area of
drug design. Although, there are many examples where structure-energy correlations hold [52,
53], there are also numerous reports about large discrepancies between measured and predicted
values. Several papers published in 2006 re-fuel the debate about how good structure-based
predictions of ∆Cp are, and discuss possible reasons for the observed “anomalous” ∆Cp values.
Kozlov and Lohman report a dramatic example [55]. They have measured binding of the
E. coli SBB tetramer to single-stranded DNA. Previous work of these authors demonstrated large
contributions to the apparent ∆H and ∆Cp from temperature-dependent changes in the
protonation state of protein side chains and base unstacking of DNA. In the much wider
temperature interval studied now, ∆Cp exhibits a strong temperature dependence (which is
usually small and can be neglected). The negative slope of ∆H-versus-T plots decreases upon
temperature increase. Above 35 °C the slope becomes even positive, indicating that ∆Cp changes
not only in magnitude but also its sign. Furthermore, both ∆H and ∆Cp are significantly
influenced by the concentration and type of monovalent anions. The authors propose a
thermodynamic linkage model according to which the measured temperature dependence of ∆H
and ∆Cp can be rationalized by the existence of coupled equilibria: (i) The protein undergoes
temperature- and salt-dependent conformational transition; (ii) Anions preferentially bind to the
protein and are released from the protein-DNA complex; (iii) Net protonation of the protein
occurs. All these processes add enthalpy and heat capacity to the “genuine” ∆H and ∆Cp (an
estimation of the magnitude is attempted in the paper), yet cannot be captured by
parameterization schemes using “fixed” molecular structures. The discussed “anomalies” might
be widely present in protein-DNA recognition. Unfortunately, characterization of DNA binding
over a large temperature interval and at various solvent conditions has been attempted only
occasionally.
Experimental heat capacity changes larger than the structure-based predictions are typical
for protein-DNA complexes. The Klenow polymerase is no exception: ∆Cp determined for the
association to primed-template DNA is twice higher than the expected one on the basis of
surface burial/dehydration [56]. Large ∆Cp of a protein-DNA complex is thought to reflect
sequence-specific binding, since almost all of the nonsequence-specific complexes exhibit small
∆Cp. Interestingly, Klenow polymerase shows no sequential preferences, as all type I
polymerases. Rather, it recognizes the primed-template structure while looking for molecular
reasons which may explain an “extra” ∆Cp, the authors note that Rg of Klenow decreases by ~1
Ǻ upon DNA binding and that the protein conformation is more ordered in certain regions of the
co-crystal structure compared to the non-bound enzyme, indicating compaction within the
protein-DNA complex. However, the decrease in Rg is too small to account for the missing part
of ∆Cp stemming from additional surface burial.
Interesting thoughts on the putative links between structure and energetic changes can be
found in ref. [31]. Cognate and non-cognate complexes of immunity proteins (Im2, Im7, Im8 and
Im9) with the DNAse domains of colicins (E2, E7, E8 and E9) have been characterized by ITC.
Structurally, the Im2/E7, Im7/E7 and Im8/E8 complexes exhibit a higher hydrogen bond density
at the binding interface than the Im9/E9 complex. Furthermore, although the interface areas of
Im7/E7 and Im9/E9 are comparable, the proportion of buried polar surface is higher for Im7/E7.
The specificity determining polar and charged side chains in Im7/E7 are replaced by non-polar
specificity-determining side chains in Im9/E9. Not surprisingly, enthalpic stabilization of the
more polar complexes is stronger, in line with the low enthalpic content of hydrophobic contacts
(at 25 °C). For all cognate pairs, the buried surface-based prediction underestimates the
experimental ∆Cp by a factor of 10. Intriguingly, the most non-polar pair (Im9/E9) has the
smallest ∆Cp, contra to the assumption that the dehydration of non-polar groups dominates the
negative ∆Cp of association. Five and seven water molecules are present at the Im9/E9 and
Im7/E7 interfaces, respectively. Bound water may possibly cause a ∆Cp decrease, but the effect
is too small to explain the experimental observations. The authors suggest as an additional source
of negative ∆Cp, global “rigidification” of the complex structure. The more polar cognate
complexes have a larger favorable ∆H and larger negative ∆Cp than the non-cognate pairs. The
situation is different for E9, where the cognate complex is entropically favored in comparison to
non-cognate complexes, due to the high degree of surface complementarity between non-polar
surfaces. The conclusion is that a high level of discrimination/specificity can be achieved by very
different thermodynamic mechanisms.
CONCLUDING REMARKS
ITC is a fast and robust method to determine the energetics of association reactions in
solution. New theoretical developments help to overcome the intrinsic limitations of the method
and to devise new applications. Both in basic biomedical and biotechnology-oriented research it
is now widely recognized that the magnitude of the changes in enthalpy, entropy and heat
capacity that accompany binding provides unique insights into the balance of forces underlying
biologically-relevant processes. There are conceptual difficulties in interpreting the observed
energetic changes in terms of discrete events at the molecular level and the correlations between
intermolecular contacts and their energetic content are still incompletely understood. The reasons
for this unfortunate situation can be found in the very nature of biological macromolecules, as
well as in the role played by ubiquitous water in tuning the energetics of chemical reactions in
the condensed aqueous phase. Macromolecules are large, cooperative systems which react to
small perturbations in a still largely unpredictable way. Large energetic changes can be caused
by structural changes that are on the limit of sensitivity of structural observations. Nevertheless,
the year 2006 has brought instructive examples of the synergy between energetic and structural
approaches and it seems likely that the coming years will follow the same trend!
Acknowledgments
This work was funded in part by the Swiss National Center of Competence in Research
“Structural Biology”.
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