Microcalorimetry for biological chemistry: experimental design, data analysis, and interpretation

Targeting pleckstrin-2/Akt signaling reduces proliferation in myeloproliferative neoplasm models

Myeloproliferative neoplasms (MPNs) are characterized by the activated JAK2/STAT pathway. Pleckstrin-2 (Plek2) is a downstream target of the JAK2/STAT5 pathway and is overexpressed in patients with MPNs. We previously revealed that Plek2 plays critical roles in the pathogenesis of JAK2-mutated MPNs. The nonessential roles of Plek2 under physiologic conditions make it an ideal target for MPN therapy. Here, we identified first-in-class Plek2 inhibitors through an in silico high-throughput screening approach and cell-based assays, followed by the synthesis of analogs. Plek2-specific small-molecule inhibitors showed potent inhibitory effects on cell proliferation. Mechanistically, Plek2 interacts with and enhances the activity of Akt through the recruitment of downstream effector proteins. The Plek2-signaling complex also includes Hsp72, which protects Akt from degradation. These functions were blocked by Plek2 inhibitors via their direct binding to the Plek2 dishevelled, Egl-10 and pleckstrin (DEP) domain. The role of Plek2 in activating Akt signaling was further confirmed in vivo using a hematopoietic-specific Pten-knockout mouse model. We next tested Plek2 inhibitors alone or in combination with an Akt inhibitor in various MPN mouse models, which showed significant therapeutic efficacies similar to that seen with the genetic depletion of Plek2. The Plek2 inhibitor was also effective in reducing proliferation of CD34-positive cells from MPN patients. Our studies reveal a Plek2/Akt complex that drives cell proliferation and can be targeted by a class of antiproliferative compounds for MPN therapy.

Identification and Characterization of a Novel Indoleamine 2,3-Dioxygenase 1 Protein Degrader for Glioblastoma

Indoleamine 2,3-dioxygenase 1 (IDO1) is a potent immunosuppressive enzyme that inhibits the antitumor immune response through both tryptophan metabolism and non-enzymatic functions. To date, most IDO1-targeted approaches have focused on inhibiting tryptophan metabolism. However, this class of drugs has failed to improve the overall survival of patients with cancer. Here, we developed and characterized proteolysis targeting chimeras (PROTACs) that degrade the IDO1 protein. IDO1-PROTACs were tested for their effects on IDO1 enzyme and non-enzyme activities. After screening a library of IDO1-PROTAC derivatives, a compound was identified that potently degraded the IDO1 protein through cereblon-mediated proteasomal degradation. The IDO1-PROTAC: (i) inhibited IDO1 enzyme activity and IDO1-mediated NF-κB phosphorylation in cultured human glioblastoma (GBM) cells, (ii) degraded the IDO1 protein within intracranial brain tumors in vivo, and (iii) mediated a survival benefit in mice with well-established brain tumors. This study identified and characterized a new IDO1 protein degrader with therapeutic potential for patients with glioblastoma.

Hierarchical integration of mitochondrial and nuclear positioning pathways by the Num1 EF hand

Positioning organelles at the right place and time is critical for their function and inheritance. In budding yeast, mitochondrial and nuclear positioning require the anchoring of mitochondria and dynein to the cell cortex by clusters of Num1. We have previously shown that mitochondria drive the assembly of cortical Num1 clusters, which then serve as anchoring sites for mitochondria and dynein. When mitochondrial inheritance is inhibited, mitochondrial-driven assembly of Num1 in buds is disrupted and defects in dynein-mediated spindle positioning are observed. Using a structure-function approach to dissect the mechanism of mitochondria-dependent dynein anchoring, we found that the EF hand–like motif (EFLM) of Num1 and its ability to bind calcium are required to bias dynein anchoring on mitochondria-associated Num1 clusters. Consistently, when the EFLM is disrupted, we no longer observe defects in dynein activity following inhibition of mitochondrial inheritance. Thus, the Num1 EFLM functions to bias dynein anchoring and activity in nuclear inheritance subsequent to mitochondrial inheritance. We hypothesize that this hierarchical integration of organelle positioning pathways by the Num1 EFLM contributes to the regulated order of organelle inheritance during the cell cycle.

