Design and synthesis of a dimeric derivative of RK-682 with increased inhibitory activity against VHR, a dual-specificity ERK phosphatase: implications for the molecular mechanism of the inhibition.

BACKGROUND: VHR is a dual-specificity phosphatase, which dephosphorylates activated ERK1/2 and weakens the ERK signaling cascade in mammalian cells. A selective inhibitor is expected to be useful for revealing the physiological function of VHR. RESULTS: First, we investigated the molecular mechanism of VHR inhibition by a known natural product, RK-682. Kinetic analysis indicated that inhibition was competitive toward the substrate, and two molecules of RK-682 were required to inhibit one molecule of VHR. Based on the structure-activity relationships for VHR inhibition by RK-682 derivatives, we constructed a binding model using molecular dynamics calculation. Based on this model, we designed and synthesized a novel dimeric derivative. As expected, the dimeric derivative showed increased inhibition of VHR, supporting our proposed mechanism of VHR inhibition by RK-682. CONCLUSION: We have developed a novel inhibitor of VHR based on the results of kinetic analysis and docking simulation.

Folding energetics of a multidomain protein, flagellin.

Thermodynamic investigations of flagellin from Salmonella typhimurium and its proteolytic fragments were conducted by differential scanning calorimetry (DSC) and circular dichroism (CD) melting measurements. A new method of analysis for a multi-state transition based on our original theoretical treatment of thermodynamic equations has been developed to analyze those data. The analysis of DSC curves confirmed the three thermodynamic domains of flagellin. The thermodynamic parameters of each domain were revised from those previously reported and the new values of the parameters have a good correlation to the apparent molecular masses of the morphological domains. CD melting measurements at far and near-UV wavelengths showed sequential unfolding of the domains. Therefore, we could reasonably assign the thermodynamically identified domains to the morphological domains. Further analysis of both DSC and CD data provided insights into the folding energetics of the multidomain structure of flagellin. An inner domain (Df1) of flagellin in the filament unfolds through a relatively broad transition, while the two outer domains unfold cooperatively and show sharp transitions. This indicates that the interdomain interactions between Df1 and D2 has different characteristics from the apparently more intimate interactions between D2 and D3. These characteristics suggest that flagellin is organized with relatively flexible domains and rigid domains, which appears to be responsible for the well-regulated assembly mechanism of the bacterial flagellar filament.

Biological activities of 1,1,6-trisubstituted indanes: beyond magainin 2.

MSI-78 is a peptide analog of naturally occurring magainin 2 isolated from the skin of Xenopus laevis. The peptide is known to have one of the strongest antibacterial activities in magainin 2 analogs against methicillin-resistant Staphylococcus aureus (MRSA). To find novel compounds superior to MSI-78, we have further designed, synthesizing 1,1-di(4-aminobutyl)-6-benzylindane (PM4) and 1,1-dibenzyl-6-(4-aminobutyl) indane (PM5), and tested their inhibitory ability of the growth of S. aureus. In an in vitro assay, PM4 showed the same antibacterial activity against the bacterium as MSI-78, and non-hemolytic activity against human red blood cells (RBCs) at the MIC (minimum inhibitory concentration) value, in contrast to the latter. On the other hand, PM5 showed stronger antibacterial activity than MSI-78, but being still accompanied with hemolysis at the MIC value. Otherwise, stronger decarboxylase activity for oxaloacetate was observed in PM5, rather than magainin 2 analogs or Oxaldie 1 as a control peptide, but not in PM4.

Single-point amino acid substitutions at the 119th residue of thermolysin and their pressure-induced activation.

The effect of amino acid substitution at the 119th site of thermolysin (TLN) on the pressure activation behavior of this enzyme was studied for four mutants at pressures < 300 MPa. For Q119Q, Q119N and Q119R, the highest activation was observed to be over 30 times that at atmospheric pressure and the activation volumes (deltaV++) were about -75 ml/mol. However, we obtained only 10 times higher activation for Q119E and Q119D (deltaV++ approximately -60 ml/mol). The intrinsic fluorescence of TLN changed at pressures > 300 MPa, and the latter two mutants showed a smaller deltaGapp and deltaVapp of transition than the wild type. These results are discussed with respect to the hydration change in the enzyme protein around the substituted region.

Design of protein function by physical perturbation method.

Based on three-dimensional structure of proteins, a rational strategy to design the protein function by physical perturbation method was proposed and tested on one of the well-examined enzymes, thermolysin for higher catalytic activity. An attempt was made to change the electrostatic potential and the dynamic property of three-dimensional structure around the active sites by single-amino-acid mutations, and the physical property of the mutants was then evaluated. Several mutants were found to have remarkably higher enzymatic activity than wild type. The multiple mutation was introduced and the logarithm of the activity was found to be almost additive. A ten times higher active mutant was realized by simultaneously introducing three single-mutations. This strategy can be easily extended to not only other enzymes but also other kinds of proteins than enzymes to modify or control the protein function based on their three-dimensional structures.

