Design and synthesis of novel chiral molecular tweezers based on deoxycholic acid

A novel type of chiral molecular tweezers has been designed and synthesized by using deoxycholic acid as backbone and ethanoyl and the chiral unsymmetrical urea unit as arms. Their structures were characterized by 1H NMR, IR, MS spectra and elemental analysis. These molecular tweezers showed good binding ability for neutral molecules and chiral molecules.     

Microdialysis-liquid chromatographic study on competitive binding of drugs to protein

A new method to determine the interaction between drug and protein has been developed by utilizing the technique of microdialysis sampling with the ketoprofen and the human serum albumin (HSA) as the model of drug and protein.Two kinds of binding sites of HSA to ketoprofen have been observed.The binding constants and number of binding sites obtained by the Scatchard equation are 0.799,3.18×106 mol-1 L and 2.15,2.01×105 mol-1 L,respectively The displacement binding of drugs to HSA has also been studied.The strong displacement of competitive binding of ibuprofen with ketoprofen to HSA was observed,which means that the primary binding site of HSA to ketoprofen and that to ibuprofen are the same.However,only a weaker displacement of warfarin for the association of ketoprofen with HSA was observed,which may suggest that the primary binding site of HSA to ketoprofen is different from that to warfarin.Such a displacement effect for competitive binding of drugs to HSA was explained by the displacement model i     

Infrared Absorption Intensity Analysis as a New Tool for Investigation of Salt Effect on Proteins

The native protein structures in buffer solution are maintained by the electrostatic force as well as the hydrophobic force, salt ions play an important role in maintaining the protein native structures, and their effect on the protein stability has attracted tremendous interests. Infrared spectroscopy has been generally used in molecular structure analysis due to its fingerprint resolution for different species including macromolecules as proteins. However spectral intensities have received much less attention than the vibrational frequencies. Here we report that the spectral intensities of protein amide I band, the finger prints for the protein secondary structures, are very sensitive to the local electric field known as Onsager reaction field caused by salt ions. IR absorbance thermal titrations have been conducted for a series of samples including simple water soluble amino acids, water soluble monomeric protein cytochrome c and dimeric protein DsbC and its single-site mutant G49R. We found that at lower temperature range （10-20℃）, there exists a thermal activated salting-in process, where the IR intensity increases with a rise in the temperature, corresponding to the ions binding of the hydrophobic surface of protein. This process is absent for the amino acids. When further raising the temperature, the IR intensity decreases, this is interpreted as the thermal activated breaking of the ion-protein surface binding. Applying Van＇t Hoff plot to the thermal titration curves, the thermodynamic parameters such as AH and AS for salting-in and ion unbinding processes can be derived for various protein secondary structural components, revealing quantitatively the extent of hydrophobic interaction as well as the strength of the ion-protein binding.     

Theoretical Study on Co^3＋ in Aqueous Solution in Terms of ABEEM/MM Model

A detailed theoretical investigation on Co^3＋ hydration in aqueous solution has been carded out by means of molecular dynamics （MD） simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics （ABEEM/MM）. The effective Co^3＋ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co^3＋（aq.） solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties （radial distribution function, angular distribution function and solvation energy） obtained for Co^3＋ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model.     

Discovery of Anti-SARS Coronavirus Drug Based on Molecular Docking and Database Screening

The active site of 3CL proteinase (3CL^por) for coronavirus was identified by comparing the crystal structures of human and porcine coronavirus. The inhibitor of the main protein of rhinovirus (Ag7088) could bind with 3CL^pro of human coronavirus, then it was selected as the reference for molecular docking and database screening. The ligands from two databases were used to search potential lead structures with molecular docking. Several structures from natural products and ACD-SC databases were found to have lower binding free energy with 3CL^pro than that of Ag7088. These structures have similar hydrophobicity to Ag7088. They have complementary electrostatic potential and hydrogen bond aeceptor and donor with 3CL^pro, showing that the strategy of anti-SARS drug design based on molecular docking and database screening is feasible.     

