Hydrophobic effect in protein folding and other noncovalent processes involving proteins

Modifying the N-terminus of polyamides: PyImPyIm has improved sequence specificity over f-ImPyIm

Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f-ImPyIm, 1) were synthesized and the biochemical and biophysical chemistry evaluated. These compounds were synthesized with the aim of attaining a higher level of sequence selectivity over f-ImPyIm (1), a previously published strong minor-groove binder. Two compounds possessing a furan or a benzofuran moiety at the N-terminus showed a footprint of 0.5microM at the cognate ACGCGT site (determined by DNase I footprinting); however, the specificity of these compounds was not improved. In contrast, PyImPyIm (4) produced a footprint of 0.5microM but showed a superior specificity using the same technique. When evaluated by thermal melting experiments and circular dichroism using ACGCGT and the non-cognate AAATTT sequence, all compounds were shown to bind in the minor-groove of DNA and stabilize the cognate sequence much better than the non-cognate (except for the non-amido-compound that did not bind either sequence, as expected). PyImPyIm (4) was interesting as the DeltaT(m) for this compound was only 4 degrees C but the footprint was very selective. No binding was observed for this compound with a third DNA (non-cognate, ACCGGT). ITC studies on compound 4 showed exothermic binding with ACGCGT and no heat change was observed for titrating the compound to the other two DNA sequences. The heat capacity (DeltaC(p)) of the PIPI/ACGCGT complex calculated from the hydrophobic interactions and SASA calculations was comparable to the experimental value obtained from ITC (-146calmol(-1)K(-1)). SPR results provided confirmation of the sequence specificity of PyImPyIm (4), with a K(eq) value determined to be 7.1x10(6) M(-1) for the cognate sequence and no observable binding to AAATTT and ACCGGT. Molecular dynamic simulations affirmed that PyImPyIm (4) binds as a dimer in an overlapped conformation, and it fits snugly in the minor-groove of the ACGCGT oligonucleotide. PyImPyIm (4) is an especially interesting molecule, because although the binding affinity is slightly reduced, the specificity with respect to f-ImPyIm (1) is significantly improved.

Coupling of folding and DNA-binding in the bZIP domains of Jun-Fos heterodimeric transcription factor

In response to mitogenic stimuli, the heterodimeric transcription factor Jun-Fos binds to the promoters of a diverse array of genes involved in critical cellular responses such as cell growth and proliferation, cell cycle regulation, embryogenic development and cancer. In so doing, Jun-Fos heterodimer regulates gene expression central to physiology and pathology of the cell in a specific and timely manner. Here, using the technique of isothermal titration calorimetry (ITC), we report detailed thermodynamics of the bZIP domains of Jun-Fos heterodimer to synthetic dsDNA oligos containing the TRE and CRE consensus promoter elements. Our data suggest that binding of the bZIP domains to both TRE and CRE is under enthalpic control and accompanied by entropic penalty at physiological temperatures. Although the bZIP domains bind to both TRE and CRE with very similar affinities, the enthalpic contributions to the free energy of binding to CRE are more favorable than TRE, while the entropic penalty to the free energy of binding to TRE is smaller than CRE. Despite such differences in their thermodynamic signatures, enthalpy and entropy of binding of the bZIP domains to both TRE and CRE are highly temperature-dependent and largely compensate each other resulting in negligible effect of temperature on the free energy of binding. From the plot of enthalpy change versus temperature, the magnitude of heat capacity change determined is much larger than that expected from the direct association of bZIP domains with DNA. This observation is interpreted to suggest that the basic regions in the bZIP domains are largely unstructured in the absence of DNA and only become structured upon interaction with DNA in a coupled folding and binding manner. Our new findings are rationalized in the context of 3D structural models of bZIP domains of Jun-Fos heterodimer in complex with dsDNA oligos containing the TRE and CRE consensus sequences. Taken together, our study demonstrates that enthalpy is the major driving force for a key protein-DNA interaction pertinent to cellular signaling and that protein-DNA interactions with similar binding affinities may be accompanied by differential thermodynamic signatures. Our data corroborate the notion that the DNA-induced protein structural changes are a general feature of the bZIP family of transcription factors.

Ligand binding induces a conformational change in ifnar1 that is propagated to its membrane-proximal domain

The type I interferon (IFN) receptor plays a key role in innate immunity against viral and bacterial infections. Here, we show by intramolecular Förster resonance energy transfer spectroscopy that ligand binding induces substantial conformational changes in the ectodomain of ifnar1 (ifnar1-EC). Binding of IFN alpha 2 and IFN beta induce very similar conformations of ifnar1, which were confirmed by single-particle electron microscopy analysis of the ternary complexes formed by IFN alpha 2 or IFN beta with the two receptor subunits ifnar1-EC and ifnar2-EC. Photo-induced electron-transfer-based fluorescence quenching and single-molecule fluorescence lifetime measurements revealed that the ligand-induced conformational change in the membrane-distal domains of ifnar1-EC is propagated to its membrane-proximal domain, which is not involved in ligand recognition but is essential for signal activation. Temperature-dependent ligand binding studies as well as stopped-flow fluorescence experiments corroborated a multistep conformational change in ifnar1 upon ligand binding. Our results thus suggest that the relatively intricate architecture of the type I IFN receptor complex is designed to propagate the ligand binding event to and possibly even across the membrane by conformational changes.

Computational methods for biomolecular electrostatics

An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate, and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion, and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems, with a particular focus on how computational tools can be used to investigate these types of interactions.

Heat-Capacity Changes in Host–Guest Complexation by Coulomb Interactions in Aqueous Solution

Heat-capacity changes (deltaC(p)0) were determined for the complexation of 1-alkanecarboxylates with protonated hexakis(6-amino-6-deoxy)-alpha-cyclodextrin (per-NH3(+)-alpha-CD) and heptakis(6-amino-6-deoxy)-beta-cyclodextrin (per-NH3(+)-beta-CD). DeltaC(p)0 decreased with an increase in the binding constant (K) and plateaued at K = 4000 M(-1). The complexes of 1-pentanoate, 1-hexanoate, and 1-heptanoate with per-NH3(+)-alpha-CD are classified as the host-guest system in which the size of the guest fits the CD cavity well. In such a system, van der Waals interaction is the major force for complexation, leading to a negative deltaH0 value. Simultaneously, the water molecules around the hydrophobic alkyl chain of the guest and inside the CD cavity are released to the aqueous bulk phase, leading to a positive deltaS0 value. The negative deltaC(p)0 value in such complexation is ascribed to dehydration of the hydrophobic alkyl chain of the guest and extrusion of the water molecules inside the CD cavity. Meanwhile, the complexes that show positive deltaC(p)0 values are characterized by complexation in which the guest molecules are significantly smaller than the CD cavities. In such a case, the complexation is endothermic and driven by the entropy gain. When the guest is much smaller than the CD cavity, the main binding force should be Coulomb interaction. To form an ionic bond, dehydration of the charged groups must occur. This process is endothermic and leads to positive deltaH0 and deltaS0 values. As the top of the CD cavity is capped by a small but hydrophobic alkyl chain, the water molecules inside the CD cavity may form the iceberg structure. This process must be accompanied by a positive deltaC(p)0 value. Hence, the complexation of a small guest with the CD with a large cavity through Coulomb interactions shows positive and large deltaC(p)0 values. These conclusions were applied to the electrostatic binding of proteins with an anionic ligand.

