Binding Thermodynamic Parameters Research Articles

Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers

Fluorescent DNA dyes are broadly used in many biotechnological applications for detecting and imaging DNA in cells and gels. Their binding alters the structural and nanomechanical properties of DNA and affects the biological processes that are associated with it. Although interaction modes like intercalation and minor groove binding already have been identified, associated mechanic effects like local elongation, unwinding, and softening of the DNA often remain in question. We used magnetic tweezers to quantitatively investigate the impact of three DNA-binding dyes (YOYO-1, DAPI, and DRAQ5) in a concentration-dependent manner. By extending and overwinding individual, torsionally constrained, nick-free dsDNA molecules, we measured the contour lengths and molecular forces that allow estimation of thermodynamic and nanomechanical binding parameters. Whereas for YOYO-1 and DAPI the binding mechanisms could be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both binding modes in a concentration-dependent manner.

Comparative study on the interaction of two binuclear Pt (II) complexes with human serum albumin: Spectroscopic and docking simulation assessments

Human serum albumin (HSA) principally tasks as a transport carrier for a vast variety of natural compounds and pharmaceutical drugs. In the present study, two structurally related binuclear Pt (II) complexes containing cis, cis-[Me2Pt (μ-NN) (μ-dppm) PtMe2] (1), and cis, cis-[Me2Pt(μ-NN)(μ dppm) Pt((CH2)4)] (2) in which NN=phthalazine and dppm=bis (diphenylphosphino) methane were used to investigate their interaction with HSA, using UV–Vis absorption spectroscopy, fluorescence, circular dichroism and molecular dynamic analyses. The spectroscopic results suggest that upon binding to HSA, the binuclear Pt (II) complexes could effectively induce structural alteration of this protein. These complexes can bind to HSA with the binding affinities of the following order: complex 2>complex 1. Moreover, the thermodynamic parameters of binding between these complexes and HSA suggested the existence of entropy-driven spontaneous interaction, which mostly dominated with the hydrophobic forces. The ANS fluorescence results also indicated that two binuclear Pt (II) complexes were competing for the binding to the hydrophobic regions on HSA. In addition, competitive displacement assay and docking simulation study revealed that complexes 1 and 2 bind to the drug binding sites II and I on HSA, respectively. Furthermore, complex 2, with the higher binding affinity for HSA, shows more denaturing effect on this protein. Considering the protein structural damages in the pathway of harmful side effects of platinum drugs, complex 1 with the moderate binding affinity and low denaturing effect might be of high significance.

Quercetin Influence on Thermal Denaturation of Bovine Serum Albumin.

The effect of quercetin (QUER) binding on bovine serum albumin (BSA) thermal denaturation was systematically investigated by means of differential scanning calorimetry (DSC). Additional information concerning thermodynamic and structural binding parameters was provided by isothermal titration calorimetry (ITC) and molecular docking. The most relevant effect of QUER is manifested in the modification of the two-step thermal fingerprint of protein denaturation. Higher QUER concentrations result in a single-step denaturation thermogram, ascribed to the interplay between specific and nonspecific binding and enhancement of the solvent unfolding action. Analysis of ITC data indicate sequential binding of two molecules of QUER occurring spontaneously at different binding sites of BSA involving hydrophobic, electrostatic and hydrogen binding forces. Identification of QUER binding sites was possible through corroboration of DSC runs in the presence of site markers and molecular docking. Modeling of ligand-protein interaction confirmed the experimental data. On one hand, a neutral form of QUER binds in a nonplanar conformation to Sudlow's site I, a large hydrophobic cavity of subdomain IIA of BSA and decreases its thermal stability. On the other hand, a second molecule of QUER, the anionic form, is bound in planar conformation to Sudlow's site II, situated in the subdomain IIIA of the folded protein, and increases the thermal stability of the corresponding structural domain of the protein.

Spectral Study of the Interaction of Myoglobin with Tannin

The interaction of myoglobin with tannin (tannic acid) at 298.15 and 303.15 K was studied by fluorescence and absorption spectroscopy in the UV region. The physicochemical and thermodynamic binding parameters (the fluorescence quenching mechanism, the bonding constant, the number of binding sites, the type of interaction) and parameters of the formed complex were determined. It was found that binding of myoglobin with tannic acid does not lead to significant changes in the electronic state of the heme ring of myoglobin.