Accurate and Real-Time Detection Method for the Exothermic Behavior of Enzymatic Nano-Microregions Using Temperature-Sensitive Amino-AgInS2 Quantum Dots

The thermal behavior of enzymes in nanoscale is of great significance to life phenomena. This nonequilibrium state real-time thermal behavior of enzymes at nanoscale cannot be accurately detected by existing methods. Herein, a novel method is developed for the detection of this thermal behavior. The enzyme-quantum dot (QD) conjugates can be obtained by chemically grafting temperature-sensitive amino-AgInS₂ QDs to the enzyme, where the QDs act as nanothermometers with a sensitivity of -2.82% °C^-1 . Detecting the photoluminescence intensity changes of the enzyme-QD conjugates, the real-time thermal behavior of enzymes can be obtained. The enzyme-QD conjugates show a temperature difference as high as 6 °C above ambient temperature in nano-microregions with good reproducibility (maximum error of 4%) during catalysis, while solution temperature hardly changed. This method has a temperature resolution of ≈0.5 °C with a detection limit of 0.02 mg mL^-1 of enzyme, and spatially ensured that the amino-AgInS₂ QDs are quantitatively bound to the enzyme; thus, it can accurately detect the exothermic behavior of the enzyme and can be extended to other organisms' detection. This method has high sensitivity, good stability, and reliability, indicating its great potential application in investigating the thermal behavior of organisms in nanoscale and related life phenomena.

Characterization of protein-protein interactions by isothermal titration calorimetry

The analysis of protein-protein interactions has attracted the attention of many researchers from both a fundamental point of view and a practical point of view. From a fundamental point of view, the development of an understanding of the signaling events triggered by the interaction of two or more proteins provides key information to elucidate the functioning of many cell processes. From a practical point of view, understanding protein-protein interactions at a quantitative level provides the foundation for the development of antagonists or agonists of those interactions. Isothermal Titration Calorimetry (ITC) is the only technique with the capability of measuring not only binding affinity but the enthalpic and entropic components that define affinity. Over the years, isothermal titration calorimeters have evolved in sensitivity and accuracy. Today, TA Instruments and MicroCal market instruments with the performance required to evaluate protein-protein interactions. In this methods paper, we describe general procedures to analyze heterodimeric (porcine pancreatic trypsin binding to soybean trypsin inhibitor) and homodimeric (bovine pancreatic α-chymotrypsin) protein associations by ITC.

2'-O,4'-C-ethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability under physiological condition

Since pyrimidine motif triplex DNA is unstable at physiological neutral pH, triplex stabilization at physiological neutral pH is important for improvement of its potential to be applied to various methods in vivo, such as repression of gene expression, mapping of genomic DNA and gene-targeted mutagenesis. For this purpose, we studied the thermodynamic and kinetic effects of a chemical modification, 2'-O,4'-C-ethylene bridged nucleic acid (ENA) modification of triplex-forming oligonucleotide (TFO), on pyrimidine motif triplex formation at physiological neutral pH. Thermodynamic investigations indicated that the modification achieved more than 10-fold increase in the binding constant of the triplex formation. The increased number of the modification in TFO enhanced the increased magnitude of the binding constant. On the basis of the obtained thermodynamic parameters, we suggested that the remarkably increased binding constant by the modification may result from the increased stiffness of TFO in the unbound state. Kinetic studies showed that the considerably decreased dissociation rate constant resulted in the observed increased binding constant by the modification. We conclude that ENA modification of TFO could be a useful chemical modification to promote the triplex formation under physiological neutral condition, and may advance various triplex formation-based methods in vivo.