Hydrophobic potential of mean force as a solvation function for protein structure prediction

We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.

Nucleation of an allosteric response via ligand-induced loop folding

The Escherichia coli biotin repressor BirA is an allosteric transcription regulatory protein to which binding of the small ligand corepressor biotinyl-5'-AMP promotes homodimerization and subsequent DNA binding. Structural data indicate that the apo or unliganded repressor is characterized by four partially disordered loops that are ordered in the ligand-bound dimer. While three of these loops participate directly in the dimerization, the fourth, consisting of residues 212-234 is distal to the interface. This loop, which is ordered around the adenine ring of the adenylate moiety in the BirA.adenylate structure, is referred to as the adenylate-binding loop (ABL). Although residues in the loop do not interact directly with the ligand, a hydrophobic cluster consisting of a tryptophan and two valine side-chains assembles over the adenine base. Results of previous measurements suggest that folding of the ABL is integral to the allosteric response. This idea and the role of the hydrophobic cluster in the process were investigated by systematic replacement of each side-chain in the cluster with alanine and analysis of the mutant proteins for small ligand binding and dimerization. Isothermal titration calorimetry measurements indicate defects in adenylate binding for all ABL variants. Additionally, sedimentation equilibrium measurements reveal that coupling between adenylate binding and dimerization is compromised in each mutant. Partial proteolysis measurements indicate that the mutants are defective in ligand-linked folding of the ABL. These results indicate that the hydrophobic cluster is critical to the ligand-induced disorder-to-order transition in the ABL and that this transition is integral to the allosteric response in the biotin repressor.

Heat capacity and compactness of denatured proteins

One of the striking results of protein thermodynamics is that the heat capacity change upon denaturation is large and positive. This change is generally ascribed to the exposure of non-polar groups to water on denaturation, in analogy to the large heat capacity change for the transfer of small non-polar molecules from hydrocarbons to water. Calculations of the heat capacity based on the exposed surface area of the completely unfolded denatured state give good agreement with experimental data. This result is difficult to reconcile with evidence that the heat denatured state in the absence of denaturants is reasonably compact. In this work, sample conformations for the denatured state of truncated CI2 are obtained by use of an effective energy function for proteins in solution. The energy function gives denatured conformations that are compact with radii of gyration that are slightly larger than that of the native state. The model is used to estimate the heat capacity, as well as that of the native state, at 300 and 350 K via finite enthalpy differences. The calculations show that the heat capacity of denaturation can have large positive contributions from non-covalent intraprotein interactions because these interactions change more with temperature in non-native conformations than in the native state. Including this contribution, which has been neglected in empirical surface area models, leads to heat capacities of unfolding for compact denatured states that are consistent with the experimental heat capacity data. Estimates of the stability curve of CI2 made with the effective energy function support the present model.

Strategies for targeting HIV-1 envelope glycoprotein gp120 in the development of new antivirals

The efficacy of highly active antiretroviral therapy for the treatment of HIV-1/AIDS is continuously threatened by viral mutations that lower the potency of one or more of its components and by the occurrence of severe side effects that lead to poor patient compliance. There is an urgent need for the development of drugs against new viral targets. Among the most attractive targets for drug development is the viral envelope glycoprotein gp120, responsible for the initial step in viral infection. gp120 binds to the cell surface receptor CD4 and initiates the cascade of events that culminates with the entry of the virus into the cell. Two classes of drugs are being developed against gp120, drugs that block the attachment of the virus and drugs that inhibit the subsequent activation mechanism. Both approaches are discussed in this article.

A Swift All-Atom Energy-Based Computational Protocol to Predict DNA−Ligand Binding Affinity and ΔTm

A hybrid molecular mechanics-statistical mechanics-solvent accessibility-based computational protocol is developed to calculate DNA-ligand binding affinity without any database training and is validated on 50 DNA-ligand complexes. The calculated binding energies yield high correlation coefficients of 0.95 (R2 = 0.90) and 0.96 (R2 = 0.93) in linear plots against experimental binding free energies (DeltaGo) and DeltaTm, respectively. The protocol is translated into a swift, web-enabled, freely accessible computational tool, http://www.scfbio-iitd.res.in/preddicta, for DeltaGo and DeltaTm prediction for DNA-ligand complexes to aid and expedite rational drug design attempts.

Uptake and release protocol for assessing membrane binding and permeation by way of isothermal titration calorimetry

The activity of many biomolecules and drugs crucially depends on whether they bind to biological membranes and whether they translocate to the opposite lipid leaflet and trans aqueous compartment. A general strategy to measure membrane binding and permeation is the uptake and release assay, which compares two apparent equilibrium situations established either by the addition or by the extraction of the solute of interest. Only solutes that permeate the membrane sufficiently fast do not show any dependence on the history of sample preparation. This strategy can be pursued for virtually all membrane-binding solutes, using any method suitable for detecting binding. Here, we present in detail one example that is particularly well developed, namely the nonspecific membrane partitioning and flip-flop of small, nonionic solutes as characterized by isothermal titration calorimetry. A complete set of experiments, including all sample preparation procedures, can typically be accomplished within 2 days. Analogous protocols for studying charged solutes, virtually water-insoluble, hydrophobic compounds or specific ligands are also considered.

Thermal Stability of Humicola insolens Cutinase in aqueous SDS

Cutinase from Humicola insolens (HiC) has previously been shown to bind anomalously low amounts of the anionic surfactant sodium dodecylsulfate (SDS). In the current work, we have applied scanning and titration calorimetry to investigate possible relationships between this weak interaction and the effect of SDS on the equilibrium and kinetic stability of HiC. The results are presented in a "state-diagram," which specifies the stable form of the protein as a function of temperature and SDS concentration. In comparison with other proteins, the equilibrium stability HiC is strongly decreased by SDS. For low SDS concentrations (SDS:HiC molar ratio, MR < 8) this trait is also found for the kinetically controlled thermal aggregation of the protein. At higher MR, however, SDS stabilizes noticeably against irreversible aggregation. We suggest that this relies on electrostatic repulsion of the increasingly negatively charged HiC-SDS complexes. The combined interpretation of calorimetric and binding data allowed the calculation of the changes in enthalpy and heat capacity for the association of HiC and SDS near the saturation point. The latter function was about -410 J mol(-1) K(-1) or similar to the heat capacity change for micelle formation (-470 J mol(-1) K(-1)). This suggests that SDS is hydrated to a similar extent in the micellar and protein associated forms. The results are discussed in terms of the Wyman theory for linked equilibria. Quantitative analysis along these lines suggests that the reversible thermal unfolding of the protein couples to the binding of 2-3 additional SDS molecules. This corresponds to a 15-20% increase in the binding number. Wyman theory also rationalizes relationships between low affinity and high susceptibility observed in this study.

Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein complexes in cell signaling

Multisite interactions and the formation of ternary or higher-order protein complexes are ubiquitous features of protein interactions. Cooperativity between different ligands is a hallmark for information transfer, and is frequently critical for the biological function. We describe a new computational platform for the global analysis of isothermal titration calorimetry (ITC) data for the study of binary and ternary multisite interactions, implemented as part of the public domain multimethod analysis software SEDPHAT. The global analysis of titrations performed in different orientations was explored, and the potential for unraveling cooperativity parameters in multisite interactions was assessed in theory and experiment. To demonstrate the practical potential and limitations of global analyses of ITC titrations for the study of cooperative multiprotein interactions, we have examined the interactions of three proteins that are critical for signal transduction after T-cell activation, LAT, Grb2, and Sos1. We have shown previously that multivalent interactions between these three molecules promote the assembly of large multiprotein complexes important for T-cell receptor activation. By global analysis of the heats of binding observed in sets of ITC injections in different orientations, which allowed us to follow the formation of binary and ternary complexes, we observed negative and positive cooperativity that may be important to control the pathway of assembly and disassembly of adaptor protein particles.

Energetics in correlation with structural features: the case of micellization

Understanding micellization processes at the molecular level has direct relevance for biological self-assembly, folding, and association processes. As such, it requires complete characterization of the micellization thermodynamics, including its correlation with the corresponding structural features. In this context, micellization of a series of model non-ionic surfactants (poly(ethylene glycol) monooctyl ethers, C(8)E(gamma)) was studied by isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). The corresponding structural properties of C(8)E(gamma) micelles were investigated by small-angle X-ray scattering (SAXS). The C(8)E(gamma) micellization, characterized independently from ITC, DSC, and structural data, reveals that deltaH(M)(o) > 0, deltaS(M)(o) > 0, and deltaC(P)(M)(o) < 0, while the dissection of its energetics shows that it is primarily governed by the transfer of 20-30 C(8) alkyl chains from aqueous solution into the nonpolar core (r approximately 1.3 nm) of the spherical micelle. Moreover, thermodynamic parameters of micellization, estimated from the structural features related to the changes in solvent-accessible surface areas upon micellization, are in a good agreement with the corresponding parameters obtained from the analysis of ITC and DSC data. We have shown that the contributions to deltaS(M)(o) other than from hydration (deltaS(M)(other)(o)), estimated from experimental data, appear to be small (deltaS(M)(other)(o) < 0.1 deltaS(M)(other)(o)) and agree well with the theoretical estimates expressed as a sum of the corresponding translational, conformational, and size contributions. These deltaS(M)(other)(o) contributions are much less unfavorable than those estimated for a rigid-body association, which indicates the dynamic nature of the C(8)E(gamma) micellar aggregates. the dynamic nature of the C8EY micellar aggregates.

Volume and hydration changes of DNA–ligand interactions

We report the volumetric and other thermodynamic properties of ethidium bromide (EB), propidium iodide (PI) and daunomycin (DAU) intercalating with poly(dA).poly(dT), poly[d(A-T)].poly[d(A-T)], and poly[d(G-C)].poly[d(G-C)], respectively, as well as minor groove binder Hoechst 33258 binding with poly[d(A-T)].poly[d(A-T)]. The data were obtained using fluorescence titration and hydrostatic pressure measurements. Our thermodynamic data are combined with enthalpies from literature reports to analyze the thermodynamic characteristics of the different interactions. The differences are interpreted based on three processes related to hydration: I. burial of non-polar hydrophobic solvent accessible surface, II. burial of polar surface and formation of solute-solute H-bonds, and III. disruption of "structural" hydration. Sequence dependent conformational changes may also be important when comparing ligand binding to different DNA sequences. We conclude that a combination of different thermodynamic parameters, especially volume change, is essential in order to understand the role of hydration in the energetics of DNA-ligand interactions.

Rigidification of a flexible protease inhibitor variant upon binding to trypsin

The Tyr35-->Gly replacement in bovine pancreatic trypsin inhibitor (BPTI) has previously been shown to dramatically enhance the flexibility of the trypsin-binding region of the free inhibitor and to destabilize the interaction with the protease by about 3 kcal/mol. The effects of this replacement on the enzyme-inhibitor interaction were further studied here by X-ray crystallography and isothermal titration calorimetry (ITC). The co-crystal structure of Y35G BPTI bound to trypsin was determined using 1.65 A resolution X-ray diffraction data collected from cryopreserved crystals, and a new structure of the complex with wild-type BPTI under the same conditions was determined using 1.62 A data. These structures reveal that, in contrast to the free protein, Y35G BPTI adopts a conformation nearly identical with that of the wild-type protein, with a water-filled cavity in place of the missing Tyr side-chain. The crystallographic temperature factors for the two complexes indicate that the mutant inhibitor is nearly as rigid as the wild-type protein when bound to trypsin. Calorimetric measurements show that the change in enthalpy upon dissociation of the complex is 2.5 kcal/mol less favorable for the complex containing Y35G BPTI than for the complex with the wild-type inhibitor. Thus, the destabilization of the complex resulting from the Y35G replacement is due to a more favorable change in entropy upon dissociation. The heat capacity changes for dissociation of the mutant and wild-type complexes were very similar, suggesting that the entropic effects probably do not arise from solvation effects, but are more likely due to an increase in protein conformational entropy upon dissociation of the mutant inhibitor. These results define the biophysical role of a highly conserved core residue located outside of a protein-binding interface, demonstrating that Tyr35 has little impact on the trypsin-bound BPTI structure and acts primarily to define the structure of the free protein so as to maximize binding affinity.