Special folding pathway to tetramer only through the micelle state of the corticotropin-releasing factor.

The ovine corticotropin-releasing factor (CRF), a peptide hormone of 41 residues stimulating the secretion of adrenocorticotropic hormone, was thermodynamically investigated. By means of size exclusion chromatography and/or ultrafiltration, the CRF solution could be separated into random coil monomers and highly alpha-helical tetramers, which seem to have amphipathic helix bundle structure. Circular dichroism measurements along with diluting or concentrating the CRF solution revealed that there exists the micelle state above the concentration of 0.1 mM, which would be the critical micelle concentration (cmc). The micelle state was also proved by binding ability for 8-anilino-1-naphthalenesulfonate and endothermic change by dilution across the cmc. The tetramer showed the cooperative thermal transition at about 55 degrees C in the buffer solution (pH 7.5), so that it would have native-protein-like folding. On the other hand, the micelle undergoes gradual change to dissociated state by heating, regardless of the similar alpha-helicity to the tetramer. Above the cmc the equilibrium between the tetramer and the micelle takes place as well as that between the monomer and the micelle. Whereas, the direct conversion between the tetramer and the monomer scarcely occurred below the cmc. The titration experiment with 2,2,2-trifluoroethanol (TFE) revealed that the cmc decreases with increasing the concentration of TFE. This tendency is the same as that of general surfactants. Most of experimental results can be well explained by this three-phase model involving the monomer, the tetramer, and the micelle. The lack of the equilibrium between the monomer and the tetramer indicates that the folding pathway of the tetramer is the transformation only through the micelle state and not from the monomer. This pathway resembles the collapse model among the phenomenological models for thermodynamic protein folding. By the mathematical consideration for the dissociation of micelle, we have demonstrated that the expected content of undegradable k-mer is 2/(k + 1), which agreed well with the observed tetramer content of CRF (40%).

Remarkable activity enhancement of thermolysin mutants.

Most attempts to modify the properties of enzymes by amino acid substitution around the active sites have resulted in suppression of the biological activity, suggesting that the structure of natural enzymes should be almost optimized evolutionally to show the highest activity. In contrast, we found an interesting site of a well-known metalloendopeptidase, thermolysin (EC.3.4.24.4), where almost all the amino acid replacement causes a remarkable increase in the hydrolytic activity. Negative correlation between the activity and the thermal stability was observed. The flexibility around the substrate binding site is suggested to be a key to the correlation. Nature may have selected the amino acid at this site, which suppresses the flexibility of the molecule, to get the highest thermal stability at the expense of the activity.

Salt-induced formation of the molten globule state of cytochrome c studied by isothermal titration calorimetry.

Although the molten globule state has been proposed as a major intermediate of protein folding, it has proven difficult to obtain thermodynamic data characterizing this state. To explore another approach for characterizing the molten globule state, salt-induced formation of the molten globule state of horse cytochrome c at pH 1.8 was studied by isothermal titration calorimetry. By titrating the acid-unfolded cytochrome c with sodium perchlorate, an exothermic reaction was observed. The titration curve obtained from the heat was cooperative and agreed well with the conformational transition curve measured by CD at 222 nm. This result indicated that the salt-induced conformation change is well approximated by a two-state transition between the acid-unfolded and molten globule states. The heat for formation of the molten globule state estimated by isothermal titration calorimetry was consistent with the enthalpy change for unfolding of the sodium perchlorate-stabilized molten globule state at pH 1.8, which was measured by differential scanning calorimetry and CD. These results indicate that the heat of titration largely reflects the enthalpy change of the conformational transition. From these results, we consider that isothermal titration calorimetry will become a useful approach for investigating the molten globule state.

Cooperative deformation of a de novo designed protein.

A de novo protein design has been made to understand the unique packing of natural proteins that have a beta/alpha-barrel fold. A carefully designed 207 amino acid sequence was synthesized using an Escherichia coli expression system and the structural and thermodynamic characteristics of the purified protein were studied. At neutral pH the protein is soluble and monomeric, with large amounts of secondary structure and a hydrophobic core, although the broad resonance peaks of its NMR spectrum suggest that the designed protein does not have a unique structure with tightly packed side chains. In an H-D exchange experiment, no amido protons of the designed protein exchanged slowly with deuterons. At acidic pH, thermal unfolding was observed with a remarkable change in the excess heat capacity measured directly by a differential scanning microcalorimeter. The enthalpy and entropy differences at 110 degrees C, extrapolated from analyzed thermodynamic parameters, are approximately 1/3 of the common values for natural proteins. These measurements indicate that the folding is significantly cooperative as expected, but that the protein is still loosely packed.

