The reaction of aromatic peptides with double helical DNA. Quantitative characterisation of a two step reaction scheme

The binding of LysTrpLys and LysTyrLys to calf thymus DNA has been investigated by the field jump method using fluorescence detection. Two separate relaxation processes, clearly distinguished on the time scale and by opposite ampli- tudes, are observed for the binding of LysTrpLys to DNA with ~ 30000 base pairs. The concentration dependence of the relaxation time constants demonstrates a mechanism with a bimolecular step followed by a slow intramolecular transition with a forward rate of 6.4 X 103 s^?1 and an equilibrium constant of 11. Measurements at various degrees of peptide binding demonstrate that the binding mechanism associated with low binding rates is restricted to a rather low number of binding sites (roughly one site in 15 base pairs). The binding of LysTyrLys to the same DNA is not associated with relaxation pro- cesses of opposite amplitudes; nevertheless two processes could be identified and assigned to a two step mechanism corre- sponding to that observed in the case of LysTrpLys. In the presence of sonicated DNA both peptides show a single relaxa- tion process with characteristics similar to those observed for the slow process in the binding to high molecular DNA. The data indicate that the intramolecular step is faster for low than for high molecular DNA. These results suggest an assignment of the intramolecular step to an insertion of the aromatic residues into the DNA associated with bending of the helix. The increase in the rate of the intramolecular step with decreasing chain length of the DNA may then be explained by a higher flexibility of the double helix at lower chain lengths.     

Kinetics of binding between thermolysin and Streptomyces metalloprotease inhibitor, talopeptin (MKI)

The mechanism of binding between thermolysin with its specific inhibitor, talopeptin (MKI), was studied kinetically with the stopped-flow method by monitoring the enhancement of tryptophan fluorescence caused by the complex formation. Only one relaxation obeying first-order kinetics was observed. The dependence of the apparent first-order constant, kapp, on the inhibitor concentration is consistent with a minimum two-step mechanism, including a fast bimolecular binding step followed by a slow unimolecular step. It was found that the increase in tryptophan fluorescence occurs solely in the slow unimolecular step. The apparent second-order rate constant, (kon)app, in the low inhibitor concentration range, was determined over the pH range between 5 and 8.5 and decreases with increasing pH. The activation parameters for the overall binding process were obtained from the temperature dependence of (kon)app.     

Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation

HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)₂ is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5′-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3′ (FL-AT-1) and 5′-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3′ (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to ∼200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar.     

Kinetics of the daunomycin--DNA interaction

The kinetics of the interaction of daunomycin with calf thymus DNA are described. Stopped-flow and temperature-jump relaxation methods, using absorption detection, were used to study the binding reaction. Three relaxation times were observed, all of which are concentration dependent, although the two slower relaxations approach constant values at high reactant concentrations. Relaxation times over a wide range of concentrations were gathered, and the data were fit by a minimal mechanism in which a rapid bimolecular association step is followed by two sequential isomerization steps. The six rate constants for this mechanism were extracted from our data by relaxation analysis. The values determined for the six rate constants may be combined to calculate an overall equilibrium constant that is in excellent agreement with that obtained by independent equilibrium measurements. Additional stopped-flow experiments, using first sodium dodecyl sulfate to dissociate bound drug and second pseudo-first-order conditions to study the fast bimolecular step, provide independent verification of three of the six rate constants. The temperature dependence of four of the six rate constants was measured, allowing estimates of the activation energy of some of the steps to be made. We speculate that the three steps in the proposed mechanism may correspond to a rapid "outside" binding of daunomycin to DNA, followed by intercalation of the drug, followed by either conformational adjustment of the drug or DNA binding site or redistribution of bound drug to preferred sites.     

Solute complexation degree with human serum albumin: biochromatographic approach

A mathematical model was developed for the study of the D,L-dansylamino acid retention mechanism in reversed-phase liquid chromatography using a C18 column as a stationary phase and human serum albumin (HSA) as an eluent modifier. The solute retention factor is dependent on the HSA concentration in the eluent as well as the binding constant of the guest-HSA complex. A determination of the degree of complexation n(c) (the percent of the complexed guest) could be carried out. Different Van 't Hoff plot shapes of the degree of complexation were observed with different eluent pH, confirming a change in the solute complexation mechanism for physiological pH (between 7-7.5). Enthalpy-entropy compensation was also analysed in relation to this mathematical model to confirm the solute complexation behavior with HSA. These results finally confirmed that at physiological pH and temperature (approximately 35 degrees C) values the HSA was in a favorable structural conformation for its binding with a great majority of drugs.     