Competing binding of metal ions with protein studied by microdialysis

A method has been established to study the competing binding of metal ions with protein by a combined technique of microdialysis with high performance liquid chromatography (HPLC). Ni2+, Cd2+, Zn2+, Cu2+ and human serum albumin (HSA) were chosen as model metal ions and protein. The experimental results show that Ni2+ and Cu2+ share a common primary binding site on HSA, and Zn2+ and Cd2+ share a different common primary binding site from them, but there is a common multi-metal binding site for all of those four metal ions. This method show advantages of fast sampling, easily to be operated and especially to be useful when ideal spectroscopic probes are not available for the study of interaction between protein and metal ions.     

A viologen-urea-based anion receptor： Colorimetric sensing of dicarboxylate anions

Compound 1 bearing urea and viologen groups has been designed and synthesized.It could be used as a colorimetric receptor for dicarboxylate anions due to the significant color changes of the solution upon the addition of dicarboxylates.More importantly,the color changes were related to the chain lengths of the dicarboxylates tested.UV-vis,’H NMR and HRMS studies demonstrated that receptor 1 utilized hydrogen bonds and electrostatic interactions to form 1:1 stoichiometry complexes with these anions.In addition,the generation of cation radical 1’ during the complexation process was also detected by EPR.     

A molecular dynamics and computational study of human KAT3 involved in KYN pathway

Kynurenine aminotransferases (KATs) catalyze the transamination of kynurenine (KYN) pathway and endogenous KYNs have been suggested to highly correlate to abnormal brain diseases. HKAT3 is a key member of KAT family, while the binding mechanism of KYN and cofactor with HKAT3 has not been determined yet. In this study, we focus on the structure-function relationship among KYN, cofactor and HKAT3. The binding models of KYN complex and KYN&cofactor complex were obtained and were studied by molecular dynamics (MD) simulations. We identified several critical residues and influence of conformational changes in human kynurenine aminotransferase 3 (HKAT3) complexes. The cofactor may contribute largely not only to the catalysis, but also to the binding. In addition, a hypothesis is proposed that a strong hydrophobic interaction between Tyr159 and Lys280 may influence the binding mode and the binding region of the substrate and the cofactor. Our results will be a good starting point for further determination of the biological role.     

Aluminum Lon Removal from Monoaluminum Ovotransferrin by Pyrophosphate

The rates at which aluminum was removed from the N- and C-terminal monoaluminum ovotransferrins by pyrophosphate were evaluated by UV difference spectra in 0.01 mol/L Hepes, pH=7.4 and at 37℃. Pesudo first-order rate constants as a function of pyrophosphate concentration were measured. The results indicate that the pathways of aluminum removal are different. For the N-terminal binding site, aluminum removal follows simple saturation kinetics, while the removal of aluminum from the C-terminal binding site reverts to the combination of saturation and first-order kinetics. The saturation component is consistent with a rate-limiting conformational change in the protein as has been reported. We propose that the first-order kinetics mechanism is attributed to a pre-equilibrium process. The rate constants of saturation kinetics are accelerated from both terminals with the addition of 0.1 mol/L chloride to the monoaluminum ovotransferrin solutions, whereas the rates of the first-order kinetics are decreased for the C-terminal binding site. The effect of chloride ionic strength causes a continuing increase on kobs for the N- and C-terminal binding sites. Moreover, the kinetics behavior of the N-terminal is more easily affected by chloride than that of the C-terminal. In the experiment presumably the N-terminal site is apparently kinetically more labile than the C-terminal site.     

The lipase monolayer film self-assembly on the negatively charged poly(ethylene terephthalate) substrate

The artificial assembly of enzymes is of considerable interest in basic research fordevelopment of enzyme engineering as well as for technological applications.Since 1991, the molecular deposition developed by Decher and others has been aversatile method for the protein and enZyme molecules self.assembly as a noveltechnique of immobilized enZyme. The glucose isomerase and the bienZymes of glucoseoxidase and glucoamylase were assembled using molecular deposition on the surface ofthe canonized …     

Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L?1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.     