Chemical modification of triplex-forming oligonucleotide to promote pyrimidine motif triplex formation at physiological pH

Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in wide variety of potential applications, such as artificial regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis in vivo. Stabilization of pyrimidine motif triplex at physiological pH is, therefore, crucial for improving its potential in various triplex-formation-based strategies in vivo. To this end, we investigated the effect of 3'-amino-2'-O,4'-C-methylene bridged nucleic acid modification of triplex-forming oligonucleotide (TFO), in which 2'-O and 4'-C of the sugar moiety were bridged with the methylene chain and 3'-O was replaced by 3'-NH, on pyrimidine motif triplex formation at physiological pH. The modification not only significantly increased the thermal stability of the triplex but also increased the binding constant of triplex formation about 15-fold. The increased magnitude of the binding constant was not significantly changed when the number and position of the modification in TFO changed. The consideration of the observed thermodynamic parameters suggested that the increased rigidity of the modified TFO in the free state resulting from the bridging of different positions of the sugar moiety with an alkyl chain and the increased hydration of the modified TFO in the free state caused by the introduction of polar nitrogen atoms may significantly increase the binding constant at physiological pH. The study on the TFO viability in human serum showed that the modification significantly increased the resistance of TFO against nuclease degradation. This study presents an effective approach for designing novel chemically modified TFOs with higher binding affinity of triplex formation at physiological pH and higher nuclease resistance under physiological condition, which may eventually lead to progress in various triplex-formation-based strategies in vivo.

Interrupted 2'-o,4'-C-aminomethylene bridged nucleic acid modification enhances pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition

Due to instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex formation-based strategies in vivo, such as regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis. To this end, we investigated the effect of our previously reported chemical modification, 2'-O,4'-C-aminomethylene bridged nucleic acid (2',4'- BNA(NC)) modification, introduced into interrupted and continuous positions of triplex-forming oligonucleotide (TFO) on pyrimidine motif triplex formation at physiological pH. The interrupted 2',4'-BNA(NC) modifications of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold, and significantly increased the nuclease resistance of TFO. On the other hand, the continuous 2',4'-BNA(NC) modification of TFO showed lower ability to promote the triplex formation at physiological pH than the interrupted 2',4'-BNA(NC) modifications of TFO, and did not significantly change the nuclease resistance of TFO. Selection of the interruptedly 2',4'-BNA(NC)-modified positions in TFO was more favorable for achieving the higher binding affinity of the pyrimidine motif triplex formation at physiological pH and the higher nuclease resistance of TFO than that of the continuously 2',4'-BNA(NC)-modified positions in TFO. We conclude that the interrupted 2',4'-BNA(NC) modification of TFO could be a key chemical modification to enhance pyrimidine motif triplex-forming ability and nuclease resistance under physiological condition, and may eventually lead to progress in various triplex formation-based strategies in vivo.

2'-O,4'-C-aminomethylene-bridged nucleic acid modification with enhancement of nuclease resistance promotes pyrimidine motif triplex nucleic acid formation at physiological pH

Due to the instability of pyrimidine motif triplex DNA at physiological pH, triplex stabilization at physiological pH is crucial in improving its potential in various triplex-formation-based strategies in vivo, such as gene expression regulation, genomic DNA mapping, and gene-targeted mutagenesis. To this end, we investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNA(NC)) modification of triplex-forming oligonucleotide (TFO), on triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA(NC) modification of TFO increased the binding constant of the triplex formation at physiological pH by more than 10-fold. The number and position of the 2',4'-BNA(NC) modification in TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity and the increased degree of hydration of the 2',4'-BNA(NC)-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant. Kinetic data demonstrated that the observed increase in the binding constant by the 2',4'-BNA(NC) modification resulted mainly from the considerable decrease in the dissociation rate constant. The TFO stability in human serum showed that the 2',4'-BNA(NC) modification significantly increased the nuclease resistance of TFO. Our results support the idea that the 2',4'-BNA(NC) modification of TFO could be a key chemical modification to achieve higher binding affinity and higher nuclease resistance in the triplex formation under physiological conditions, and may lead to progress in various triplex-formation-based strategies in vivo.

Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes

The quantification of protein-ligand interactions is essential for systems biology, drug discovery, and bioengineering. Ligand-induced changes in protein thermal stability provide a general, quantifiable signature of binding and may be monitored with dyes such as Sypro Orange (SO), which increase their fluorescence emission intensities upon interaction with the unfolded protein. This method is an experimentally straightforward, economical, and high-throughput approach for observing thermal melts using commonly available real-time polymerase chain reaction instrumentation. However, quantitative analysis requires careful consideration of the dye-mediated reporting mechanism and the underlying thermodynamic model. We determine affinity constants by analysis of ligand-mediated shifts in melting-temperature midpoint values. Ligand affinity is determined in a ligand titration series from shifts in free energies of stability at a common reference temperature. Thermodynamic parameters are obtained by fitting the inverse first derivative of the experimental signal reporting on thermal denaturation with equations that incorporate linear or nonlinear baseline models. We apply these methods to fit protein melts monitored with SO that exhibit prominent nonlinear post-transition baselines. SO can perturb the equilibria on which it is reporting. We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly.

Interaction of verapamil with lipid membranes and P-glycoprotein: connecting thermodynamics and membrane structure with functional activity

Verapamil and amlodipine are calcium ion influx inhibitors of wide clinical use. They are partially charged at neutral pH and exhibit amphiphilic properties. The noncharged species can easily cross the lipid membrane. We have measured with solid-state NMR the structural changes induced by verapamil upon incorporation into phospholipid bilayers and have compared them with earlier data on amlodipine and nimodipine. Verapamil and amlodipine produce a rotation of the phosphocholine headgroup away from the membrane surface and a disordering of the fatty acid chains. We have determined the thermodynamics of verapamil partitioning into neutral and negatively charged membranes with isothermal titration calorimetry. Verapamil undergoes a pK-shift of DeltapK(a) = 1.2 units in neutral lipid membranes and the percentage of the noncharged species increases from 5% to 45%. Verapamil partitioning is increased for negatively charged membranes and the binding isotherms are strongly affected by the salt concentration. The electrostatic screening can be explained with the Gouy-Chapman theory. Using a functional phosphate assay we have measured the affinity of verapamil, amlodipine, and nimodipine for P-glycoprotein, and have calculated the free energy of drug binding from the aqueous phase to the active center of P-glycoprotein in the lipid phase. By combining the latter results with the lipid partitioning data it was possible, for the first time, to determine the true affinity of the three drugs for the P-glycoprotein active center if the reaction takes place exclusively in the lipid matrix.

Isothermal titration calorimetry

Isothermal titration calorimetry is an ideal technique for measuring biological binding interactions. It does not rely on the presence of chromophores or fluorophores, nor does it require an enzymatic assay. Because the technique relies only on the detection of a heat effect upon binding, it can be used to measure the binding constant, K, the enthalpy of binding, DeltaH degrees and the stoichiometry, or number of binding sites, n. This chapter describes instrumentation, experimental design, and the theoretical underpinnings necessary to run and analyze a calorimetric binding experiment.

High-density miniaturized thermal shift assays as a general strategy for drug discovery

More general and universally applicable drug discovery assay technologies are needed in order to keep pace with the recent advances in combinatorial chemistry and genomics-based target generation. Ligand-induced conformational stabilization of proteins is a well-understood phenomenon in which substrates, inhibitors, cofactors, and even other proteins provide enhanced stability to proteins on binding. This phenomenon is based on the energetic coupling of the ligand-binding and protein-melting reactions. In an attempt to harness these biophysical properties for drug discovery, fully automated instrumentation was designed and implemented to perform miniaturized fluorescence-based thermal shift assays in a microplate format for the high throughput screening of compound libraries. Validation of this process and instrumentation was achieved by investigating ligand binding to more than 100 protein targets. The general applicability of the thermal shift screening strategy was found to be an important advantage because it circumvents the need to design and retool new assays with each new therapeutic target. Moreover, the miniaturized thermal shift assay methodology does not require any prior knowledge of a therapeutic target's function, making it ideally suited for the quantitative high throughput drug screening and evaluation of targets derived from genomics.

