Terminal protection of small molecule-linked ssDNA-SWNT nanoassembly for sensitive detection of small molecule and protein interaction

The interactions between small molecules and proteins constitute a critical regulatory mechanism in many fundamental biological processes.A novel biosensing strategy has been developed for sensitive and selective detection of small molecule and protein interaction on the basis of terminal protection of small molecule-linked ssDNA-SWNT nanoassembly.The developed strategy is demonstrated using folate and its binding protein folate receptor(FR) as a model case.The results reveal the developed technique displays superb resistance to non-specific binding,very low detection limit as low as subnanomolar,and a wide dynamic range from 100 pmol/L to 500 nmol/L of FR.Thus,it may offer a simple,cost-effective,highly selective and sensitive platform for homogeneous fluorescence detection of small molecule-protein interaction and related biochemical studies.     

REFINED CRYSTAL STRUCTURE OF INSULIN AT 1.8A RESOLUTION——HYDROGEN BONDS AND BOUND WATER

The hydrogen bonds in insulin fall into three cases: the helical hydrogen bonds in α- or 3_(10)helices, the non-helical one formed by polar groups of insulin itself, and the hydrogen bondsformed between insulin and water. By using the information obtained, the results of a seriesof biochemical investigations on insulin analogs related to B-chain C-terminal peptide can beinterpreted and it can also be inferred that the complex behaviours of the aggregation ofinsulin may play a protective role for the unique conformation of the molecule. Water structure also appears in the refined model. About one third of the water in anasymmetric unit is hydrogen-bonded to insulin molecules or each other, which are referred toas bound water. The polar and charged groups of insulin all show the tendencies to bind towater molecules as many as possible, which is a significant factor for the stabilization of theunique conformation of the molecule. The binding way of water molecules to insulin mole-cules is also analysed.     

Theoretical Researches on the Recognizing Characteristics of Atrazine Imprinted Polymers with Different Functional Monomers

As a widely used herbicide, the threat of atrazine to both environment and health of people has become the focus. Therefore, the research and analysis of atrazine are getting more important. In this work, the MIT was used to detect atrazine theoretically. Atrazine was taken as a template molecule. MAA, MMA and TFMAA were taken as the functional monomers, respectively. The geometry optimization, the nature of hydrogen bonds, the NBO charge, and the binding energies of the imprinted molecule with the functional monomers were investigated at the B3LYP/6-31g(d,p) level. Results indicated that atrazine had the strongest interaction with TFMAA. When the ratio of atrazine and TFMAA was 1:6, the amount of H-bond formed from atrazine and TFMAA was the largest. Moreover, TFMAA owned the largest binding energy with atrazine while MMA owned the smallest. The study is helpful to interpret experiment phenomena of molecular imprinting and select better functional monomers.     

A kinetic model for the effects of vanadate on human erythrocyte membrane

The effects of vanadate on human erythrocyte membrane have been investigated with stopped-flow and equilibrium fluorescence quenching techniques. The equilibrium study showed a half-quenching concentration (K_(1/2)) of 0.27 mmol·L~(-1). The stopped-flow experiment exhibited a fast rise (t_(1、2)~f～1s) and a slow drop (t_(1/2)~s 1～2 min) in fluorescence. Based on the results and that from the across membrane transport of vanadate, a kinetic model is proposed which suggests that the membrane proteins experience a series of conformational changes before and during the quenching of the intrinsic fluorescence. These changes are induced mainly by three kinds of interactions: (i) the long-distance, non-specific interaction between the vanadate and the erythrocyte membrane surface, (ⅱ) the charge interaction between the vanadate and parts of the membrane proteins, and(ⅲ) the binding of the vanadate to some membrane proteins.     

