Isothermal Titration Calorimetry Titration Research Articles

Organic-soluble cytosine derivatives for studying base-pair interactions in nonaqueous solution

The presence of higher order G-quadruplex-DNA (G4) structures in human cells in guanine-rich DNA sequences has been well established. In cases of G4 helicase impairment or G4 stabilization via association with G4 ligands, it has been determined that arrest and/or termination of DNA transcription/replication occurs because these structures act as physical barriers to both helicase and polymerase mobility along the DNA. Truncation of transcription or replication may result in the loss of genetic material expression leading to disorders. To ameliorate G4-induced barriers, agents that destabilize or “unwind” the quadraplex structures are sought. Earlier work has shown that the cytosine analogue phenylpyrrolocytosine has potential G4-destabilizing ability. It was hypothesized that the unwinding activity was related to its ability to base pair with guanosine. To facilitate the design and evaluation of the hydrogen bonding ability of cytosine analogues, solubility in aprotic, and low-polarity solvents, e.g., deutero-chloroform (CDCl3), is needed; then, determination of association constants ( Ka) with guanine via 1H nuclear magnetic resonance (NMR) spectroscopy or isothermal titration calorimetry (ITC) will be possible. Herein, we report on the synthesis of three new chloroform-soluble, cytosine analogues: N1-cyclohexylmethyl-7-phenylimidazolocytosine, N1-cyclohexylmethyl-7-(6-(methoxycarbonyl)pyridin-2-yl)imidazolocytosine, and N1-cyclohexylmethyl-7-(6-carbamoylpyridin-2-yl)imidazolocytosine. We further report the binding interactions of each of these analogues with the guanosine derivative 2′,3′,5′- O-tris( tert-butyldimethylsilyl)guanosine through the use of both ITC and 1H NMR titration experiments in chloroform and compare the binding to persilyated ribo-cytidine.

The formation mechanism of multilayer emulsions studied by isothermal titration calorimetry and dynamic light scattering

The formation of multilayer interfaces in oil-in-water (O/W) systems has many advantages in delivering lipid-soluble active compounds. In this study, isothermal titration calorimetry (ITC) and dynamic light scattering (DLS) were used to investigate the formation mechanism of multilayer emulsions by mixing low methoxyl pectin (LMP) and sodium caseinate (CAS) stabilized O/W emulsion. Thermodynamic properties and ζ-potential curves were studied as a function of polymer ratio, suggesting that ITC could provide more accurate information about the polymer concentration effect. ITC titration confirmed that LMP binds CAS-coated droplets mainly through electrostatic forces, which was a spontaneous exothermic process (ΔG < 0). Furthermore, stable multilayer emulsions were obtained by titrating CAS-stabilized droplets into LMP instead of back-titrating. Finally, the effects of mixing methods on the stability of multilayer emulsions were evaluated. The results suggest that titration rather than direct mixing can produce uniform and smaller-sized droplets and delay the onset of droplets aggregation.

Characterizing Thermodynamics of Protein-Glycosaminoglycan Interactions Using Isothermal Titration Calorimetry.

It has now become increasingly clear that a complete atomic description of how biomacromolecules recognize each other requires knowledge not only of the structures of the complexes but also of how kinetics and thermodynamics drive the binding process. In particular, such knowledge is lacking for protein-glycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide all of the thermodynamic parameters-enthalpy, entropy, free energy (binding constant), and stoichiometry-from a single experiment. Here we describe different factors that must be taken into consideration in carrying out ITC titrations to obtain meaningful thermodynamic data of protein-GAG interactions.

A discussion on the affecting factors of the fitting procedures’ reliability in isothermal titration calorimetry analysis

The standard isothermal titration calorimetry (ITC) curve, characterized as a typical sigmoid is strictly confined by the so-called c value, which is a ratio of titrand concentration to KD. The proper c value with a range from 5 to 500 is commonly recommended as a standard protocol in routine detection process for acquiring the reliable fitting results in 1:1 binding mode. However, if the c value is less than “1” due to the weak binding or low concentration of analyte, fitting precision gets unstable and susceptible to the data noise. Herein, we first got a deep discussion into the reliability of the fitting procedure for 1:1 binding mode by data simulation, then quantized the effect of several affecting factors on the precision of parameters estimation through mathematical analysis. Finally, we proposed the value of 2~4 times KD for final ligand concentration is optimal for the ITC titration in low c system (c < 1). All the theoretical derivations were further verified by a practical experiment of Magnesium-EDTA binding test.