2'-O,4'-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies

Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in an artificial control of gene expression in vivo. Stabilization of the pyrimidine motif triplex at physiological pH is, therefore, crucial in improving its therapeutic potential. To this end, we have investigated the thermodynamic and kinetic effects of our previously reported chemical modification, 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide (TFO), on pyrimidine motif triplex formation at physiological pH. The thermodynamic analyses indicated that the 2',4'-BNA modification of TFO increased the binding constant of the pyrimidine motif triplex formation at neutral pH by approximately 20 times. The number and position of the 2',4'-BNA modification introduced into the TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity itself of the 2',4'-BNA-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant at neutral pH. Kinetic data demonstrated that the observed increase in the binding constant at neutral pH by the 2',4'-BNA modification of TFO resulted from the considerable decrease in the dissociation rate constant. Our results certainly support the idea that the 2',4'-BNA modification of TFO could be a key chemical modification and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo.

Tight ligand binding affinities determined from thermodynamic linkage to temperature by titration calorimetry

A general isothermal titration calorimetry method is described that can be used to determine equilibrium binding constants for high-affinity interactions of ligands with biological macromolecules. The method exploits the thermodynamic linkage between the ligand binding equilibrium constant and temperature. By measuring the binding enthalpy change for an interaction as a function of temperature directly, the change in affinity can be calculated with an integrated form of the van't Hoff equation that is applicable to ligand binding to biological macromolecules. When the temperature dependence of the affinity is combined with the absolute affinity determined independently at a convenient temperature (where the affinity can most accurately or most easily be measured), the absolute binding affinity over the entire temperature range is determined.

Heavy metal toxicity testing in environmental samples

The toxicity of heavy metals in the environment depends on a number of physicochemical and biological factors. The complexity of these relationships has encouraged the use of bioassays for direct measurement of the [table: see text] impact of toxic metals on selected test species. Fish and daphnid bioassays are well accepted by the scientific and regulatory communities, but their length (48 h or more) and the considerable time and effort needed to culture the test organisms make their application to sample screening problematical. Microbial and biochemical assays based on the inhibition of bioluminescence, enzyme activity, enzyme biosynthesis, growth, respiration, and heat production are typically faster and less expensive than the traditional and fish bioassays. Some of these tests approach or equal the sensitivity of daphnids to heavy metals. Since the soil acts as a sink for airborne and waste-applied metals, the uptake of metals by plants and the associated toxic impacts are important. Growth inhibition, enzyme induction, and production of stress proteins have been considered as toxicity end points. Enzymatic tests have been developed that are specific for heavy metal toxicity. Such tests can facilitate toxicity reduction evaluations. Detection of individual metals in the environment may eventually be possible using biosensors consisting of genetically engineered microorganisms. Direct solid-phase tests for soil, sediment, or sludge toxicity, using bacterial bioluminescence or enzyme activity as end points, have been developed. Such tests may complement traditional solid-phase toxicity tests using nematodes or earthworms as indicator organisms. Based on the work reviewed, we draw the following conclusions: 1. The Microtox assay is sensitive to mercury but would fail to detect the toxicity of certain metals, such as cadmium. Among all the microbial assays reviewed, the bioassay based on growth inhibition of the alga Selenastrum capricornutum appears to give the lowest EC50s, similar to those seen for daphnid bioassays. 2. Biosensors, using genetically engineered microorganisms, offer an elegant means of detecting the presence of specific heavy metals in environmental samples. However, at the present time, they are not designed for assessing heavy metal toxicity. 3. The use of bioassays specific for heavy metal toxicity can be useful for directly assessing the bioavailability of these toxicants in environmental samples, thus avoiding the need for fractionation.+4