Studies on Reaction Mechanism Between Sparfloxacin and Bovine Serum Albumin

The binding of sparfloxacin and bovine serum albumin(BSA) in aqueous solution was studied by means of fluorescence and absorbance spectra, and the interactions influenced by Fe^3 and Cu^2 were explored. Based on the Scatchard‘s site binding model and fluorescence quenching, practical formulas for a small molecule ligand attaching to a bio-macromolecule are proposed. The binding parameters were measured according to the suggested models, and the binding distance, the transfer efficiency of energy between sparfloxacin and BSA were obtained in view of the F6rster theory of non-radiation energy transfer. The effect of sparfloxacin on the conformation of BSA was analyzed by means of synchronous fluorescence spectroscopy.     

Thermally-enhanced photo-electric response of an organic semiconductor with low exciton binding energy for simultaneous and distinguishable detection of light and temperature

Simultaneous and distinguishable detection of external stimuli such as light and temperature is of great interest for a variety of scientific and industrial applications.Theoretically,an organic semiconductor with low exciton binding energy,low thermal activation energy and good charge transporting property produces thermally enhanced photo-electric response in organic phototransistors(OPTs),which thus provides an ideal and effective way to realize the simultaneous and distinguishable detection of temperature and light.However,there is no report on such a kind of organic semiconductor until now.Herein,we designed and synthesized a narrow band gap organic small molecule semiconductor 2,5-bis(2-butyloctyl)-3,6-bis(5-(4-(diphenylamino)phenyl)thiophen-2-yl)-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione(DPP-T-TPA)with low exciton binding energy(about 37 meV)and small activation energy(about 61 meV)for distinct thermal-dependence of charge carrier and exciton.The low exciton binding energy enables the semiconductor to exhibit strong thermal dependence of exciton dissociation,which contributes to the thermally-enhanced photo-electric response.Furthermore,the low thermal activation energy produces the weak thermal dependence of charge transport,which avoids the disturbance of thermally-modulated charge transport on photo-electric response.Benefiting from these two features,phototransistors based on DPP-T-TPA show great potential in simultaneous and distinguishable detection of light and temperature,which represents a novel and efficient way for bifunctional detection.     

A DFT Investigation on the Co-adsorption of H_2 and Ions inside the Carbon Nanotube

We studied the co-adsorption of hydrogen molecule and ions (Li,K,Mg,Ca) inside the single-walled carbon nanotubes (SWNTs) by using density-functional theory (DFT).The band structures (BS),density of states (DOS),charge transfer and difference charge density are presented.We discussed the interaction between the ions (Li,K,Mg,Ca) and H 2.Meanwhile,the binding energy indicates that ionization can increase the adsorption energy of H 2 in CNT.     

Sorption Removal of Pb（Ⅱ） from Solution by Uncalcined and Calcined MgAl-Layered Double Hydroxides

Layered double hydroxide （LDH） with a Mg/Al molar ratio of 1 ： 1 was synthesized by using a co-precipitation method and its calcined product （CLDH） was obtained by calcination of the MgAl-LDH at 500 ℃. The sorption removal of Pb^2＋ from solution was investigated, finding that both LDH and CLDH show good sorption ability and they could be used as a new type of environmental sorbent for the removal of Pb^2＋ from water. The sorption kinetics and the sorption isotherms of Pb^2＋ on both LDH and CLDH can be described by the pseudo-second order kinetics and Freundlich isotherm, respectively, under the studied conditions. The sorption amounts of Pb^2＋ on LDH and CLDH are independent of pH in a pH range of about 3-10. The presence of NaNO3 may inhibit the sorption of Pb^2＋ on LDH while hardly affect that on CLDH. The sorption mechanism of Pb^2＋ on LDH and CLDH may be attributed to the surface precipitation and the surface complex adsorption. The surface complex adsorption may be further distinguished to the chemical binding adsorption forming the inner-sphere surface complexes and the electrostatic binding adsorption forming the outer-sphere surface complexes. The sorption mechanism of Pb^2＋ on LDH may be attributed to the surface precipitation and the electrostatic binding adsorption, while that on CLDH may be attributed to the surface precipitation and the chemical binding adsorption.     