Determination of captopril in pharmaceutical preparation and biological fluids using two- and three-way chemometrics methods

Spectrophotometric method has been developed for the direct quantitative determination of captopril in pharmaceuticalpreparation and biological fluids(human plasma and urine)samples.The method was accomplished based on parallel factoranalysis(PARAFAC)and partial least squares(PLS).The study was carried out in the pH range from 2.0 to 12.8 and with aconcentration from 0.70 to 61.50 μg mL~(-1)of captopril.Multivariate calibration models such as PLS at various pH and PARAFACwere elaborated from ultraviolet spectra deconvolution and captopril determination.The best models for this system were obtainedwith PARAFAC and PLS at pH 2.0.The applications of the method for determination of real samples were evaluated by analysis ofcaptopril in pharmaceutical preparations and biological fluids with satisfactory results.The accuracy of the method,evaluatedthrough the RMSEP,was 0.5801 for captopril with best calibration curve by PARAFAC and 0.6168 for captopril with PLS at pH 2.0model.     

Resonance Rayleigh scattering study of the interaction of bleomycinA_5 with nucleic acids and its analytical application

The interaction of bleomycinA5 with nucleic acids has been investigated by using resonance Rayleigh scattering (RRS), molecular absorption and fluorescence spectra. The result shows that in near pH 2.2 buffer medium and absence of any metal ions, nucleic acids are capable of binding with bleomycinA5 (BLMA5) to form complexes which can remarkably enhance the RRS intensity and result in batho- chromic and hyperchromic molecular absorption of nucleic acids and fluorescence quenching of bleomycinA5. The RRS spectral characteristics for the binding products of bleomycinA5 with various DNA and RNA are similar, and the maximum RRS peaks are at 301 nm for ctDNA and sDNA, 370 nm for hsDNA, 310 nm for RNAtypeVI and RNAtypeIII, respectively. The increments of RRS intensity are greatly different in which DNA enhances greatly and RNA enhances lightly. In this work, the optimum condi- tions of the interaction and some influencing factors have been investigated. The reaction mechanism and a binding model for the interaction of BLMA5 with the nucleic acids are discussed. In addition, a highly sensitive, simple and rapid new method for the determination of DNA has been developed. The detection limits (3σ) are 5.7 ng/mL for ctDNA, 7.4 ng/mL for sDNA and 9.2 ng/mL for hsDNA, respectively. The method can be applied to determination of trace amounts of DNA.     

PURIFICATION OF Cd-BINDING PROTEIN FROM MAIZE ROOTS BY REVERSE-PHASE HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY

An efficient procedure of purification of Cd-binding protein in roots of maize has been established. Young seedlings of maize were exposed to a medium containing CdCl2 to induce the production of Cd-binding protein in their roots. The protein was purified after heat treatment by ion-exchange chromatography and reverse-phase HPLC. The resulting protein was identified as a purified product by N-terminal amino acid with the dansyl method. Its molecular weight was 3200 dalton, the cysteine content was 29.5%, about 3 Cd atoms were bound to one molecule of the protein and the Cd : cystine ratio was 1 : 2.3. According to its character, this protein could be a kind of plant metallothionein-like protein.     

Urea Decomposition Method to Synthesize Hydrotalcites

The urea decomposition property at high temperature has been used to control the pH value in the synthesis of layer compounds. The hydrotalcites of Mg-Al and Ni-Al with high crystallinity were synthesized by using this property.     