Molecular Mapping of the Chloride-binding Site in von Willebrand Factor (VWF)

Physiological concentrations of NaCl inhibit the hydrolysis of von Willebrand factor (VWF) by ADAMTS-13. This effect is because of the specific binding of chloride ions to VWF. Urea-induced unfolding was measured in the presence of NaCl, CH3COONa, and NaClO4 at pH 8.0, 25 degrees C, for multimeric VWF, the recombinant A1-A2-A3 VWF domains, and the A1 domain. Chloride stabilizes the folded conformation of the A1-A2-A3 and A1 domains more efficiently than acetate but less strongly than perchlorate. Spectroscopic evidence showed that chloride binds to both the A1 and A1-A2 domain but not to the isolated A2 domain. Binding of Cl- to both wild type (WT) and the natural mutant p.R1306W A1-A2-A3 domains of VWF has a large heat capacity change equal to -1 and -0.4 kcal mol(-1) K(-1) for WT and p.R1306W A1-A2-A3 domains, respectively. This result implies that a burial of a vast apolar surface area is caused by conformational transitions linked to chloride binding. At any temperature, chloride affinity was higher for WT than for the mutant p.R1306W form. Chloride ions inhibit hydrolysis by ADAMTS-13 of the A1-A2-A3 and A1-A2 domains in the presence of either urea or high shear stress, whereas this effect was either absent or negligible in experiments using A2 and A2-A3 domains. These findings show that the A1 domain contains the binding site of chloride ions that control allosterically the proteolysis by ADAMTS-13 of the Tyr1605-Met1606 bond in the A2 domain and that the R1306W mutation of type 2B VWD quenches the binding of chloride ion to the A1 domain.

A molecular mechanism for osmolyte-induced protein stability

Osmolytes are small organic compounds that affect protein stability and are ubiquitous in living systems. In the equilibrium protein folding reaction, unfolded (U) native (N), protecting osmolytes push the equilibrium toward N, whereas denaturing osmolytes push the equilibrium toward U. As yet, there is no universal molecular theory that can explain the mechanism by which osmolytes interact with the protein to affect protein stability. Here, we lay the groundwork for such a theory, starting with a key observation: the transfer free energy of protein backbone from water to a water/osmolyte solution, Deltagtr, is negatively correlated with an osmolyte's fractional polar surface area. Deltagtr measures the degree to which an osmolyte stabilizes a protein. Consequently, a straightforward interpretation of this correlation implies that the interaction between the protein backbone and osmolyte polar groups is more favorable than the corresponding interaction with nonpolar groups. Such an interpretation immediately suggests the existence of a universal mechanism involving osmolyte, backbone, and water. We test this idea by using it to construct a quantitative solvation model in which backbone/solvent interaction energy is a function of interactant polarity, and the number of energetically equivalent ways of realizing a given interaction is a function of interactant surface area. Using this model, calculated Deltagtr values show a strong correlation with measured values (R = 0.99). In addition, the model correctly predicts that protecting/denaturing osmolytes will be preferentially excluded/accumulated around the protein backbone. Taken together, these model-based results rationalize the dominant interactions observed in experimental studies of osmolyte-induced protein stabilization and denaturation.

Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein

The trp RNA-binding attenuation protein (TRAP) functions in many bacilli to control the expression of the tryptophan biosynthesis genes. Transcription of the trp operon is controlled by TRAP through an attenuation mechanism, in which competition between two alternative secondary-structural elements in the 5' leader sequence of the nascent mRNA is influenced by tryptophan-dependent binding of TRAP to the RNA. Previously, NMR studies of the undecamer (11-mer) suggested that tryptophan-dependent control of RNA binding by TRAP is accomplished through ligand-induced changes in protein dynamics. We now present further insights into this ligand-coupled event from hydrogen/deuterium (H/D) exchange analysis, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC). Scanning calorimetry showed tryptophan dissociation to be independent of global protein unfolding, while analysis of the temperature dependence of the binding enthalpy by ITC revealed a negative heat capacity change larger than expected from surface burial, a hallmark of binding-coupled processes. Analysis of this excess heat capacity change using parameters derived from protein folding studies corresponds to the ordering of 17-24 residues per monomer of TRAP upon tryptophan binding. This result is in agreement with qualitative analysis of residue-specific broadening observed in TROSY NMR spectra of the 91 kDa oligomer. Implications for the mechanism of ligand-mediated TRAP activation through a shift in a preexisting conformational equilibrium and an induced-fit conformational change are discussed.

Specific DNA binding by the homeodomain Nkx2.5(C56S): detection of impaired DNA or unfolded protein by isothermal titration calorimetry

Titrations of specific 18-bp duplex DNA with the cardiac-specific homeodomain Nkx2.5(C56S) have utilized an ultrasensitive isothermal titration calorimeter (ITC). As the free DNA nears depletion, we observe large apparent decreases in the binding enthalpy when the DNA is impaired or when the temperature is sufficiently high to produce some unfolding of the free protein. Either effect can be attributed to refolding of the biopolymer that occurs as a result of stabilization due to the large favorable change in free energy on the homeodomain binding to DNA (-49.4 kJ/mol at 298 K). In either case, thermodynamic parameters obtained in such ITC experiments are unreliable. By using a lower temperature (85 vs. 95 degrees C) during the annealing of complementary DNA strands, damage of the 18-bp duplex DNA (T(m) = 72 degrees C) is avoided, and titrations with the homeodomain are normal at temperatures from 10 to 40 degrees C when >95% of the protein is folded. Under the latter conditions, the heat capacity plot is linear with a DeltaC(p) value of -0.80 +/- 0.03 kJ K(-1) mol(-1), which is more negative than that calculated from the burial of solvent accessible surface areas (-0.64 +/- 0.05 kJ K(-1) mol(-1)), consistent with water structures being at the protein-DNA interfaces.

Proton exchange coupled to the specific binding of alkylsulfonates to serum albumins

We have applied isothermal titration calorimetry to investigate the linkage between ligand binding and the uptake or release of protons by human serum albumin (HSA) and bovine serum albumin (BSA). The ligands were sodium decyl sulfate (SDeS) and sodium dodecyl sulfate (SDS). Within a certain temperature range, the binding isotherm could be clearly resolved into two classes of sites (high affinity and low affinity) and modeled assuming independence and thermodynamic equivalence of the sites within each class. Measurements at pH 7.0 in different buffer systems revealed that the binding of SDS to the high affinity sites did not couple to any exchange of protons in either of the proteins. Saturation of the 6-8 low affinity sites for SDS, on the other hand, brought about the release of two protons from both HSA and BSA. In addition to elucidating the pH dependence of ligand binding, this analysis stressed that binding enthalpies for the low affinity sites measured by calorimetry must be corrected for effects due to the concomitant protonation of the buffer. The shorter ligand SDeS bound to HSA with a comparable stoichiometry but with four times lower affinity. Interestingly, no proton linkage was observed for the binding of SDeS. An empirical structural analysis suggested that His 242 in site 7 (of HSA) is a likely candidate for one of the proton donors.

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks-Chandler-Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces.

Structural cooperativity in spectrin type repeats motifs of dystrophin

Dystrophin is a member of the spectrin family of proteins, which are characterized as being predominantly composed the spectrin-type-repeat, a triple alpha-helical bundle motif present in multiple tandem copies, producing a rod-like shape. Whether or not this motif, which is determined by sequence homology, is correlated with biophysical domains in the intact protein is uncertain. The nature of the domain structure impacts the flexibility and shape of the rod region of this protein, which is a target for modification in several therapeutic approaches aimed at Duchenne Muscular Dystrophy, a common and fatal genetic disease caused by defective dystrophin. We examined three such motifs in dystrophin, expressing them recombinantly both singly and in tandem, and studying their thermodynamic properties by solvent and thermal denaturation. We have found that the degree to which they are independently stable and expressible varies considerably. The fourth motif appears to be largely stable and independent, whereas the third and second motifs interact strongly.