The rate of equine liver alcohol dehydrogenase denaturation by urea. Dependence on temperature and denaturant concentration

The kinetics of the irreversible urea denaturation of equine liver alcohol dehydrogenase have been studied as a function of temperature and urea concentration. The unfolding of the macromolecule, monitored by means of the phosphorescence properties of a deeply buried tryptophan residue, was found to be strictly a two-state process over the entire temperature range. It is characterized by a steep dependence on urea concentration typical of highly cooperative transitions and below room temperature it possesses large negative activation energies. The reaction is comparatively slow, does not seem to be preceded by a fast phase, and the rate-limiting step does not have the characteristics of proline isomerization. When the data are analyzed in terms of binding equilibria the temperature dependence results from an anomalously large change in heat capacity. Although this is a property of strong hydrophobic interactions in model compounds the slow rates of denaturation are best understood with a model of protein stability which emphasizes the cooperative nature of intramolecular interactions such as hydrogen bonding.     

Determination of Some Hydrodynamic Parameters of Ovine Serum Albumin Solutions Using Viscometric Measurements

The influence of protein concentration and temperature on the viscosity of ovine serum albumin (OSA) solutions was studied. The Mooney equation and a modified Arrhenius formula were used to described the viscosity-concentration and viscosity-temperature dependence of the solutions, respectively. The effective specific volume, the activation energy and entropy of viscous flow for hydrated OSA were calculated. The axial ratio and the dimensions of the main semi-axes of hydrated OSA were established. At low concentration limit, the temperature dependence of the intrinsic viscosity and Huggins coefficient is presented. Comparison of some hydrodynamic parameters obtained for different proteins has been made.     

Isokinetic relationships for the effect of inorganic phosphate and protons on the deoxygenation rate of human hemoglobin

The rate of hemoglobin deoxygenation is measured as a function of inorganic phosphate concentration, pH, and temperature. Isokinetic relationships (enthalpy-entropy compensation) are searched for by applying the method of O. Exner and, for comparative purposes, the conventional method of plotting the energy of activation (E*) versus the natural log of the pre-exponentional factor of the Arrhenious equation (In A). Both plots indicate compensation between the activation parameters. However, unlike the conventional plot, the Exner treatment is able to distinguish between two types of compensation. Furthermore, when extrapolated rate constants based on all the data in an Exner plot are transposed into E* vs. In A plots, so-called “turn-around” behavior is predicted for the effect of increasing phosphate concentration at constant pH. Such “turn-around” behavior in E* vs. In A plots has been observed experimentally by Beetlestone and co-workers for anion binding to human hemoglobin as a functin of pH. Lastly, the compensation temperatures obtained from these data all fall within the Vaslow-Doherty compensation range (250–350°K) which is thought to indicate that the solvent, water, is involved in the reaction mechanism. Thus, Exner plots appear to further resolve isokinetic temperatures of the Vaslow-Doherty type. Differences in the electrostriction of solvent in the activated state is suggested as one possible physical source for the Vaslow-Doherty type compensation observed in this work.     

Complex formation between the copper protein, azurin and the cytochrome c peroxidase of Pseudomonas aeruginosa.

Reduced azurin reacts with the resting, oxidized cytochrome c peroxidase of Pseudomonas aeruginosa to yield time courses observed at 420 nm, which consist of the sum of two exponential processes. Each process exhibits a hyperbolic dependence of the observed rate constant on the reduced azurin concentration. The fraction of the total optical density change which each process contributes is found to be dependent on the reduced azurin concentration. This pattern of reactivity is maintained at pH values between 5.5 and 8.0. The data has been analyzed in terms of a complex formation between the two proteins followed by an intramolecular electron exchange reaction. This analysis yields values for the binding constants at each pH value. The intramolecular exchange reaction is independent of pH, whilst the pH dependence of the binding reaction suggests the involvement of a histidine residue in this process.     