Fluorometric enzyme immunosensing system based on natural product resveratrol for horseradish peroxidase and Ag/SiO_2 nanoparticles

The properties of resveratrol (3′, 4′, 5-trihydroxystlbene, RST) were for the first time evaluated as a potential substrate for horseradish peroxidase (HRP)-catalyzed fluorogenic reaction. The properties of RST for use as fluorogenic substrates for HRP and its application in immunoassays were compared with commercially available substrates such as p-hydroxyphenylpropionic acid (pHPPA), chavicol and Amplex red by a fluoroimmunosensing method in the use of Schistosomia japonicum antibody (SjAb) as a model analyte. The fluoroimmunosensing device was constructed by dispersing Schistosomia japonicum antigen (SjAg), nano-Ag/SiO2 particles and sol-gel at low temperature. In pH 5.8 Britton-Robinson buffer (B-R), HRP-SjAb conjugates can catalyze the polymerization reaction of RST by H2O2 forming fluorescent dimmers. The increase of the fluorescence intensity of the dimmers product at emission of 462 nm (excitation: 315 nm) is proportional to the concentration of HRP-SjAb binding to the SjAg entrapped in the nano-Ag/SiO2 particles-sol-gel matrix. A competitive binding assay has been used to determine SjAb in rabbit serum with the aid of SjAb labeled with HRP. Substrate RST showed comparable ability for HRP detection and its enzyme-linked immunosensing reaction system, in a linear detection ranging of 1.5×10-6-7.3×10-4 g/L and with a detection limit of 1.5×10-6 g/L. The immobilized biocomposites surface could be regenerated by simply polishing with an alumina paper, with an excellent reproducibility (RSD = 4.7%). The proposed method has been successfully used for analysis of the rabbit serum sample with satisfactory results.     

Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immu- noglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change △H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol-1 and 132.95 J·mol-1·K-1 according to the Vant’ Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient Frster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein’s secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.     

HYDROGEN-SUPPORTED NITROGENASE ACTIVITY IN Rhodopseudomonas capsulata: THE NATURALLY OCCURRING ELECTRON CARRIERS

In vivo the hydrogenase of Rhodopseudomonas capsulata is capable of recycling molecular hydrogen, which is coupled to the nitrogenase for acetylene redaction. A ferredoxin from R. capsulata can be reduced by native hydrogenase with molecular hydrogen as electron donor. The reducing power generated by H_2-hydrogenase could couple to nitrogenase-dependent acetylene reduction via ferredoxin. A natural fraction from crude extracts of R. capsulata has been separated, which functions as an active electron carrier between H_2-hydrogenase system and acetylene reduction reaction by native nitrogenase. A low midpoint redox potential component was identified in this natural fraction. The evidence indicates that the component effective for the coupling of electron might be a cytochrome C_3. A methyl viologen-linked diaphorase activity specific to NADPH has been identified. The possible role of ferredoxincytochrome C_3 complex as an electron carrier system in the hydrogen evolution and hydrogen recycling process by     

Integration of genetic virtual screening patterns and latent multivariate modeling techniques for QSAR optimization based on combinations and/or interactions between peptides and proteins

Both the concept and the model of snug quantitative structure-activity relationship (QSAR) were pro-posed and developed for molecular design through constructing QSAR based on some known mode of receptor/ligand interactions. Many disadvantages of traditional models can be avoided by using the proposed method because the traditional models only determined upon molecular structural features in sample sets themselves. A genetic virtual screening of peptide/protein combinations (GVSPPC) is proposed for the first time by utilizing this idea to examine peptide/protein affinity activities. A genetic algorithm (GA) was developed for screening combinative targets with an interaction mode for virtual receptors. GVSPPC succeeds in disposing difficulties in rational QSAR,in order to search for the ligand/receptor interactions on conditions of unknown structures. Some bioactive oligo-/poly-peptide systems covering 58 angiotensin converting enzyme (ACE) inhibitors and 18 double site mutation residues in camel antibody protein cAb-Lys3 were investigated by GVSPPC with satisfactory results (R 2 cu>0.91,Q 2 cv > 0.86,ERMS=0.19-0.95),respectively,which demonstrates that GVSPPC is more inter-pretable in the ligand-receptor interaction than the traditional QSAR method.     

Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

The double-stranded DNA (dsDNA) probe contains two different protein binding sites. One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme. The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.