Binding-linked protonation of a DNA minor-groove agent

The energetics for binding of a diphenyl diamidine antitrypanosomal agent CGP 40215A to DNA have been studied by spectroscopy, isothermal titration calorimetry, and surface plasmon resonance biosensor methods. Both amidines are positively charged under experimental conditions, but the linking group for the two phenyl amidines has a pK(a) of 6.3 that is susceptible to a protonation process. Spectroscopic studies indicate an increase of 2.7 pK(a) units in the linking group when the compound binds to an A/T minor-groove site. Calorimetric titrations in different buffers and pH conditions support the proton-linkage process and are in a good agreement with spectroscopic titrations. The two methods established a proton-uptake profile as a function of pH. The exothermic enthalpy of complex formation varies with different pH conditions. The observed binding enthalpy increases as a function of temperature indicating a negative heat capacity change that is typical for DNA minor-groove binders. Solvent accessible surface area calculations suggest that surface burial accounts for about one-half of the observed intrinsic negative heat capacity change. Biosensor and calorimetric experiments indicate that the binding affinities vary with pH values and salt concentrations due to protonation and electrostatic interactions. The surface plasmon resonance binding studies indicate that the charge density per phosphate in DNA hairpins is smaller than that in polymers. Energetic contributions from different factors were also estimated for the ligand/DNA complex.

Designing allosteric peptide ligands targeting a globular protein

Patented signal analytic algorithms applied to hydrophobically transformed, numerical amino acid sequences have previously been used to design short, protein-targeted, L or D retro-inverso peptides. These peptides have demonstrated allosteric and/or indirect agonist effects on a variety of G-protein and tyrosine kinase coupled membrane receptors with 30% to over 80% hit rates. Here we extend these approaches to a globular protein target. We designed eight peptide ligands targeting an ELISA antibody responsive protein, beta-galactosidase, betaGAL. Three of the eight 14mer peptides allosterically activated betaGAL with ELISA methodology. Using Bayesian statistics, this 38% hit rate would have occurred 2 x 10(-9) by chance. These peptides demonstrated binding site competitive or noncompetitive interactions, suggesting allosteric site multiplicity with respect to their betaGAL binding-mediated ELISA signal. Kinetic studies demonstrated the temperature dependence of the betaGAL peptide binding functions. Using the van't Hoff relation, we found evidence for enthalpy-entropy compensation. This relation is often found for hydrophobic interactions in aqueous media, and is consistent with the postulated hydrophobic series encoding underlying our protein-targeted, peptide design methods. It appears that our algorithmic, hydrophobic autocovariance eigenvector template approach to the design of allosteric peptides targeting membrane receptors may also be applicable to the design of peptide ligands targeting nonmembrane involved globular proteins.

Ligand-induced thermostability in proteins: thermodynamic analysis of ANS-albumin interaction

A comparative thermodynamic study of the interaction of anilinonaphthalene sulfonate (ANS) derivatives with bovine serum albumin (BSA) was performed by using differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). The chemically related ligands, 1,8-ANS and 2,6-ANS, present a similar affinity for BSA with different binding energetics. The analysis of the binding driving forces suggests that not only hydrophobic effect but also electrostatic interactions are relevant, even though they have been extensively used as probes for non-polar domains in proteins. Ligand association leads to an increase in protein thermostability, indicating that both dyes interact mainly with native BSA. ITC data show that 1,8-ANS and 2,6-ANS have a moderate affinity for BSA, with an association constant of around 1-9x10(5) M(-1) for the high-affinity site. Ligand binding is disfavoured by conformational entropy. The theoretical model used to simulate DSC data satisfactorily reproduces experimental thermograms, validating this approach as one which provides new insights into the interaction between one or more ligands with a protein. By comparison with 1,8-ANS, 2,6-ANS appears as a more "inert" probe to assess processes which involve conformational changes in proteins.

Resonance Character of Hydrogen-bonding Interactions in Water and Other H-bonded Species

Hydrogen bonding underlies the structure of water and all biochemical processes in aqueous medium. Analysis of modern ab initio wave functions in terms of natural bond orbitals (NBOs) strongly suggests the resonance-type "charge transfer" (CT) character of H-bonding, contrary to the widely held classical-electrostatic viewpoint that underlies current molecular dynamics (MD) modeling technology. Quantum cluster equilibrium (QCE) theory provides an alternative ab initio-based picture of liquid water that predicts proton-ordered two-coordinate H-bonding patterns, dramatically different from the ice-like picture of electrostatics-based MD simulations. Recent X-ray absorption and Raman scattering experiments of Nilsson and co-workers confirm the microstructural two-coordinate picture of liquid water. We show how such cooperative "unsaturated" ring/chain topologies arise naturally from the fundamental resonance-CT nature of B:cdots, three dots, centeredHA hydrogen bonding, which is expressed in NBO language as n(B)-->sigma(AH)(*) intermolecular delocalization from a filled lone pair n(B) of the Lewis base (B:) into the proximal antibond sigma(AH)(*) of the Lewis acid (HA). Stabilizing n(O)-->sigma(OH)(*) orbital delocalization, equivalent to partial mixing of resonance structures H(2)O:cdots, three dots, centeredHOH H(3)O(+) cdots, three dots, centered(-):OH, is thereby seen to be the electronic origin of general enthalpic and entropic propensities that favor relatively small cyclic clusters such as water pentamers W(5c) in the QCE liquid phase. We also discuss the thermodynamically competitive three-coordinate clusters (e.g., icosahedral water buckyballs, W(24)), which appear to play a role in hydrophobic solvation phenomena. We conclude with suggestions for incorporating resonance-CT aspects of H-bonding into empirical MD simulation potentials in a computationally tractable manner.

Stabilization of beta-hairpin peptides by salt bridges: role of preorganization in the energetic contribution of weak interactions

A model beta-hairpin peptide has been used to investigate the context-dependent contribution of cross-strand Lys-Glu interactions to hairpin stability. We have mutated two Ser-Lys interstrand pairs to Glu-Lys salt bridges, one close to the type I' Asn-Gly turn sequence (Ser6 --> Glu), and one close to the N- and C-termini (Ser15 --> Glu). Each individual interaction contributes approximately 1.2-1.3 kJ mol(-1) to stability; however, introducing the two salt bridges simultaneously produces a much larger overall contribution (-3.6 kJ mol(-1)) consistent with an important role for preorganization and cooperativity in determining the energetics of weak interactions. We compare and contrast CD and NMR data on the highly folded hairpin with the two Glu-Lys pairs to shed light on the nature of the folded state in water. We show that large cosolvent-induced changes in the CD spectrum, in contrast with the modest effects observed on Halpha chemical shifts, support a hydrophobically collapsed entropy-driven conformation in water whose stability is modulated by long-range Coulombic interactions from the Glu-Lys interactions. Cosolvent stabilizes the structure enthalpically, as is evident from CD melting profiles.