Thermodynamics of inhibitor binding to the catalytic site of glucoamylase from Aspergillus niger determined by displacement titration calorimetry

The binding of different inhibitors to glucoamylase G2 from Aspergillus niger and its temperature and pH dependencies have been studied by titration calorimetry. The enzyme binds the inhibitors 1-deoxynojirimycin and the pseudo-tetrasaccharide acarbose with association constants of 3 x 10(4) and 9 x 10(11) M-1, respectively, at 27 degrees C. The binding free energy for both ligands is remarkably temperature-invariant in the interval from 9 to 54 degrees C as the result of large compensating changes in enthalpy and entropy. Acarbose and 1-deoxynojirimycin bound with slightly different free energy-pH profiles, with optima at 5.5 and 5.5-7.0, respectively. Variations in delta H degrees and T delta S degrees as a function of pH were substantially larger than variations in delta G degrees in a partly compensatory manner. Two titratable groups at or near subsite 1 of the catalytic site were found to change their pKa slightly upon binding. The hydrogenated forms of acarbose, D-gluco- and L-ido-dihydroacarbose, bind with greatly reduced association constants of 3 x 10(7) and 2 x 10(5) M-1, respectively, and the pseudo-disaccharide methyl acarviosinide, lacking the two glucose units at the reducing end compared to acarbose, has a binding constant of 8 x 10(6) M-1; these values all result from losses in both enthalpy and entropy compared to acarbose. Three thio analogues of the substrate maltose, methyl alpha- and beta-4-thiomaltoside and methyl alpha-4,5'-dithiomaltoside, bind with affinities from 3 x 10(3) to 6 x 10(4) M-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Regeneration of immobilized antibodies on fiber optic probes

The regeneration of antibodies covalently immobilized to an optical fibre surface was investigated by dissociation of the antibody-antigen complex with three different solvents: (a) an acidic solution (0.1 M glycine hydrochloride in 50% (v/v) ethylene glycol, pH 1.75), (b) a basic solution (0.05 M tetraethylamine in 50% (v/v) ethylene glycol, pH 11.0) and (c) 50% (v/v) ethanol in PBS. The fibres coated with polyclonal rabbit anti-goat antibody against a large protein retained 70% and 65% of the original signal after five consecutive regenerations with acidic and basic solvent systems, respectively. The fibres coated with monoclonal mouse anti-trinitrobenzene antibody specific for a small organic molecule, retained over 90% of the original signal when regenerated with basic and ethanol solutions. This study evaluated regeneration and reuse of antibody-coated fibre optic biosensors as a means of reducing routine laboratory analysis costs and time.

Electrostatic and nonpolar peptide-membrane interactions. Lipid binding and functional properties of somatostatin analogues of charge z = +1 to z = +3

The interaction of four structurally related somatostatin analogues (effective electric charge +0.4 < or = < or = +3) with lipid membranes was studied with titration calorimetry and was compared with the functional activity of the peptides. Surface activity measurements provided average cross-sections of 70 or 135 A2, indicating that the cyclic molecules orient at the air-water interface with their ring system either parallel (z = +3) or perpendicular (z = +1) to the surface or switching between the two orientations according to the surface density (z = +2). The nonspecific binding of the peptides to sonified lipid vesicles was enthalpy-driven with a delta H of -4 to -7.5 kcal/mol. A consistent quantitative analysis of the binding isotherms was achieved by combining electrostatic attractions, calculated via the Gouy-Chapman theory, with a nonspecific surface partition equilibrium for the nonpolar interactions. The electrostatic attraction of the cationic peptides varied strongly according to the peptide charge. Due to the flat ring structure of the cyclic peptides, their true physical charge was sensed at the membrane surface, and no "charge screening" was observed. Peptide binding to the negative charged membrane was accompanied by a proton-uptake of the N-terminal amino group of 0.23-0.38 H+/peptide. Deviations from the theoretical prediction of 0.39 H+/peptide can be explained by a preferential binding of the nonprotonated species. The nonpolar interactions, as described by the surface partition coefficients of the four peptides, fell into a narrow range of K congruent to 50-230 M-1 whereas the apparent overall binding constants were between 200 and 5000 M-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Thermodynamics of binding of the CO2-competitive inhibitor imidazole and related compounds to human carbonic anhydrase I: an isothermal titration calorimetry approach to studying weak binding by displacement with strong inhibitors