Self-assembly study of type I collagen extracted from male Wistar Hannover rat tail tendons

BackgroundCollagen, the most abundant protein in the animal kingdom, represents a promising biomaterial for regenerative medicine applications due to its structural diversity and self-assembling complexity. Despite collagen’s widely known structural and functional features, the thermodynamics behind its fibrillogenic self-assembling process is still to be fully understood. In this work we report on a series of spectroscopic, mechanical, morphological and thermodynamic characterizations of high purity type I collagen (with a D-pattern of 65 nm) extracted from Wistar Hannover rat tail. Our herein reported results can be of help to elucidate differences in self-assembly states of proteins using ITC to improve the design of energy responsive and dynamic materials for applications in tissue engineering and regenerative medicine.MethodsHerein we report the systematic study on the self-assembling fibrillogenesis mechanism of type I collagen, we provide morphological and thermodynamic evidence associated to different self-assembly events using ITC titrations. We provide thorough characterization of the effect of pH, effect of salts and protein conformation on self-assembled collagen samples via several complementary biophysical techniques, including circular dichroism (CD), Fourier Transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic mechanical thermal analysis (DMTA) and thermogravimetric analysis (TGA).ResultsEmphasis was made on the use of isothermal titration calorimetry (ITC) for the thermodynamic monitoring of fibrillogenesis stages of the protein. An overall self-assembly enthalpy value of 3.27 ± 0.85 J/mol was found. Different stages of the self-assembly mechanism were identified, initial stages take place at pH values lower than the protein isoelectric point (pI), however, higher energy release events were recorded at collagen’s pI. Denatured collagen employed as a control exhibited higher energy absorption at its pI, suggesting different energy exchange mechanisms as a consequence of different aggregation routes.Graphical abstract

Thermodynamics of ferredoxin binding to cyanobacterial nitrate reductase.

The role of the seven negatively charged amino acids of Synechocystis sp. PCC 6803 ferredoxin (Fd), i.e., Glu29, Glu30, Asp60, Asp65, Asp66, Glu92, and Glu93, predicted to form complex with nitrate reductase (NR), was investigated using site-directed mutagenesis and isothermal titration calorimetry (ITC). These experiments identified four Fd amino acids, i.e., Glu29, Asp60, Glu92, and Glu93, that are essential for the Fd binding and efficient electron transfer to the NR. ITC measurements showed that the most likely stoichiometry for the wild-type NR/wild-type Fd complex is 1:1, a Kd value 4.7μM for the complex at low ionic strength residues and both the enthalpic and entropic components are associated with complex formation. ITC titrations of wild-type NR with four Fd variants, E29N, D60N, E92Q, and E93N demonstrated that the complex formation, although favorable, was less energetically favorable when compared to complex formation between the two wild-type proteins, suggesting that these negatively charged Fd residues at these positions are important for the effective and productive interaction with wild-type enzyme.

Exopolysaccharides from yoghurt fermented by Lactobacillus paracasei: Production, purification and its binding to sodium caseinate

Lactobacillus paracasei that could release exopolysaccharide (EPS), was used as starter to prepare yoghurt under optimal fermented conditions. It was found that the viscosity of yoghurt increased exponentially with EPS production, and to elucidate this phenomen, the binding of EPS-S11 extracted and purified from yoghurt to casein was evaluated by turbidity and particle size analysis, zeta potential study, confocal laser scanning microscopy (CLSM) imaging, and isothermal titration calorimetry (ITC) determination. Results indicated that EPS-S11 with an average molecular weight of 1.68 × 107 Da, was mainly composed of mannose, glucose, galactose and glucuronic acid in a molar ratio of 0.87:0.92:1:0.24. Upon the addition of EPS-S11, the turbidity and particle size of casein solution both decreased in a dose-dependent manner, while the zeta potential was dose-dependently increased, suggesting that EPS-S11 might inhibit the aggregation of casein and thus enhanced its stability. ITC titration and CLSM imaging confirmed the existence of interactions between EPS-S11 and casein, which mainly involved in electrostatic interaction as well as hydrophobic interaction.