Degradation products of the artificial azo dye, Allura red, inhibit esterase activity of carbonic anhydrase II: A basic in vitro study on the food safety of the colorant in terms of enzyme inhibition

Allura red is a widely used food colorant, but there is debate on its potential security risk. In the present study, we found that degradation products of the dye were more potent agents with higher carbonic anhydrase inhibitory action than the parent dye. The mechanism by which the compounds inhibit the enzyme activity has been determined as competitive mode. In addition, the enzyme binding properties of the compounds were investigated employing different spectroscopic techniques and molecular docking. The analyses of fluorescence quenching data revealed the existence of the same binding site for the compounds on the enzyme molecule. The thermodynamic parameters of ligand binding were not similar, which indicates that different interactions are responsible in binding of the parent dye and degradation products to the enzyme. It appears that enzyme inhibition should be considered, more seriously, as a new opened dimension in food safety.

Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis

The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb=(7.6±0.21)×105) between complex and protein have been obtained at 298K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2±0.11)×106M−1. Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.

Structural⿿functional insights and studies on saccharide binding of Sophora japonica seed lectin

Functional and conformational transitions of the Sophora japonica seed lectin (SJL) were studied in detail using bioinformatics and biophysical tools. Homology model of the lectin displayed all the characteristics of the legume lectin monomer and the experimental observations correlated well with the structural information. In silico studies were performed by protein-ligand docking, calculating the respective binding energies and the residues involved in the interactions were derived from LigPlot+ analysis. Fluorescence titrations showed three times higher affinity of T-antigen disaccharide than N-acetyl galactosamine (GalNAc) towards SJL indicating extended sugar binding site of the lectin. Thermodynamic parameters of T-antigen binding to SJL indicated the process to be endothermic and entropically driven while those of GalNAc showed biphasic process. SDS-PAGE showed post-translationally modified homotetrameric species of the lectin under native conditions. In presence of guanidine hydrochloride (0.5⿿5.0M), the tetramer first dissociated into dimers followed by unfolding of the protein as indicated by size exclusion chromatography, fluorescence and CD spectroscopy. Different structural rearrangements were observed during thermal denaturation of SJL at physiological pH 7.2, native pH 8.5 and molten globule inducing pH 1.0. Topological information revealed by solute quenching studies at respective pH indicated differential hydrophobic environment and charge density around tryptophan residues.

New Computational Approach for External Entropy in Protein-Protein Binding.

Molecular recognition through the noncovalent association of biomolecules is of central importance in biology and pharmacology. Developing reliable computational methods for estimating binding thermodynamic parameters is therefore of great practical value. However, considerable uncertainty remains regarding the external entropy that is associated with the reduction in the external (positional and orientational) degrees of freedom upon complex formation. Here, we present a novel statistical mechanical method for computing the external entropy by extending the energetic approach we have developed for unimolecular processes to association processes. We find that, in contrary to what is postulated in most of the previous methods, intrinsic couplings between the internal and external degrees of freedom of bound complex cannot in general be neglected in the determination of the external entropy. Nevertheless, there exists the best choice of the external coordinates with which those couplings are minimized. With such a choice of the external coordinates, the lowest upper bound of the external entropy is obtained from a tractable expression, which serves as an estimate of the external entropy. Our method can be implemented in a straightforward manner with molecular dynamics simulations, and its applicability is demonstrated through the application to the barnase-barstar complex.

Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters

Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation), and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB on double-stranded DNA has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction.

Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry.

Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.

Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes

Isothermal titration calorimetry was applied to determine the thermodynamic parameters for the specific binding of Ag(I) ions to a series of DNA duplexes comprising Im:Im or Tr:Tr mispairs to form metal-mediated Im–Ag(I)–Im or Tr–Ag(I)–Tr base pairs (Im=imidazole nucleoside; Tr=1.2,4-triazole nucleoside). A total of seven different duplexes are discussed, incorporating one to three artificial base pairs in neighboring or non-neighboring positions. The association constant related to the formation of Tr–Ag(I)–Tr base pairs is estimated to be <103M−1. In contrast, Im–Ag(I)–Im base pairs are much more stable. The intrinsic association constant for their formation is in the order of 106M−1 and is therefore larger than that for the formation of T–Hg(II)–T and C–Ag(I)–C base pairs consisting of natural nucleobases. Two neighboring Im–Ag(I)–Im base pairs form cooperatively, whereas two remotely located Im–Ag(I)–Im base pairs form non-cooperatively. In general, the specific binding of Ag(I) to Im:Im-containing duplexes is enthalpically driven, with a significant additional entropic contribution in most cases.

Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches

ABSTRACTRiboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.