Spectroscopic investigation of the anticancer alkaloid piperlongumine binding to human serum albumin from the viewpoint of drug delivery

Piperlongumine (PL) is a very promising natural agent with a high potential for cancer treatment. To overcome the poor water solubility of PL, there is a need to develop a novel water‐soluble formulation in which PL is non‐covalently bound to human serum albumin (HSA). PL binding to HSA was studied by various spectroscopic techniques under simulated physiological conditions. Spectroscopic evidence showed that the interaction of PL with HSA could form a PL–HSA complex. The binding constant (K_a) values increased with increasing temperature, and a similar dependence was observed for the number of binding sites (n) values. The number of PL molecules bound to HSA reached 8.1 when the temperature was raised to 308 K. Thermodynamic calculation results suggested that the binding reaction occurred spontaneously but was an entropy‐driven process, and hydrophobic forces played a major role in stabilizing the complex. Furthermore, PL binding induced conformational and microenvironmental changes in HSA. Displacement studies indicated that PL and warfarin had separate binding regions in site I. Therefore, it would be possible to develop a novel water‐soluble formulation involving PL and HSA. This study may provide some valuable information in terms of improving the poor water solubility of PL.     

Water relations in the malonamide-induced haemolysis of mammalian erythrocytes

A revised procedure is described for deriving enthalpy-entropy relations in the haemolysis kinetics of mammalian erythrocytes and its application demonstrates that previously reported linear enthalpy-entropy correlations are statistical artefacts with no real physical basis.Physically valid linear enthalpy-entropy relations do exist between species at constant osmotic concentration, but these are the result of the mutual dependence of the activation parameters on erythrocyte solvent volume. Non-linear enthalpy-entropy dependence on osmotic concentration, which is also physically valid and occurs within species, is attributed to erythrocyte solvent volume variation due to the osmotic properties of haemoglobin.Further development of the data indicates that malonamide-induced haemolysis is essentially an osmotic phenomenon and that the water permeability of all those cells is probably the same.From a consideration of the process in relation to the molecular dynamics of water it appears that the activation enthalpy, entropy and internal energy of haemolysis may refer to the molecular mobility of water during osmosis.     

Electron spin resonance study of the copper(II) complexes of human and dog serum albumins and some peptide analogs

Electron spin resonance spectra of the first Cu(II) complexes of human serum albumin, dog serum albumin, l-aspartyl-l-histidine N-methylamide and glycyl-glycyl-l-histidine N-methylamide have been studied using isotopically pure ⁶⁵Cu in its chloride form. At 77° K, the esr spectra of Cu(II) complex of human serum albumin exhibited only one form of esr signal between pH 6.5 and 11. No intermediate forms were detected. The presence of an equally spaced nine-line superhyperfine structure with spacing ～15 G indicated considerable covalent bonding between Cu(II) and four nitrogen atoms derived from the protein. The esr spectrum form of Cu(II) bound to human serum albumin detected at neutral pH would be consistent with the participation of four nitrogens from the α-NH₂ group, two peptide groups, and the imidazole group of a histidine residue. In contrast, the esr spectra of Cu(II)-dog serum albumin complex showed a transition from a low pH form to a high pH form as the pH was increased to 9.5. These spectral changes were found to be reversible upon lowering the pH. Ligand superhyperfine splittings in the low pH form of the esr signal of Cu(II)-dog albumin were not resolved. The distinct pH dependence of the esr signals observed in human and dog serum albumin complexes could be correlated to their respective optical spectra changes as a function of pH. At room temperature and in the pH range between 6 and 11, the esr spectra of Cu(II) complexes of l-aspartyl-l-alanyl-l-histidine N-methylamide and glycyl-glycyl-l-histidine N-methylamide exhibited a well-resolved nine-line superhyperfine structure indicating metal coordination with four equivalent nitrogen atoms of peptide.     