MONTE CARLO SIMULATION ON AQUEOUS SOLUTION OF BIOLOGICAL MOLECULES——ALANINE SOLUTION

The Monte Carlo simulation is performed for a cluster consisting of a neutral alanine molecule surrounded by 56 water molecules. The average water-water and alanine-water interaction energies are found. The space surrounding the alanine molecule is divided into three regions, where the central atoms are C' atom for the earboxyl group region, N atom for the amino group region and C~β atom for the methyl group region. The water-water and water-alanine interaction energies as functions of the distance between the oxygen atom in a water molecule and the central atom in each region are calculated. In each region the orientational correlation function for the dipole moments of water molecules, the radial distribution function for the oxygen and hydrogen atoms of water molecules are evaluated. In addition, the numbers of water molecules in the first solvation shells of each region and of entire alanine molecule are also counted.     

A Density Functional Theory Study on Electronic Structure and Second—order Nonlinear Optical Properties of Some Push—Pull Molecules

Time-dependent density-functional theory(TDDFT)has been applied to calculate the electronic structure and second-order nonlinear optical(NLO) properties of some organic molecules.The two-dimensional(2-D)charge transfer charateristics of calculated molecules were studied and compared with corresponding experimental results.All the theoretical results agree well with the measurement.For 2-D molecule with two-fold symmetry,the dominant charge transfer is off-diagonal,while for three-fold symmetry 2-D molecule,the dominant charge transfer is not only between branches and central group but also among branches.     

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.     

STUDY ON BINDING MODE OF CISPLATIN TO F-ACTIN ON THE BASIS OF LIGAND-METAL CHARGE TRANSFER SPECTRA

The binding mode and configuration of cisplatin with F-actin were studied on the basisof charge transfer bands of cisplatin-F-actin complex The binding mode was discussed on the basis ofthe results of LMCT.Raman and fluorescence spectra.     

Molecular electronegativity in density functional theory(Ⅷ)——Charge polarization modes in a closed system

Based on the density functional theory and the atom-bond electronegativity equalization model (ABEEM), a method is proposed to construct the softness matrix and to obtain the electron population normal modes (PNMs) for a closed system. Using this method the information about the bond charge polarization in a molecule can be obtained easily. The test calculation shows that the PNM obtained by this method includes all the modes about the bond charge polarization explicitly. And the bond charge polarization mode characterized by the biggest eigenvalue, which is the softest one of all modes related with chemical bonds, can describe the charge polarization process in a molecule as exquisitely as the corresponding ab initio method.     

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     

Simulation and Preparation of Molecular Imprinting System with Atrazine as Template

In this work, atrazine functions as a template molecule, and trifluoromethacrylic acid(TFMAA), methacrylic acid(MAA), methyl methacrylate(MMA), and acrylamide(AM) serve as functional monomers, respectively. By using density functional theory(DFT), the computational approach was carried out to simulate the self-assembly system of template and functional monomer. The geometry optimization, action sites, binding energies, and molecular imprinting mechanism of complexes with different functional monomers in different proportions were predicted. The simulation results showed that atrazine and the functional monomers interacted through hydrogen bond. Among the 4 functional monomers, the imprinted complex formed by TFMAA and atrazine with a ratio of(1:6) has the lowest binding energy and the best imprinting effect. Then, the microspheres of molecularly imprinted polymer(MIPs) were prepared by precipitating polymerization using atrazine as the template molecule and TFMAA as the functional monomer. The microspheres were observed by scanning electron microscopy(SEM). The results showed that atrazine MIP microspheres had average particle size of 400 nm, which was greater than the non-imprinted polymeric microspheres(NIPs). Dynamic adsorption experiments of MIPs showed that the adsorption reaction reached balance after 200 min. Analysis of the Scatchard plot revealed that the binding sites of MIPs to atrazine were equal class under the studied concentration range. The dissociation constant(Kd) and apparent maximum adsorption quantity(Qmax) of MIPs were 3.6×10-5 mol/L and 4.83 μmol/g, respectively. The study of selective adsorption between atrazine and metribuzin showed that imprinted microspheres had high selectivity for the template molecule atrazine.     