Temperature dependence of the thermodynamics of helix-coil transition

The temperature-induced helix to coil transition in a series of host peptides was monitored using circular dichroism spectroscopy (CD) and differential scanning calorimetry (DSC). Combination of these two techniques allowed direct determination of the enthalpy of helix-coil transition for the studied peptides. It was found that the enthalpy of the helix-coil transition differs for different peptides and this difference is related to the difference in the temperature for the midpoint of helix-coil transition. The enthalpy of the helix-coil transition decreases with the increase in temperature, thus providing the first experimental estimate for the heat capacity changes upon helix-coil transition, DeltaC(p). The values for DeltaC(p) of helix-coil transition are found to be negative, which is in contrast to the positive DeltaC(p) for protein unfolding. Analysis suggests that this negative DeltaC(p) of helix-coil transition is due to the exposure of the polar peptide backbone to solvent upon helix unfolding.

Heat Capacity Effects of Water Molecules and Ions at a Protein–DNA Interface

The interaction of the TATA-box binding protein from the thermophilic and halophilic archaea Pyrococcus woesei (PwTBP) with an oligonucleotide containing a specific binding site is stable over a very broad range of temperatures and ionic strengths, and is consequently an outstanding system for characterising general features of protein-DNA thermodynamics. In common with other specific protein-DNA recognition events, the PwTBP-TATA box interaction is accompanied by a large negative change in heat capacity (deltaCp) arising from the total change in solvation that occurs upon binding, which in this case involves a net uptake of cations. Contrary to previous hypotheses, we find no overall effect of ionic strength on this heat capacity change. We investigate the local contributions of site-specific ion and water binding to the overall change in heat capacity by means of a series of site-directed mutations of PwTBP. We find that although changes in the local ion binding capacity affect the enthalpic and entropic contributions to the free energy of the interaction, they do not affect the change in heat capacity. In contrast, we find remarkably large heat capacity effects arising from two particular symmetry-related mutations. The great magnitude of these effects is not explicable in terms of current semi-empirical models of heat capacity change. Previously reported X-ray crystal structures show that these mutated residues are at the centre of an evolutionarily conserved network of water-mediated hydrogen bonds between the protein and the DNA backbone. Consequently, we conclude that, in addition to water molecules buried in the protein-DNA interface that have been previously shown to influence heat capacity, bridging water molecules in a highly polar surface environment can also contribute substantially to negative heat capacity change on formation of a protein-DNA complex.

Thermodynamics of protein folding: a microscopic view

Statistical thermodynamics provides a powerful theoretical framework for analyzing, understanding and predicting the conformational properties of biomolecules. The central quantity is the potential of mean force or effective energy as a function of conformation, which consists of the intramolecular energy and the solvation free energy. The intramolecular energy can be reasonably described by molecular mechanics-type functions. While the solvation free energy is more difficult to model, useful results can be obtained with simple approximations. Such functions have been used to estimate the intramolecular energy contribution to protein stability and obtain insights into the origin of thermodynamic functions of protein folding, such as the heat capacity. With reasonable decompositions of the various energy terms, one can obtain meaningful values for the contribution of one type of interaction or one chemical group to stability. Future developments will allow the thermodynamic characterization of ever more complex biological processes.

Phenomenological similarities between protein denaturation and small-molecule dissolution: Insights into the mechanism driving the thermal resistance of globular proteins

This article shows that the stability profiles of thermophilic proteins are significantly displaced toward higher temperatures as compared to those of mesophilic proteins. A similar trend characterizes the aqueous transfer of N-alkyl amides. In fact, as a general feature of transfer processes, liquid dissolution profiles are centered at temperatures higher than those of solid ones. This behavior is governed by packing contributions. A partition of the unfolding thermodynamics based on the analysis of phenomenological temperatures common to dissolution and unfolding phenomena provides a clue to understanding the mechanism of thermal stabilization. In fact, the position of stability profiles along the temperature axis does not appear to depend on solvation of internal residues. Instead, it is notably affected by solidlike components, whose progressive decrease appears to drive the heat denaturation temperature increase of most thermostable proteins. As a corollary, it is shown that there are actually two limiting mechanisms of thermal stabilization.

Thermodynamic description of the effect of the mutation Y49F on human glutathione transferase P1-1 in binding with glutathione and the inhibitor S-hexylglutathione

The thermodynamics of binding of both the substrate glutathione (GSH) and the competitive inhibitor S-hexylglutathione to the mutant Y49F of human glutathione S-transferase (hGST P1-1), a key residue at the dimer interface, has been investigated by isothermal titration calorimetry and fluorescence spectroscopy. Calorimetric measurements indicated that the binding of these ligands to both the Y49F mutant and wild-type enzyme is enthalpically favorable and entropically unfavorable over the temperature range studied. The affinity of these ligands for the Y49F mutant is lower than those for the wild-type enzyme due mainly to an entropy change. Therefore, the thermodynamic effect of this mutation is to decrease the entropy loss due to binding. Calorimetric titrations in several buffers with different ionization heat amounts indicate a release of protons when the mutant binds GSH, whereas protons are taken up in binding S-hexylglutathione at pH 6.5. This suggests that the thiol group of GSH releases protons to buffer media during binding and a group with low pKa (such as Asp98) is responsible for the uptake of protons. The temperature dependence of the free energy of binding, DeltaG0, is weak because of the enthalpy-entropy compensation caused by a large heat capacity change. The heat capacity change is -199.5 +/- 26.9 cal K-1 mol-1 for GSH binding and -333.6 +/- 28.8 cal K-1 mol-1 for S-hexylglutathione binding. The thermodynamic parameters are consistent with the mutation Tyr49 --> Phe, producing a slight conformational change in the active site.

Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA

DNA binding of the Type 1 DNA polymerase from Thermus aquaticus (Taq polymerase) and its Klentaq large fragment domain have been studied as a function of temperature. Equilibrium binding assays were performed from 5 to 70 degrees C using a fluorescence anisotropy assay and from 10 to 60 degrees C using isothermal titration calorimetry. In contrast to the usual behavior of thermophilic proteins at low temperatures, Taq and Klentaq bind DNA with high affinity at temperatures down to 5 degrees C. The affinity is maximal at 40-50 degrees C. The DeltaH and DeltaS of binding are highly temperature dependent, and the DeltaCp of binding is -0.7 to -0.8 kcal/mol K, for both Taq and Klentaq, with good agreement between van't Hoff and calorimetric values. Such a thermodynamic profile, however, is generally associated with sequence-specific DNA binding and not non- specific binding. Circular dichroism spectra show conformational rearrangements of both the DNA and the protein upon binding. The high DeltaCp of Taq/Klentaq DNA binding may be correlated with structure-specific binding in analogy to sequence- specific binding, or may be a general characteristic of proteins that primarily bind non-specifically to DNA. The low temperature DNA binding of Taq/Klentaq is suggested to be a general characteristic of thermophilic DNA binding proteins.