Fluorinated Bambusurils as Highly Effective and Selective Transmembrane Cl−/HCO3− Antiporters

Summary The exchange of chloride and bicarbonate across lipid bilayers is an important biological process. Synthetic molecules can act as mobile carriers for these anions, although most show little selectivity. Here we report on three bambus[6]uril macrocycles functionalized with fluorinated benzyl groups, which are able to exchange Cl− and HCO3− efficiently. Remarkably, rates for Cl−/NO3− exchange are two orders of magnitude lower. The higher rates of Cl−/HCO3− transport can be explained by the ability of the bambusurils to complex Cl− and HCO3− simultaneously, facilitating their exchange at the bilayer interface. Furthermore, the exceptionally high affinity and selectivity of these systems for NO3− appear to contribute to the poor Cl−/NO3− exchange. This work not only demonstrates the importance of anion binding characteristics on anion transport but also the potential relevance of bambusurils for anion transport applications considering the high rate observed for Cl−/HCO3− exchange.

Thermodynamic selectivity of functional agents on zeolite for sodium dodecyl sulfate sequestration

This study proposes a thermodynamic approach to effectively select functional agents onto zeolite for sodium dodecyl sulfate (SDS) sequestration in greywater reuse. We combine isothermal titration calorimetry (ITC) and quantum chemistry simulation (QCS) to identify the interactions between SDS and agents at the molecular level. Three potential agents, cetyl trimethyl ammonium bromide (CTAB), N,N,N-trimethyltetradecan-1-aminium bromide (C14TAB), and 14-hydroxy-N,N,N-trimethyltetradecan-1-aminium bromide (C14HTAB), differ in carbon chain length and hydrophilic groups. The ITC titration of SDS with CTAB released the highest heat, followed by those with C14TAB and C14HTAB, as was the same trend for the amounts of SDS adsorbed by the respective functionalized-zeolites. Results suggest that the favorable SDS sorption occurred at the bilayer CTAB-zeolite is driven by enthalpy as similar as the SDS…CTAB interaction found, regardless of the contribution from electrostatic and/or hydrophobic behaviors, while the declined sorption is entropy-driven via the predominant hydrophobic interaction onto the monolayer CTAB-zeolite. The data presented here interpret the nature of molecularly thermodynamic quantities and enable the manipulation of sorption capacity optimization.

Increased Flexibility of Local Conformation in the N-Terminal Domain of MdmX Enhances Ligand-Binding Affinity

The overexpression of Mdm2 and MdmX ultimately impairs the cancer suppression of p53 function in approximately half of human cancers. Discovery of Mdm2 inhibitors has been made tremendous progress and some potent prodrugs have been considered for clinical investigation. Although MdmX is homologous to Mdm2 regarding their amino acid sequences and three-dimensional structures, the Mdm2 inhibitors exhibit weak affinity binding to MdmX. In order to aid in designing of MdmX inhibitors based on the Mdm2 inhibitor scaffolds, we engineered a disulfide bond to tie up the N-terminus and the C-terminus of the N-terminal domain of MdmX (N-MdmX) so that the pre-defined ligand-binding pocket on N-MdmX would be rigidified for docking an inhibitor. The resultant N-MdmX mutant was defined as N-MdmX2C and its interaction with nutlin-3a (a potent Mdm2 inhibitor) was characterized with isothermal titration calorimetry (ITC), circular dichroism spectroscopy (CD) and nuclear magnetic resonance (NMR) spectroscopy. The ITC data reveal that N-MdmX2C exhibits relatively-strong affinity binding to nutlin-3a compared to N-MdmX. The CD analysis indicates that both N-MdmX2C and N-MdmX have similar secondary structure content while their tertiary structures show difference. However, the 15N-1H HSQC NMR spectra reveal that the conformation of N-MdmX2C becomes more flexible compared to N-MdmX unexpectedly. Nevertheless, the 15N-1H HSQC NMR titration confirms that N-MdmX2C has higher binding affinity for nutlin-3a than N-MdmX. On the other hand, both N-MdmX2C and N-MdmX exhibit the same binding affinity to p53p investigated with ITC and NMR titration. Taken together, the current results suggest the confirmation of N-MdmX2C resembles a binding intermediate state for ligand binding, providing an ideal model for anticancer drug design targeting MdmX/Mdm2. (∗Corresponding authors)