Prediction of the active sites of proteins from amino acid sequences.

The discriminant analysis of complementary units and repeated sequences of amino acids in an initial sample of 48 different enzymes produces practically useful empirical-functions which allow catalytic sites to be distinguished from non-catalytic sites. The independent variables in the discriminant functions were almost all composed of complementary units of amino acids, that is amino acid sequences whose nucleotide coding sequences were complementary to each other. In order to evaluate the validity of the functions, we applied them to the amino acid sequences of 17 different kinds of enzymes as well as 30 non-enzymes such as receptors, oncoproteins, cytokines, hormones and so on. The functions proved to be effective in predicting not only the catalytic sites of enzymes but also the binding sites of the other proteins. The result suggests that complementary units are evolutionarily conserved as a signal around the active sites of various proteins.

Enthalpic destabilization of a mutant human lysozyme lacking a disulfide bridge between cysteine-77 and cysteine-95.

To understand the role of disulfide bridges in protein stability, the thermodynamic changes in the denaturation of two mutant human lysozymes lacking a disulfide bridge between Cys-77 and Cys-95 (C77A and C77/95A) were analyzed using differential scanning calorimetry (DSC). At pH 3.0 and 57 degrees C, the stabilities of both the C77A and C77/95A mutants were decreased about 4.6 kcal.mol-1 in Gibbs free energy change. Under the same conditions, the enthalpy changes (delta H) were 94.8 and 90.8 kcal.mol-1, respectively, which were smaller than that of the wild type (100.8 kcal.mol-1). The destabilization of the mutants was caused by enthalpic factors. Although X-ray crystallography indicated that the mutants preserve the wild-type tertiary structure, removal of the disulfide bridge increased the flexibility of the native state of the mutants. This was indicated both by an increase in the crystallographic thermal factors (B-factors) and by a decrease in the affinity of N-acetylglucosamine trimer [(NAG)3] observed using isothermal titration calorimetry (DTC) due to entropic effects. Thus, the effect of cross-linking on the stability of a protein is not solely explained by the entropy change in denaturation.

Thermodynamic characterization of cytochrome c at low pH. Observation of the molten globule state and of the cold denaturation process.

Several reports have pointed out the existence of intermediate states (both kinetic and equilibrium intermediate) between the native and the denatured states. The molten globule state, a compact intermediate state in which the secondary structure is formed but the tertiary structure fluctuates considerably, is currently being studied intensively because of its possible implication in the folding process of several proteins. We have examined the thermal stability of horse cytochrome c at low pH between 2.0 and 3.2 and different potassium chloride concentrations by absorbance of the Soret band, far and near-ultraviolet circular dichroism (u.v. c.d.) and tryptophan fluorescence using a multidimensional spectrophotometer. The concentration of potassium chloride ranged from 0 M to 0.5 M. The experimental thermal denaturation curves show that: (1) the helical content of cytochrome c remains stable at higher temperature when the concentration of salt is increased; whereas (2) the extent of ordering of the tertiary structure is weakly dependent on salt concentration; and (3) for cytochrome c, the stabilization of the molten globule state is induced by the binding of anions. Other salts such as NaCl, LiCl, potassium ferricyanide (K3Fe(CN)6) and Na2SO4 may also be used to stabilize the molten globule state. The thermodynamic analysis of the denaturation curves of c.d. at 222 nm and c.d. at 282 nm shows that, whereas a two-state (native and denatured) transition is observed at low-salt concentration, the far and near-u.v. c.d. melting curves of cytochrome c do not coincide with each other at high-salt concentration, and a minimum of three different thermodynamic states (IIb, intermediate or IIc, and denatured) is necessary to achieve a sufficient analysis. The intermediate state (called IIc) is attributed to the molten globule state because of its high secondary structure content and the absence of tertiary structure. Therefore, at low pH, cytochrome c is present in at least four states (native, IIb, IIc and denatured) depending on the salt concentration and temperature. The thermodynamic parameters, i.e. the Gibbs free energy differences (delta G), the enthalpy differences (delta H), the midpoint temperatures (Tm) of the transition (IIb in equilibrium intermediate (IIc in equilibrium denatured) are determined. We also give estimates of the heat capacity differences (delta Cp) from the temperature dependence of the enthalpy differences. The enthalpy change and the heat capacity difference of the IIc in equilibrium denatured transition are non-zero. The number of charges (protons or chloride anions) released upon transitions are determined by analysing the pH and chloride anion concentration dependence of the Gibbs free energy.(ABSTRACT TRUNCATED AT 400 WORDS)

Spectroscopic studies on lambda cro protein-DNA interactions.