Design,synthesis and antifungal activities in vitro of novel tetralin compounds

Novel chiral tetralin compounds were designed and synthesized, and their antifungal activities in vitro were tested. The results showed that all of target compounds had potent antifungal activities, and were stronger than that of control compounds tetrahydroisoquinolines. The binding model of lead molecules in the active site of CYP51 of Candida albicans showed that lead compound specifically interacted with the amino acids residues in the active site, without binding with the heme of CYP51, which was different from azole antifungal drugs. The present study might afford a novel lead molecule to develop non-azole CYP51 inhihitars of fungi.     

A High Performance Theory for Thermodynamic Study on the Binding of Human Serum Albumin with Erbium Chloride

A thermodynamic study of the interaction between erbium(III) chloride (Er3＋) and human serum albumin (HSA) was studied at pH＝7.0, 27 and 37 ℃ in phosphate buffer by isothermal titration calorimetry (ITC). The present study reports the thermodynamic parameters that govern HSA-Er3＋ interactions. The extended solvation theory was used to reproduce the enthalpies of HSA-Er3＋ interactions over the whole range of Er3＋ concentrations. The binding parameters recovered from the new model were attributed to the structural change of HSA and its biological activity. The results obtained indicate that there is a set of two identical binding sites for Er3＋ ions with negative cooperativity. The enhancement of complex formation by Er3＋ and concomitant increase in ∆S suggest that the metal ion plays a role in increasing the number of hydrophobic contacts. The binding parameters discovered from the extended solvation model indicate that the stability of HSA molecule is increased as a result of its interaction with Er3＋ ions.     

Fast kinetic studies of reduction of ferricytochrome c by a series of Fe(EDTA)-type complexes

The reductions of cytochrome c by a series of derivatives of Fe(EDTA)2- complex have been studied by a stopped-flow technique. The reactions of cytochrome c with Fe(EDTA)2-, Fe (CDTA)2- and Fe(IDA)22- present typical outer sphere mechanism, meanwhile the cytochrome c(III) and Fe(NTA)- system shows abnormal kinetic behavior, including the rate saturation, big negative entropy and lower overall charge and binding site charge calculated from the dependence of electron transfer rate on ionic strength. On the basis of these observations a semi-inner-sphere mechanism is proposed to illustrate the kinetics.     

PHOTOPHYSICAL BEHAVI0RS OF OLIGOMER BASED ON 1, 1′-BINAPHTHOL WITH 3, 3′-ACETYLENE SPACER*

The photophysical behaviors of the oligomer based on 1,1'-binaphthol with3,3'-acetylene spacer were investigated. The oligomer molecule has a naphthyl-acetylene-naphthyl effective conjugation segment. The atropic of the 1,1'-binaphthyl moiety led totwisted and rigid main chain in the oligomer. With the changes of the external environ-ment such as solvents used, solvent viscosity and ambient temperature, the wavelengthsof absorption and the intensities of fluorescence and absorption are changed slightly, butthe fluorescent intensity and quantum yield can be influenced. The luminescent behav-iors of the oligomer exhibit twisted intramolecular charge transfer characteristics, whichcould have a potential application in wavelength-stable light emitting material adaptableto ambient temperature and the solvents used in wide range.     

Theoretical Study on the Charge Transport Properties of Coronene and Its Derivatives

Molecular structures, reorganization energies and charge transport matrix elements of coronene and its fluoro-, hydroxyl- and sulfhydryl-substituted derivatives have been studied at the B3LYP/6-31G＊＊ level. Based on the semi-classical model of electron transfer, charge transport rate constants of the title molecules have been calculated. The results indicate that the coronene molecule is helpful to the transport of negative charge, and the transport rate of positive charge is between those of hexaazatriphenylene and triphenylene.