Regulation of Mammalian Dynein Intermediate Chain

Cytoplasmic dynein is a protein complex responsible for transporting cellular cargos on microtubules. Dynein's activities are regulated by other proteins including dynactin which mediates dynein-cargo interactions and increases dynein's processivity. The intermediate chain (IC) of dynein binds to dynactin p150Glued subunit, an interaction central to dynein regulation. The N-terminal domain of IC, N-IC is partially disordered, and contains binding site for a coiled-coil domain of p150Glued and a serine-rich region known to undergo phosphorylation in vivo. There are conflicting results to the effect of phosphorylation on dynactin binding. Using different techniques, one group showed phosphorylated S84 and a phosphomimetic mutant S84D abolished p150Glued binding in vitro while another group demonstrated S84D was still able to bind. We use mutagenesis, constructs of varying length, isothermal titration calorimetry (ITC) and NMR spectroscopy to identify the effect of phosphomimetic S84D on structure of IC and its ability to bind p150Glued. Backbone assignments of IC2C1-96 and secondary chemical shifts show residues 4-38 (helix 1) and 52-66 (helix 2) adopt helical structures and the rest of the protein is disordered. NMR and ITC titration studies identify the first 44 residues as sufficient for binding. The phosphomimetic mutant IC2CS84D abolishes p150Glued binding, without causing major changes in structure and dynamics as detected from NMR measurements. Chemical shift comparison between WT and S84D shows long-range effects on residues in the linker between helix 1 and 2, suggesting conformational changes in the linker. Mutations in the linker region restore p150Glued binding. Together, these results demonstrate for the first time phosphorylation in a disordered region affects binding at a distant site in the sequence, and is fine-tuned by changes in a disordered linker separating two structured domains. This regulatory control of dynein-dynactin interactions is key to cargo- and temporal-specific alterations in dynein transport.

ITC Methods for Assessing Buffer/Protein Interactions from the Perturbation of Steady-State Kinetics: A Reactivity Study of Homoprotocatechuate 2,3-Dioxygenase.

Isothermal titration calorimetry (ITC) can be used to study the thermodynamics of enzyme substrate binding or the kinetics of substrate turnover (or both). Substrate-binding interactions are observed in a typical ITC titration experiment in which the heat change for the addition of an aliquot of substrate to a solution containing the enzyme is determined for a number of titrant (i.e., substrate) injections and the data fit for the thermodynamic parameters (ΔG, ΔH, and -TΔS) for substrate binding. Of course, these measurements must be made under conditions where the substrate binds but does not turnover. In the ITC "kinetics" experiment, the power change observed after injection of an excess of substrate into a solution of the enzyme is a direct measure of the rate at which substrate is converted to product, and the ITC data can be analyzed for the kinetic parameters (Vmax, kcat, KM, and kcat/KM). The ITC technique is particularly versatile in that it can be applied to systems where there might not be a change in a spectroscopic signal for either substrate binding or the reaction of the substrate to form product. A complication is that if there are competing reactions, for example, buffer protonation, or product binding, to name just two, the enthalpy change measured for either substrate binding or for substrate turnover will be a summation of all of the reaction heats. Enzyme studies are typically done in buffered solutions at constant pH. The general, and often incorrect, assumption is that the buffer components are simply spectators and not participants in either substrate binding or substrate turnover. This chapter describes how we have used ITC measurements to identify problem buffers that impact the kinetics for an enzyme catalyzed reaction. Herein, we show the effects of several buffers on the steady-state kinetics for the conversion of the substrate, 3,4-dihydroxyphenyl acetate (homoprotocatechuate), to the ring-opened product, 5-carboxymethyl-2-hydroxymuconic semialdehyde by the nonheme iron(II) metalloenzyme, homoprotocatechuate 2,3-dioxygenase. Several buffers were observed to engage in buffer/enzyme interactions within the active site pocket. These enzyme-buffer interactions were shown to inhibit substrate turnover and to contribute additional enthalpy terms to the overall heat of reaction observed for substrate turnover (and for substrate binding).

Measuring Multivalent Binding Interactions by Isothermal Titration Calorimetry.