The visible spectrum of Co(II)-substituted human carbonic anhydrase I (HCA I) complexed with the unique CO2-competitive inhibitor imidazole undergoes a marked alkaline intensification, with a midpoint near pH 8 [Bauer, R., Limkilde, P., & Johansen, J. T. (1977) Carlsberg Res. Commun. 42, 325-339]. This change was first attributed to the ionization of a nondisplaced water ligand of the active-site metal in a five-coordinate complex. Later proposals favored assigning it to the deprotonation of the bound imidazole itself to give a tetrahedrally coordinated imidazolate anion at high pH. We have determined by isothermal titration calorimetry the pH dependence of the enthalpy of binding of imidazole and its analogues to HCA I and Co(II)HCA I. We devised an indirect strategy whereby the enthalpy of binding of the strong sulfonamide inhibitor methazolamide was determined in the absence and presence of a constant high concentration of the competing imidazole or its analogues. The standard enthalpy of binding of deprotonated methazolamide to the "acid" form of HCA I and Co(II)HCA I was found to be pH independent over the pH range of 6.5-9.5, as expected. It was also identical for both the zinc (-13.5 +/- 1.1 kcal M-1) and the cobalt (-13.7 +/- 0.4 kcal M-1) forms. The standard enthalpy of binding of neutral imidazole (average value -6.1 +/- 0.8 kcal M-1) surprisingly did not show any marked pH dependence, varying by about 1.1 and 2.6 kcal M-1 for the zinc and cobalt enzymes, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Organization of glycosphingolipids in phosphatidylcholine bilayers: use of antibody molecules and Fab fragments as morphologic markers

The techniques of ultrafast freezing and freeze-etch electron microscopy have been successfully employed to visualize IgG molecules and Fab fragments specifically bound to the neutral glycosphingolipids Forssman and asialo-GM1 incorporated into phosphatidylcholine liposomes. Monovalent Fab is the superior marker because of its small size and because it does not cause liposomal aggregation with concomitant glycolipid reorganization. Analysis of Fab labeling of liposomes containing these neutral glycosphingolipids leads to the conclusion that the Forssman glycosphingolipid is dispersed in clusters of not more than several molecules when present at low mole fraction in fluid-phase 1-palmitoyl-2-oleoylphosphatidylcholine liposomes. In contrast to this, asialo-GM1 under the same conditions is present in clusters of about 15 molecules in this phospholipid matrix.

A study on the allosteric interaction between the major binding sites of human serum albumin using microcalorimetry

The binding of warfarin and oxyphenbutazone to albumin has been studied at pH 6.8 and pH 9.2 by measuring the heat of binding of these ligands to their high-affinity binding sites on albumin (delta Ho'1). The -delta Ho'1 values for the binding of warfarin at pH 6.8 and 9.2 and oxyphenbutazone at pH 6.8 and 9.2 were found to be 16.9(+/- 0.6), 28.8(+/- 0.6), 10.5(+/- 0.4) and 17.4(+/- 0.6) kJmol-1, respectively. The Gibbs energies (delta Go'1) corresponding to these delta Ho'1 values cover a much smaller range. The pH dependences of delta Go'1 and delta Ho'1 are explained in terms of pK shifts in the albumin upon binding warfarin or oxyphenbutazone. Diazepam, which binds to a site on albumin which is different from the warfarin-oxyphenbutazone binding site, increases - delta Ho'1 for the binding of warfarin and oxyphenbutazone to albumin at pH 6.8, but it does not influence the -delta Ho'1 at pH 9.2. This phenomenon may be attributed to an allosteric interaction between the diazepam binding site and the warfarin binding site. This allosteric interaction must have its origin in a phenomenon other than the N-B transition.