香菇中麦角钙化甾醇含量的测定及其在人体内的传输机制

在阳光照射和自然阴干两种干燥方式下,测定了香菇中麦角钙化甾醇的含量。在不同实验条件下,测定了麦角甾醇转化为麦角钙化甾醇的转化率。在模拟生理条件下,通过荧光光谱、同步荧光光谱、三维荧光光谱、位点竞争实验、紫外可见吸收光谱和分子对接方法对麦角钙化甾醇与人血清白蛋白相互作用过程中的机制和构象变化进行了系统研究,从而揭示了麦角钙化甾醇在体内的传输机制。结果表明,阳光照射能够提高香菇中麦角钙化甾醇含量。麦角甾醇在溶液状态下经过紫外光照射4h,麦角甾醇转化为麦角钙化甾醇的转化率为21%。荧光光谱表明麦角钙化甾醇通过静态猝灭机制猝灭人血清白蛋白的内源荧光。在288K时有利于麦角钙化甾醇与人血清白蛋白的结合,在较高温度下麦角钙化甾醇不能与人血清白蛋白结合。热力学参数分析和分子对接结果表明,疏水作用、氢键和范德华力是结合过程中的主要作用力。位点竞争实验和同步荧光光谱表明位点I是麦角钙化甾醇和人血清白蛋白相互作用的主要结合位点。结合过程中能够发生能量转移,结合距离是3.46nm。结合过程轻微地改变人血清白蛋白的结构和微环境。     

Elementary processes in the interaction of serine protease with a possible transition state analog. Subtillisin-benzeneboronic acid system.

The interaction of benzeneboronic acid(BBA), a possible transition state analog, with subtilisin BPN' [EC 3.4.21.14] was studied by the temperature-jump method at various pH's, temperatures and in D2O as well as H2O. From analysis of the concentration dependence of the relaxation times, it was suggested that the subtillsin-BBA interactions consist of at least two elementary steps, a fast bimolecular association followed by a slow unimolecular process. Similar concentration dependence was observed at pH 6.1-6.7 at 25degrees. However, in D2O the reciprocal relaxation times generally decreased compared to those in H2O and became concentration-independent below pD 6.5. The relaxation times were influenced considerably by the temperature. From these results, the slow unimolecular process was assigned to the trigonal-tetrahedral interconversion of BBA at the active site of the enzyme.     

Chromatographic study of magnesium and calcium binding to immobilized human serum albumin

The use of immobilized human serum albumin (HSA) as a stationary phase in affinity chromatography has been shown to be useful in resolving optical antipodes or to investigate interactions between drugs and protein. However, to our knowledge, no inorganic ion binding has been studied on this immobilized protein type. To do this, the human serum albumin stationary phase was assimilated to a weak cation-exchanger by working with a mobile phase pH equal to 6.5. A study of the eluent ionic strength effect on ion retention was carried out by varying the buffer concentrations and the column temperatures. The thermodynamic parameters for magnesium and calcium transfer from the mobile to the stationary phase were determined from linear van’t Hoff plots. An enthalpy–entropy compensation study revealed that the type of interaction was independent of the mobile phase composition. A simple model based on the Gouy–Chapman theory was considered in order to describe the retention behavior of the test cations with the mobile phase ionic strength. From this theoretical approach, the relative charge densities of the human serum albumin surface implied in the binding process were estimated at different column temperatures.     

Size as a parameter for solvent effects on Candida antarctica lipase B enantioselectivity

Changes in solvent type were shown to yield significant improvement of enzyme enantioselectivity. The resolution of 3-methyl-2-butanol catalyzed by Candida antarctica lipase B, CALB, was studied in eight liquid organic solvents and supercritical carbon dioxide, SCCO(2). Studies of the temperature dependence of the enantiomeric ratio allowed determination of the enthalpic (Delta(R-S)Delta H(++)) as well as the entropic (Delta(R-S)Delta S(++)) contribution to the overall enantioselectivity (Delta(R-S)Delta G(++)= -RTlnE). A correlation of the enantiomeric ratio, E, to the van der Waals volume of the solvent molecules was observed and suggested as one of the parameters that govern solvent effects on enzyme catalysis. An enthalpy-entropy compensation relationship was indicated between the studied liquid solvents. The enzymatic mechanism must be of a somewhat different nature in SCCO(2), as this reaction in this medium did not follow the enthalpy-entropy compensation relation.     

Kinetic studies of the interaction of methyl orange with poly(L-lysine) by stopped-flow with circular dichroism detection

The interaction of methyl orange with poly(L -lysine) was studied kinetically by the stopped-flow technique with CD detection, as well as by static CD titration experiments. In the static experiments, the differences observed in the polymer-to-dye ratio dependences of the CD spectra and absorption spectra suggested at least two kinds of bound states of the methyl orange attached to the polymer. The kinetic experiments using the stopped-flow apparatus, however, revealed four distinct reaction processes. The reaction mechanism was elucidated from the concentration dependence of the time constant for each process as follows: the first process was attributed to the bimolecular binding step of methyl orange to the side chain of poly(L -lysine), the second and third process were ascribed to the intramolecular reaction of the polymer–dye complex, and the fourth process was found to be the intermolecular aggregation of the polymer–dye complex. The origin of the stacking of methyl orange on poly(L -lysine) is discussed on the basis of the characteristics of signal amplitudes obtained from the kinetic experiments for these processes.     