Multivalent glycoconjugate-protein interactions are central to many important biological processes. Isothermal titration calorimetry (ITC) can potentially reveal the molecular and thermodynamic basis of such interactions. However, calorimetric investigation of multivalency is challenging. Binding of multivalent glycoconjugates to proteins (lectins) often leads to a stoichiometry-dependent precipitation process due to noncovalent cross-linking between the reactants. Precipitation during ITC titration severely affects the quality of the baseline as well as the signals. Hence, the resulting thermodynamic data are not dependable. We have made some modifications to address this problem and successfully studied multivalent glycoconjugate binding to lectins. We have also modified the Hill plot equation to analyze high quality ITC raw data obtained from multivalent binding. As described in this chapter, ITC-driven thermodynamic parameters and Hill plot analysis of ITC raw data can provide valuable information about the molecular mechanism of multivalent lectin-glycoconjugate interactions. The methods described herein revealed (i) the importance of functional valence of multivalent glycoconjugates, (ii) that favorable entropic effects contribute to the enhanced affinities associated with multivalent binding, (iii) that with the progression of lectin binding, the microscopic affinities of the glycan epitopes of a multivalent glycoconjugate decrease (negative cooperativity), (iv) that lectin binding to multivalent glycoconjugates, especially to mucins, involves internal diffusion jumps, (bind and jump) and (v) that scaffolds of glycoconjugates influence their entropy of binding.

Linear starch and hexanoic acid complexation evaluated by isothermal titration calorimetry

Linear starch form inclusion complexes with fatty acids through hydrophobic interaction. The complexation between starch and fatty acid is affected by many factors, such as starch degree of polymerization (DP), fatty acid structure, and complexation conditions. There is limited information on the use of isothermal titration calorimetry (ITC) in understanding starch‐fatty acid interactions. The effects of temperature and concentration of hexanoic acid on the complexation of debranched waxy maize starch and potato amylose were investigated using ITC. The starch samples were characterized for their molecular size distribution and iodine affinity. Potato amylose and debranched waxy maize starch displayed a major peak DP of 330 and 25, and iodine affinity of 2.9 and 13.9, respectively. The ITC titration data were fitted best to a one set of binding site model. Complexation was exothermic and spontaneous for all reactions based on changes in enthalpy of free energy (ΔG). The binding affinity (Ka) of debranched waxy maize starch for hexanoic acid decreased with an increase in temperature from 25 to 45°C. The Ka and number of binding sites (n) for debranched waxy maize exceeded those of potato amylose, indicating a higher complexation of debranched waxy maize for hexanoic acid. The number of binding sites (n) and enthalpy of binding (ΔH) values for both starches remained independent of temperature change. The ITC results demonstrated that debranched waxy maize starch was favored over potato amylose to complex hexanoic acid.

Investigation into the molecular and thermodynamic basis of protein interactions in multimodal chromatography using functionalized nanoparticles.

Although multimodal chromatography offers significant potential for bioseparations, there is a lack of molecular level understanding of the nature of protein binding in these systems. In this study a nanoparticle system is employed that can simulate a chromatographic resin surface while also being amenable to isothermal titration calorimetry (ITC) and solution NMR. ITC and NMR titration experiments are carried out with (15)N-labeled ubiquitin to investigate the interactions of ubiquitin with nanoparticles functionalized with two industrially important multimodal ligands. The ITC results suggest that binding to both multimodal ligand surfaces is entropically driven over a range of temperatures and that this is due primarily to the release of surface bound waters. In order to reveal structural details of the interaction process, binding-induced chemical shift changes obtained from the NMR experiments are employed to obtain dissociation constants of individual amino acid residues on the protein surface. The residue level information obtained from NMR is then used to identify a preferred binding face on ubiquitin for interaction to both multimodal ligand surfaces. In addition, electrostatic potential and spatial aggregation propensity maps are used to determine important protein surface property data that are shown to correlate well with the molecular level information obtained from NMR. Importantly, the data demonstrate that the cluster of interacting residues on the protein surface act co-operatively to give rise to multimodal binding affinities several orders of magnitude greater than those obtained previously for interactions with free solution ligands. The use of NMR and ITC to study protein interactions with functionalized nanoparticles offers a new tool for obtaining important molecular and thermodynamic insights into protein affinity in multimodal chromatographic systems.

Zinc(II) complexation by some biologically relevant pH buffers.

The isothermal titration calorimetry (ITC) technique supported by potentiometric titration data was used to study the interaction of zinc ions with pH buffer substances, namely 2-(N-morpholino)ethanesulfonic acid (Mes), piperazine-N,N'-bis(2-ethanesulfonic acid) (Pipes), and dimethylarsenic acid (Caco). The displacement ITC titration method with nitrilotriacetic acid as a strong, competitive ligand was applied to determine conditional-independent thermodynamic parameters for the binding of Zn(II) to Mes, Pipes, and Caco. Furthermore, the relationship between the proposed coordination mode of the buffers and the binding enthalpy has been discussed.

Thermodynamics of host-guest interactions between fullerenes and a buckycatcher.