Effect of calcium ions on the irreversible denaturation of a recombinant Bacillus halmapalus alpha-amylase: a calorimetric investigation

The effect of temperature and calcium ions on the denaturation of a recombinant alpha-amylase from Bacillus halmapalus alpha-amylase (BHA) has been studied using calorimetry. It was found that thermal inactivation of BHA is irreversible and that calcium ions have a significant effect on stability. Thus an apparent denaturation temperature ( T (d)) of 83 degrees C in the presence of excess calcium ions was observed, whereas T (d) decreased to 48 degrees C when calcium was removed. The difference in thermal stability with and without calcium ions has been used to develop an isothermal titration calorimetric (ITC) procedure that allows simultaneous determination of kinetic parameters and enthalpy changes of the denaturation of calcium-depleted BHA. An activation energy E (A) of 101 kJ/mol was found for the denaturation of calcium-depleted BHA. The results support a kinetic denaturation mechanism where the calcium-depleted amylase denatures irreversibly at low temperature and if calcium ions are in excess, the amylase denatures irreversibly at high temperatures. The two denaturation reactions are coupled with the calcium-binding equilibrium between calcium-bound and -depleted amylase. A combination of the kinetic denaturation results and calcium-binding constants, determined by isothermal titration calorimetry, has been used to estimate kinetic stability, expressed in terms of the half-life of BHA as a function of temperature and free-calcium-ion concentration. Thus it is estimated that the apparent E (A) can be increased to approx. 123 kJ/mol by increasing the free-calcium concentration.

On the dissection of the unfolding reaction by the dissolution thermodynamics of N-alkyl amides

Dissection of the unfolding thermodynamics based on small molecule dissolution led to controversial interpretations. It is proposed here that uncertainty about water transfer processes to be used in first approximation analyses of protein stability may be removed (i) separating liquid-dissolution-like effects from solid-like packing contributions; (ii) taking into account both peptide and side chain dissolution; and (iii) analysing the water-dependent part of the denaturation reaction by the dissolution thermodynamics of liquid N-alkyl amides. Based on these criteria, this paper analyses the entropy of the aqueous transfer of liquid N-alkyl amides filling a gap in a recent model of the unfolding energetics, which was limited to the enthalpy. Both enthalpic and entropic changes accompanying the liquid-dissolution-like immersion of internal amino acid residues in water during unfolding may be unambiguously described within this context. Although the model developed does not deepen our knowledge of protein unfolding, it may be of help in the analysis of whether liquid-dissolution-like effects or solid-like packing contributions play the major role in determining protein stability at elevated temperatures.

Relationships between the temperature dependence of solvent denaturation and the denaturant dependence of protein stability curves

We have used a simple binding model to consider how the thermodynamics of denaturant-protein interactions might influence the shape of protein stability curves (free energy change as a function of temperature), and how these effects translate into a temperature dependence of the apparent m-value (sensitivity of unfolding free energy to denaturant). We find that for an exothermic binding reaction with no binding heat capacity increment, increasing denaturant concentrations produces an apparent increase in curvature in the protein stability curve, giving rise to an increase in the heat capacity increment of unfolding. Similar increases are seen if the binding heat capacity increment is taken as positive. However, for a negative binding heat capacity increment, increasing denaturant concentrations decreases the curvature of the stability curve, giving rise to a decrease in the heat capacity of unfolding. At very high denaturant concentrations (above which the heat capacity of denaturation becomes negative) the stability curve becomes dimpled, showing two separate maxima rather than one. These three models result in very different temperature dependencies of apparent m-values. For urea-induced unfolding of the ankyrin-domain of the Drosophila Notch protein, we find a dependence of experimental m-values on temperature that is similar to that produced by a negative binding heat capacity increment. This temperature dependence is consistent with the observed decrease in heat capacity of unfolding as denaturant is added.

Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function

Structural genomics is a new approach in functional assignment of proteins identified via whole-genome sequencing programs. Its rationale is that nonhomologous proteins performing similar or related biological functions might have similar tertiary structure. We used dye pseudoaffinity chromatography, two-dimensional gel electrophoresis, and mass spectrometry to identify two novel Escherichia coli nucleotide-binding proteins, YnaF and YajQ. YnaF exhibited significant sequence identity with MJ0577, an ATP-binding protein from a hyperthermophile (Methanococcus jannaschii), and with UspA, a protein from Haemophilus influenzae that belongs to the Universal Stress Protein family. YnaF conserves the ATP-binding site and the dimeric structure observed in the crystal of MJ0577. The protein YajQ, present in many bacterial genomes, is missing in eukaryotes. In the absence of significant similarities of YajQ to any solved structure, we determined its structural and ligand-binding properties by NMR and isothermal titration calorimetry. We demonstrate that YajQ is composed of two domains, each centered on a beta-sheet, that are connected by two helical segments. NMR studies, corroborated with local sequence conservation among YajQ homologs in various bacteria, indicate that one of the beta-sheets is mostly involved in biological activity.

Thermodynamics of drug-DNA interactions

Many anticancer, antibiotic, and antiviral drugs exert their primary biological effects by reversibly interacting with nucleic acids. Therefore, these biomolecules represent a major target in drug development strategies designed to produce next generation therapeutics for diseases such as cancer. In order to improve the clinical efficacy of existing drugs and also to design new ones it is necessary to understand the molecular basis of drug-DNA interactions in structural, thermodynamic, and kinetic detail. The past decade has witnessed an increase in the number of rigorous biophysical studies of drug-DNA systems and considerable knowledge has been gained in the energetics of these binding reactions. This is, in part, due to the increased availability of high-sensitivity calorimetric techniques, which have allowed the thermodynamics of drug-DNA interactions to be probed directly and accurately. The focus of this article is to review thermodynamic approaches to examining drug-DNA recognition. Specifically, an overview of a recently developed method of analysis that dissects the binding free energy of these reactions into five component terms is presented. The results of applying this analysis to the DNA binding interactions of both minor groove drugs and intercalators are discussed. The solvent water plays a key role in nucleic acid structure and consequently in the binding of ligands to these biomolecules. Any rational approach to DNA-targeted drug design requires an understanding of how water participates in recognition and binding events. Recent studies examining hydration changes that accompany DNA binding by intercalators will be reviewed. Finally some aspects of cooperativity in drug-DNA interactions are described and the importance of considering cooperative effects when examining these reactions is highlighted.