Intrinsic thermodynamics of inhibitor binding to human carbonic anhydrase IX

BackgroundHuman carbonic anhydrase 9th isoform (CA IX) is an important marker of numerous cancers and is increasingly interesting as a potential anticancer drug target. Various synthetic aromatic sulfonamide-bearing compounds are being designed as potent inhibitors of CA IX. However, sulfonamide compound binding to CA IX is linked to several reactions, the deprotonation of the sulfonamide amino group and the protonation of the CA active site Zn(II)-bound hydroxide. These linked reactions significantly affect the affinities and other thermodynamic parameters such as enthalpies and entropies of binding. MethodsThe observed and intrinsic affinities of compound binding to CA IX were determined by the fluorescent thermal shift assay. The enthalpies and entropies of binding were determined by the isothermal titration calorimetry. ResultsThe pKa of CA IX was determined to be 6.8 and the enthalpy of CA IX-Zn(II)-bound hydroxide protonation was −24kJ/mol. These values enabled the analysis of intrinsic thermodynamics of a library of compounds binding to CA IX. The most strongly binding compounds exhibited the intrinsic affinity of 0.01nM and the observed affinity of 2nM. ConclusionsThe intrinsic thermodynamic parameters of compound binding to CA IX helped to draw the compound structure to thermodynamics relationship. General significanceIt is important to distinguish the intrinsic from observed parameters of any disease target protein interaction with its inhibitors as drug candidates when drawing detailed compound structure to thermodynamics correlations.

Fabrication of High-Performance Magnetic Lysozyme-Imprinted Microsphere and Its NIR-Responsive Controlled Release Property.

The preparation of efficient and practical biomacromolecules imprinted polymer materials is still a challenging task because of the spatial hindrance caused by the large size of template and target molecules in the imprinting and recognition process. Herein, we provided a novel pathway to coat a NIR-light responsive lysozyme-imprinted polydopamine (PDA) layer on a fibrous SiO2 (F-SiO2) microsphere grown up from a magnetic Fe3O4 core nanoparticle. The magnetic core-shell structured lysozyme-imprinted Fe3O4@F-SiO2@PDA microspheres (MIP-lysozyme) can be easily separated by a magnet and have a high saturation adsorption capacity of lysozyme of 700 mg/g within 30 min because of the high surface area of 570 m(2)/g and the mesopore size of 12 nm of the Fe3O4@F-SiO2 support. The MIP-lysozyme microspheres also show an excellent selective adsorption of lysozyme (IF > 4). The binding thermodynamic parameters studied by ITC proves that the lysozyme should be restricted by the well-defined 3D structure of MIP-lysozyme microspheres. The MIP-lysozyme can extract lysozyme efficiently from real egg white. Owing to the efficient NIR light photothermal effect of PDA layer, the MIP-lysozyme microspheres show the controlled release property triggered by NIR laser. The released lysozyme molecules still maintain good bioactivity, which can efficiently decompose E. coli. Therefore, this work provides a novel strategy to build practical NIR-light-responsive MIPs for the extraction and application of biomacromolecules.

Study on the interaction of three structurally related cationic Pt(II) complexes with human serum albumin: importance of binding affinity and denaturing properties

Human serum albumin (HSA) primarily functions as a transport carrier for a vast variety of natural ligands and pharmaceutical drugs. In the present study, three structurally related cationic Pt(II) complexes ([Pt(ppy)(dppe)]CF3CO2: 1, Pt(bhq)(dppe)]CF3CO2: 2, and [Pt(bhq)(dppf)]CF3CO2: 3) were used to evaluate their interaction with HSA under different experimental setups, using UV–Vis absorption spectroscopy, fluorescence and circular dichroism techniques. The spectroscopic results suggest that upon binding to HSA, the Pt(II) complexes could effectively induce structural alteration of the protein. The complexes can bind to HSA with the binding affinities of the following order: 3 > 2 > 1. Also, thermodynamic parameters of binding between these complexes and HSA indicated the existence of entropy-driven spontaneous interaction which primarily dominated with the hydrophobic forces. Also, docking simulation study revealed the binding details of these complexes on HSA. Complex 3 with highest binding affinity for HSA indicates lowest denaturing effect on this protein. The low denaturation properties of 3 appear important in the terms of lower susceptibility of this platinum complex for possible development of deleterious side effects.

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).

A combined binding mechanism of nonionic ethoxylated surfactants to bovine serum albumin revealed by fluorescence and circular dichroism

The study systematically investigates aqueous mixtures of fixed bovine serum albumin (BSA) and various ethoxylated nonionic surfactants belonging to a homologous series or not. Mono-disperse tetra-(C12E4), hexa-(C12E6) and octa-ethyleneglycol mono-n-dodecyl ether (C12E8), and poly-disperse eicosa-ethyleneglycol mono-n-tetradecyl ether (C14EO20) are respectively employed. Fluorescence and circular dichroism measurements are performed at surfactant/protein molar ratios (rm)s lower and higher than one. We aim to get new insights into the binding mechanism of these species and to differentiate among the interaction abilities of these surfactants. The relative magnitude of the binding thermodynamic parameters by fluorescence, and the increase of α-helix prove that hydrogen bonding drives the interaction next to the hydrophobic attraction. C12En (n=4,6,8) develop more H bonds with the albumin than C14EO20 owing to a zigzag conformation of their short ethyleneoxide chains. Among the homologous surfactants, C12E6 has a slightly stronger interaction with BSA due to a maximal number of H bonds at a minimal hindering. Static fluorescence and dynamic fluorescence indicate an inter-conversion between the tryptophan (Trp) rotamers which happens around the surfactants critical micellar concentration. For C14EO20, the meander conformation of the polar group determines a less evident conversion of the Trp rotamers and smaller α-helix rise. Binding isotherms of the homologous surfactants and the fluorescence quenching mechanism by C12E6 are also provided.