1H NMR and isothermal titration calorimetry (ITC) experiments were employed to obtain reliable thermodynamic data for the formation of the 1:1 inclusion complexes of fullerenes C60 and C70 with the buckycatcher (C60H28). NMR measurements were done in toluene-d8 and chlorobenzene-d5 at 288, 298, and 308 K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane at temperatures from 278 to 323 K. The association constants, Ka, obtained with both techniques are in very good agreement. The thermodynamic data obtained by ITC indicate that generally the host–guest association is enthalpy-driven. Interestingly, the entropy contributions are, with rare exceptions, slightly stabilizing or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these thermodynamic functions exhibit classical enthalpy/entropy compensation. The ΔCp values calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes with the buckycatcher in toluene. The negative ΔCp values are consistent with some desolvation of the host-cavity and the guest in the inclusion complexes, C60@C60H28 and C70@C60H28.

Using isothermal titration calorimetry to determine thermodynamic parameters of protein-glycosaminoglycan interactions.

It has now become increasingly clear that a complete atomic description of how biomacromolecules recognize each other requires knowledge not only of the structures of the complexes but also of how kinetics and thermodynamics drive the binding process. In particular, such knowledge is lacking for protein-glycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide various thermodynamic parameters-enthalpy, entropy, free energy (binding constant), and stoichiometry-from a single experiment. Here we describe different factors that must be taken into consideration in carrying out ITC titrations to obtain meaningful thermodynamic data of protein-GAG interactions.

Shape readout of AT‐rich DNA by carbohydrates

Gene expression can be altered by small molecules that target DNA; sequence as well as shape selectivities are both extremely important for DNA recognition by intercalating and groove-binding ligands. We have characterized a carbohydrate scaffold (1) exhibiting DNA "shape readout" properties. Thermodynamic studies with 1 and model duplex DNAs demonstrate the molecule's high affinity and selectivity towards B* form (continuous AT-rich) DNA. Isothermal titration calorimetry (ITC), circular dichroism (CD) titration, ultraviolet (UV) thermal denaturation, and Differential Scanning Calorimetry were used to characterize the binding of 1 with a B* form AT-rich DNA duplex d[5'-G2 A6 T6 C2 -3']. The binding constant was determined using ITC at various temperatures, salt concentrations, and pH. ITC titrations were fit using a two-binding site model. The first binding event was shown to have a 1:1 binding stoichiometry and was predominantly entropy-driven with a binding constant of approximately 10(8) M(-1) . ITC-derived binding enthalpies were used to obtain the binding-induced change in heat capacity (ΔCp ) of -225 ± 19 cal/mol·K. The ionic strength dependence of the binding constant indicated a significant electrolytic contribution in ligand:DNA binding, with approximately four to five ion pairs involved in binding. Ligand 1 displayed a significantly higher affinity towards AT-tract DNA over sequences containing GC inserts, and binding experiments revealed the order of binding affinity for 1 with DNA duplexes: contiguous B* form AT-rich DNA (d[5'-G2 A6 T6 C2 -3']) >B form alternate AT-rich DNA (d[5'-G2 (AT)6 C2- 3']) > A form GC-rich DNA (d[5'-A2 G6 C6 T2 -3']), demonstrating the preference of ligand 1 for B* form DNA.

Thermodynamic Analysis of the Binding of 2F5 (Fab and Immunoglobulin G Forms) to Its gp41 Epitope Reveals a Strong Influence of the Immunoglobulin Fc Region on Affinity

Immunotherapies and vaccines based on the induction of broadly neutralizing monoclonal antibodies (bNAbs) have become outstanding strategies against HIV-1. Diverse bNAbs recognizing different regions of the HIV-1 envelope have been identified and extensively studied. However, there is little information about the thermodynamics of binding of these bNAbs and their epitopes. We used isothermal titration calorimetry to characterize thermodynamically the interactions between bNAb2F5 (in both the IgG and Fab forms) and its functional and core epitope peptides. We found that these interactions are enthalpically driven and opposed by a negative entropy change. The highest affinity was found for 2F5 IgG for its functional epitope, indicating that additional interactions involving residues flanking the core epitope contribute strongly to higher affinity. In addition, the strong influence of the Fc region on the binding affinity suggests long-range allosteric effects within IgG. Our results provide useful information for developing new therapeutics against HIV-1 and, in a broader scope, contribute to a better understanding of antigen-antibody recognition.