Temperature-dependent delta C0p generated by a shift in equilibrium between macrostates of an enzyme

Substantial negative heat capacity changes (delta C0p' s) have frequently been observed to accompany the formation of protein-ligand complexes. Glutamate dehydrogenase and horse liver alcohol dehydrogenase, however, have been reported to form binary complexes with coenzyme with negligible delta H0p' and only small delta C0p' s. Although many intriguing mechanisms have been proposed to account for the observed phenomena, there is little direct experimental evidence available which might provide a basis for evaluating the contributions of delta C0p' s of complex formation from the various mechanistic sources or even for distinguishing between them. However, if, as Eftink and Biltonen have suggested, a shift in equilibrium between macrostates contributes significantly to an observed delta C0p' s for a given reaction, it should be possible to characterize such a system by measuring the temperature dependence of the delta C0p'. Despite this, few studies have determined delta H0' values at more than two temperatures. We have now measured the temperature dependence of the delta H0' (and, thereby, that of the delta C0p') of the formation of an enzyme-reduced coenzyme complex in an attempt to provide such a basis and have found that the entire delta C0p' of complex formation is accounted for by a temperature-induced shift of an equilibrium between the different forms of the free enzyme.

Calorimetric study of concanavalin A binding to saccharides

The binding of concanavalin A in the dimer form to various saccharides has been studied by calorimetry, and estimates of the binding enthalpy and binding constants have been calculated. Methyl alpha-D-mannoside and methyl alpha-D-glucoside have a -- delta H0 of 21.5 and 11.5 kJ/mol, respectively, at both pH 4 and 4.5. The p-nitrophenyl derivatives react with enthalpic values of 15.6 and 14.6 kJ/mol. The galactosepyranosides show no heat effects during mixing with the protein solutions. The apparent binding enthalpies calculated from the variations of the equilibrium constants with temperature are in good agreement with the values measured experimentally. The two binding sites of the dimer form of concanavalin A are equal and independent, and the low enthalpies obtained do not justify a large conformational change during the reaction. The binding reaction has also been estimated for other sugars normally contained in glycoproteins.

The thermodynamics of nucleotide binding to proteins

Models describing the interaction of a small molecule with a protein are typically couched in terms of the stoichiometry, cooperativity, and binding free-energy change. These parameters are readily available from equilibrium dialysis experiments (or appropriate variations). With the recent advent of extremely sensitive calorimeters, it is possible to obtain thermal data for the binding reaction and, thus, the entire set of thermodynamic parameters, delta G', delta H', delta S', delta C', become readily available. This review is limited to the binding of nucleotides and nucleotide analogs to proteins for which complete thermal data are available. While the majority of such systems have been characterized by calorimetry, we have not excluded, per se, van't Hoff enthalpy determinations. The systems we have considered include, but are not limited to, thymidylate synthetase, phosphorylase, several dehydrogenases, aldolase, glutamine synthetase, hemoglobin, asparate transcarbamylase, and ribonuclease. A variety of forces contribute to the total free-energy change upon ligand binding. These forces include ionic, van der Waals, hydrogen bond, and hydrophobic. In several cases, properly designed experiments have allowed a partial resolution of the individual contributions of these various forces. Variation of easily accessible conditions such as temperature, pH, ionic strength, or solvent third component produce changes in the set of thermodynamic parameters which lead to the resolution of the forces. The generality of heat effects makes this method very useful for studying the involvement of protons in binding reactions. The variation in the magnitude and direction (release or uptake) of the proton flux is readily studied by determining the apparent heat of reaction at constant pH, ionic strength, and temperature in two or more buffers of differing heat of ionization. This application has been exploited in several cases and is examined in great detail. An overview of the results in these systems to date suggests that several trends observed in the thermodynamic parameters need to be confirmed by further experimentation and, if they hold, an appropriate theoretical basis must be developed to aid in their interpretation.