Spectroscopic (circular dichroism and fluorescence) and thermodynamic studies were conducted on lambda Cro-DNA interactions. Some base substitutions were introduced to the operator and the effects on the conformation of the complex and thermodynamic parameters for dissociation of the complex were examined. It was found that, (1) in the specific binding of Cro with DNA which has a (pseudo) consensus sequence, DNA is overwound, while in non-specific binding it is unchanged, or rather unwound; (2) substitution of central base-pairs or the introduction of a mismatched base-pair at the center of the operator reduces the extent of DNA conformational change on Cro binding and lessens the stability of the Cro-DNA complex, even though there is apparently no direct interaction between Cro and DNA at these positions; (3) stability of the complex increases with the degree of DNA conformational change of the same type during binding; (4) in some cases of specific binding, there are three states in the dissociation of the complex as observed by salt titration: two conformational states for the complex depending on salt concentration and, in non-specific binding, dissociation is a two-state transition; (5) the number of ions involved in interactions between Cro and 17 base-pair DNA is about 7.7 for NaCl titrations; (6) dissociation free energy prediction of the Cro-DNA complex by simple addition of the dissociation free energy change of a single base-pair substitution agrees with our experimental results when DNA overwinding occurs during binding, i.e. in specific binding.

Structural organization of flagellin.

The terminal regions of flagellin from Salmonella typhimurium have been reported to be disordered in solution, whereas the central part of the molecule contains protease-resistant, compact structural units. Here, conformational properties of flagellin and its proteolytic fragments were investigated and compared to characterize the domain organization and secondary structure of flagellin. Deconvolution analysis of the calorimetric melting profiles of flagellin and its fragments suggests that flagellin is composed of three co-operative units or domains. The central part of the molecule, residues 179 to 418, consists of two domains (G1 and G2), whereas the third domain (G3) is discontinuous, constructed from segments 67 to 178 and 419 to 448. Secondary structure prediction and analysis of far-ultraviolet circular dichroic spectra have revealed that G1 and G2 consist predominantly of beta-structure with a little alpha-helical content. G3 contains almost equal amounts of alpha and beta-structure, while in the terminal parts of flagellin the ordered secondary structure seems to be entirely alpha-helical.

Thermal stability of dihydrofolate reductase and its fused proteins with oligopeptides.

Two fused proteins of dihydrofolate reductase (DHFR) with oligopeptides were prepared by a recombinant DNA method. One of these, DHFR-IQI, has three (Ile-Gln-Ile) and the other, DHFR-lek, has eight (Ile-Arg-Met-Tyr-Gly-Gly-Phe-Leu) additional amino acid residues at the C terminals; in both proteins, Cys152 of wild DHFR is replaced by Glu. The thermal transition of the proteins was measured by CD and DSC at pH 7.0 and compared with that of wild DHFR. The results show that the thermal stability of DHFR-IQI is the same as that of the wild DHFR and that of DHFR-lek is less than that of the former two DHFRs. Analysis of the DSC data of DHFR-IQI indicates that the thermal transition is a three-state one. Data from both DSC and CD measurements suggest the association of DHFR-lek molecules.

[The effect of calcium hydroxide eugenol agents on pulp of primary teeth of young dogs. The view of early stages].

Eugenol has such effective anti-corrosion and pain-killing properties that it is widely used for dentistry clinically. We focused our attention on eugenol and made agents for pulpotomy which were mixtures of calcium hydroxide, eugenol and polyethylene glycol 4000 for a base. We attempted to use them for the pulpotomy of primary teeth of young dogs and observed the healing progress of the treated teeth during the early stages. The experiment utilized four young dogs whose primary teeth were pulpotomized by the usual method. Agents of the pulpotomy were mixed calcium hydroxide (1.0 g), eugenol (0.8 ml) and polyethylene glycol 4000 (1.2 ml). After 3 days and 7 days, these teeth were taken out to be made into histopathological specimens. We inspected them microscopically. The results obtained were as follows. 1) After 3 days, the amputated pulp which was in contact with the agents turned into necrotic layers. Degenerative, necrotic, and non-structural states were widely observed. Under the necrotic layers, there were hematoxyline dark stained layers. Also the hematoxyline dark stained layers separated from the proper pulp. In the proper pulp, there were no abnormalities. 2) After 7 days, the necrotic layers were atrophied. In the dark stained layers, the stained areas were darker than that of after 3 days and increased in degeneration. In the proper pulp, round cells appeared and with a chronic inflammatory appearance along with vacuole, atrophy and degeneration. It seemed to be affected by eugenol. Dentin bridges still has not yet formed.