Thermodynamic characterization of variants of mesophilic cytochrome c and its thermophilic counterpart

Thermal stability was measured for variants of cytochrome c-551 (PA c-551) from a mesophile, Pseudomonas aeruginosa, and a thermophilic counterpart, Hydrogenobacter thermophilus cytochrome c-552 (HT c-552), by differential scanning calorimetry (DSC) at pH 3.6. The mutated residues in PA c-551, selected with reference to the corresponding residues in HT c-552, were located in three spatially separated regions: region I, Phe7 to Ala/Val13 to Met; region II, Glu34 to Tyr/Phe43 to Tyr; and region III, Val78 to Ile. The thermodynamic parameters determined indicated that the mutations in regions I and III caused enhanced stability through not only enthalpic but also entropic contributions, which reflected improved packing of the side chains. Meanwhile, the mutated region II made enthalpic contributions to the stability through electrostatic interactions. The obtained differences in the Gibbs free energy changes of unfolding [Delta(DeltaG)] showed that the three regions contributed to the overall stability in an additive manner. HT c-552 had the smallest heat capacity change (DeltaC(P)), resulting in higher DeltaG values over a wide temperature range (0-100 degrees C), compared to the PA c-551 variants; this contributed to the highest stability of HT c-552. Our DSC measurement results, in conjunction with mutagenesis and structural studies on the homologous mesophilic and thermophilic cytochromes c, provided an extended thermodynamic view of protein stabilization.

Thermodynamics of E. coli cytidine repressor interactions with DNA: distinct modes of binding to different operators suggests a role in differential gene regulation

Interactions between the Escherichia coli cytidine repressor protein (CytR) and its operator sites at the different promoters that comprise the CytR regulon, play an important role in the regulation of these promoters. The natural operators are palindromes separated by variable length central spacers (0-9 bp). We have suggested that this variability affects the flexibility of CytR-DNA contacts, thereby affecting the critical protein-protein interactions between CytR and the cAMP receptor protein (CRP) that underlie differential repression and activation of CytR-regulated genes. To assess this hypothesis, we investigated the thermodynamics of CytR binding to the natural operator sequences found in udpP and deoP2. To separate effects due to spacing from effects due to the differing sequences of the recognition half-sites of these two operators, we also investigated CytR binding to artificial hybrid operators, in which the half-site sequences of udpP and deoP2 were exchanged. Thermodynamic parameters, DeltaS(o), DeltaH(o) and DeltaC(o)(p), were determined by van't Hoff analysis of CytR binding, monitored by changes in the steady-state fluorescence anisotropy of dye-conjugated, operator-containing oligonucleotides. Large differences in thermodynamics were observed that depend primarily on the central spacer rather than the sequences of the recognition half-sites. Binding to operators with deoP2 spacing results in a very large, negative DeltaC(o)(p). Association is strongly favored enthalpically and strongly disfavored entropically at ambient temperature. By contrast, binding to operators with udpP spacing results in a small, negative DeltaC(o)(p). Association is weakly favored both enthalpically and entropically at ambient temperature. A difference of such magnitude in DeltaDeltaC(o)(p) has not been reported previously for specific binding of a transcription factor to different sites. The identical salt dependence of CytR binding to deoP2 and udpP operators indicates that ion-dependent processes do not contribute significantly to this difference. Thus, the different thermodynamic effects appear to reflect distinctly different modes of site-specific DNA binding. We discuss similarities to operator binding by CytR homologs among LacI family repressors, and we consider how different CytR binding modes might affect interactions with other components of the gene regulatory machinery that contribute to differential gene regulation.

Isothermal titration calorimetry in drug discovery

Isothermal titration calorimetry (ITC) follows the heat change when a test compound binds to a target protein. It allows precise measurement of affinity. The method is direct, making interpretation facile, because there is no requirement for competing molecules. Titration in the presence of other ligands rapidly provides information on the mechanism of action of the test compound, identifying the intermolecular complexes that are relevant for structure-based design. Calorimetry allows measurement of stoichiometry and so evaluation of the proportion of the sample that is functional. ITC can characterize protein fragments and catalytically inactive mutant enzymes. It is the only technique which directly measures the enthalpy of binding (delta H degree). Interpretation of delta H degree and its temperature dependence (delta Cp) is usually qualitative, not quantitative. This is because of complicated contributions from linked equilibria and a single change in structure giving modification of several physicochemical properties. Measured delta H degree values allow characterization of proton movement linked to the association of protein and ligand, giving information on the ionization of groups involved in binding. Biochemical systems characteristically exhibit enthalpy-entropy compensation where increased bonding is offset by an entropic penalty, reducing the magnitude of change in affinity. This also causes a lack of correlation between the free energy of binding (delta G degree) and delta H degree. When characterizing structure-activity relationships (SAR), most groups involved in binding can be detected as contributing to delta H degree, but not to affinity. Large enthalpy changes may reflect a modified binding mode, or protein conformation changes. Thus, delta H degree values may highlight a potential discontinuity in SAR, so that experimental structural data are likely to be particularly valuable in molecular design.

Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area

To interpret effects of urea and guanidinium (GuH(+)) salts on processes that involve large changes in protein water-accessible surface area (ASA), and to predict these effects from structural information, a thermodynamic characterization of the interactions of these solutes with different types of protein surface is required. In the present work we quantify the interactions of urea, GuHCl, GuHSCN, and, for comparison, KCl with native bovine serum albumin (BSA) surface, using vapor pressure osmometry (VPO) to obtain preferential interaction coefficients (Gamma(mu3)) as functions of nondenaturing concentrations of these solutes (0-1 molal). From analysis of Gamma(mu3) using the local-bulk domain model, we obtain concentration-independent partition coefficients K(nat)(P) that characterize the accumulation of these solutes near native protein (BSA) surface: K(nat)(P,urea)= 1.10 +/- 0.04, K(nat)(P,SCN(-)) = 2.4 +/- 0.2, K(nat)(P,GuH(+)) = 1.60 +/- 0.08, relative to K(nat)(P,K(+)) identical with 1 and K(nat)(P,Cl(-)) = 1.0 +/- 0.08. The relative magnitudes of K(nat)(P) are consistent with the relative effectiveness of these solutes as perturbants of protein processes. From a comparison of partition coefficients for these solutes and native surface (K(nat)(P)) with those determined by us previously for unfolded protein and alanine-based peptide surface K(unf)(P), we dissect K(P) into contributions from polar peptide backbone and other types of protein surface. For globular protein-urea interactions, we find K(nat)(P,urea) = K(unf)(P,urea). We propose that this equality arises because polar peptide backbone is the same fraction (0.13) of total ASA for both classes of surface. The analysis presented here quantifies and provides a physical basis for understanding Hofmeister effects of salt ions and the effects of uncharged solutes on protein processes in terms of K(P) and the change in protein ASA.