Kinetic and thermodynamic parameters for oxygen binding to the allosteric states of Panulirus interruptus hemocyanin

The temperature dependence of the oxygen binding equilibria and kinetics of Panulirus interruptus hemocyanin has been analyzed within the context of the two-state allosteric model. Oxygenation of the T-state is characterized by a more negative value of DeltaH than that of the R-state; therefore, cooperative effects in oxygen binding to P. interruptus hemocyanin are thermodynamically governed by favorable entropy changes. The allosteric transition in the unliganded derivative shows an enthalpy-entropy compensation effect. The activation enthalpies for oxygenation and deoxygenation of the T-state are larger than those for the R-state, while the activation entropies are favorable for the T-state and unfavorable for the R-state. Thus, the activation free energies for oxygen binding to the T- and R-states are similar, while for the deoxygenation reaction DeltaG++ is smaller for the T-state. The analysis reported confirms the applicability of the Monod-Wyman-Changeux two-state allosteric model to P. interruptus hemocyanin and yields a complete thermodynamic characterization of oxygen binding under both equilibrium and dynamic regimes.     

Studies of copper(II) binding to glycylglycyl-L-tyrosine-N-methyl amide, a peptide mimicking the NH2-terminal copper(II)-binding site of dog serum albumin by analytical potentiometry, spectrophotometry, CD, and NMR spectroscopy

Unlike human serum albumin (HSA), dog serum albumin (DSA) does not possess the characteristics of the specific first binding site for Cu(II). In DSA, the important histidine residue in the third position, responsible for the Cu(II)-binding specificity in HSA, is replaced by a tyrosine residue. In order to study the influence of the tyrosine residue in the third position of DSA, a simple model of the NH2-terminal native sequence tripeptide of DSA, glycylglycyl-L-tyrosine-N-methylamide (GGTNMA) was synthesized and its Cu(II)-binding properties studied by analytical potentiometry, spectrophotometry, CD, and NMR spectroscopy. The species analysis indicated the existence of five mono-complexes at different protonation states: MHA, MA, MH-1A, MH-2A, MH-3A, and only one bis-complex MH-2A-2. The complexing ability of GGTNMA to Cu(II) was found to be weaker than that of the Cu(II) binding peptide models of HSA. The visible absorption spectra of Cu(II)-GGTNMA complexes are similar to those observed in the case of DSA-Cu(II) complexes. The weaker binding and the spectral properties of Cu(II)-GGTNMA complexes are consistent with less specific Cu(II)-binding properties of the peptide of this sequence similar to what was noted with DSA. CD results are in excellent agreement with species analysis and visible spectra where it is clearly evident that Cu(II) binds to GGTNMA starting from the alpha-NH2 group and step by step to deprotonated amide nitrogens as the pH is raised. The absence of any charge transfer band around 400 nm strongly indicates that Cu(II) does not bind to the phenolate group. Furthermore, NMR results are consistent with the noninvolvement of the tyrosine residue of GGTNMA in Cu(II) complexation. Thus, it is clear that the low Cu(II)-binding affinity of DSA is due to the genetic substitution of tyrosine for histidine at the NH2-terminal region of the protein.     

Na~(+)、Ca~(2+)、Cu~(2+)和Zn~(2+)与HSA相互作用的~(23)(Na)-NMR研究

 本文应用~23Na-NMR波谱技术,研究了Na~(+)、Ca~(2+)、Cu~(2+)和Zn~(2+)与人体血清白蛋白(HSA)的相互作用。在实验基础上,通过引入两位快交换模型,拟合计算获得了Na~(+)与HSA相互作用的结合常数和处于结合状态Na~(+)的相关时间;实验表明Ca~(2+)能与Na~(+)竞争同HSA结合,拟合计算获得了两者与HSA相互作用结合常数的比值,棕榈酸钠能增强Ca~(2+)同Na~(+)竞争与HSA结合的能力;从实验上未能观察到Cu~(2+)、Zn~(2+)能同Na~(+)竞争与HSA相互作用的证据。