Thermal analysis of ligand-DNA interaction: determination of binding parameters

The review discusses the methods of thermodynamic analysis of reactions of non-covalent binding of biologically active compounds with DNA, which is a key constituent of cell chromatin. Knowledge of thermodynamic profile of ligand binding with nucleic acids is important for understanding the mechanism of medico-biological action of the currently existing drugs and for designing of new drugs with improved medical effect. Thermodynamic analysis of ligand binding with DNA is based on analysis of experimentally measured changes of Gibbs free energy (ΔG), enthalpy (ΔH), entropy (ΔS) and heat capacity (ΔCр). Right selection of the methods of measurement of these parameters and understanding of limitations of currently existing approaches for numerical data analysis are crucially important for correct interpretation of the obtained results and getting insight into the mechanism of drug-DNA interaction. In the present work the currently existing methods of determination of thermodynamic parameters of ligand binding with DNA were divided into two main groups. The first group is associated with the approaches used in cases when the heating of the system does not cause melting of the biopolymer. The main focus is given to the second group of the methods which are based on description of helix-coil transition of DNA-ligand complexes with further comparison of the same transition for «free» biopolymer. The methods of computation of the binding parameters utilizing the Ising-type models and models based on the equations of chemical equilibrium are discussed.

β-Lactoglobulin (BLG) binding to highly charged cationic polymer-grafted magnetic nanoparticles: Effect of ionic strength

Poly(2-(methacryloyloxy)ethyltrimethyl ammonium chloride) (PMATAC) modified magnetic nanoparticles (NPs) with a high zeta potential of ca. 50mV were synthesized by atom transfer radical polymerization (ATRP). The prepared NPs consist of a magnetic core around 13nm and a PMATAC shell around 20nm attached on the surface of magnetic nanoparticles. Thermodynamic binding parameters between β-lactoglobulin and these polycationic NPs were investigated at different ionic strengths by high-resolution turbidimetry, dynamic light scattering (DLS), and isothermal titration calorimetry (ITC). Both turbidity and ITC show that binding affinities for BLG display a non-monotonic ionic strength dependence trend and a maximum appears at ionic strength of 50mM. Such observation should arise from the coeffects of protein charge anisotropy visualized by DelPhi electrostatic modeling and the strong electrostatic repulsion among highly charged NPs at a variety of ionic strengths.

Thermodynamics of substrate binding to the metal site in homoprotocatechuate 2,3-dioxygenase: Using ITC under anaerobic conditions to study enzyme–substrate interactions

BackgroundExtradiol dioxygenases are a family of nonheme iron (and sometimes manganese) enzymes that catalyze an O2-dependent ring-opening reaction in a biodegradation pathway of aromatic compounds. Here we characterize the thermodynamics of two substrates binding in homoprotocatechuate 2,3-dioxygenase (HPCD) prior to the O2 activation step. MethodsThis study uses microcalorimetry under an inert atmosphere to measure thermodynamic parameters associated with catechol binding to nonheme metal centers in HPCD. Several stopped-flow rapid mixing experiments were used to support the calorimetry experiments. ResultsThe equilibria constant for 4-nitrocatechol and homoprotocatechuate binding to the iron(II) and manganese(II) forms of HPCD range from 2×104 to 1×106, suggesting there are distinctive differences in how the enzyme–substrate complexes are stabilized. Further experiments in multiple buffers allowed us to correct the experimental ΔH for substrate ionization and to fully derive the pH and buffer independent thermodynamic parameters for substrate binding to HPCD. Fewer protons are released from the iron(II) dependent processes than their manganese(II) counterparts. ConclusionsCondition independent thermodynamic parameters for 4-nitrocatechol and homoprotocatechuate binding to HPCD are highly consistent with each other, suggesting these enzyme–substrate complexes are more similar than once thought, and the ionization state of metal coordinated waters may be playing a role in tuning redox potential and in governing reactivity. General significanceSubstrate binding to HPCD is a complex set of equilibria that includes ionization of substrate and water release, yet it is also the key step in O2 activation. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.