Quantitative structure-activity relationship of compounds binding to estrogen receptor β based on heuristic method

Estrogen compounds may pose a serious threat to the health of humans and wildlife.The estrogen receptor (ER) exists as two subtypes,ERβ and ERβ.Compounds might have different relative affinities and binding modes for ERβ and ERβ.In this study,the heuristic method was performed on 31 compounds binding to ERβ to select 5 variances most related to the activity (LogRBA) from 1524 variances,which were then employed to develop the best model with the significant correlation and the best predictive power (r2 = 0.8...     

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.     

Activation free energy of Zn（Ⅱ）,Co（Ⅱ） binding to metallo-β-lactamase ImiS

In an effort to understand the recombination of a B2 metallo-β-lactamase（MβL）,the binding of metals to apo-ImiS was studied by isothermal titration calorimetry and fluorescence spectra.The binding of Zn（Ⅱ）,Co（Ⅱ） to apo-lmiS resulted in activation free energies △G_≠~θ values of 93.719 and 92.948 kJ mol~（-1）,respectively,and increasing of fluorescence intensity at maxima emission of 340 nm.     

Periodic tables of diatomic and triatomic molecules

The Mendeleev periodic table of atoms is one of the most important principles in natural science. However, there is shortage of analog for molecules. Here we propose two periodic tables, one for diatomic molecules and one for triatomic molecules. The form of the molecular periodic tables is analogous to that of Mendeleev periodic table of atoms. In the table, molecules are classified and arranged by their group number G, which is the number of valence electrons, and the periodic number P, which represents the size of the molecules. The basic molecular properties, including bond length, binding energy, force constant, ionization potential, spin multiplicity, chemical reactivity, and bond angle, change periodically within the tables. The periodicities of diatomic and triatomic molecules are thus revealed. We also demonstrate that the periodicity originates from the shell-like electronic configurations of the molecules. The periodic tables not only contain free molecules, but also the "virtual" molecules present in polyatomic molecules. The periodic tables can be used to classify molecules, to predict unknown molecular properties, to understand the role of virtual molecules in polyatomic molecules, and to initiate new research fields, such as the periodicities of aromatic species, clusters, or nanoparticles. The tables should be of interest not only to scientists in a variety of disciplines, but also to undergraduates studying natural sciences.     

FKBP23 in ER binds to BiP specifically

FKBP23 was found in mouse endoplasmic reticulum (ER) in 1998. It consists of an N-terminal peptidyl-prolyl cis-trans isomerase (PPIase) domain and a C-terminal domain with Ca2+ binding sites. The fusion protein of mouse FKBP23 and glutathione S-transferase (GST), GST-FKBP23, and the fusion protein of BiP, a member of heat shock protein 70 (Hsp 70) in ER, and GST, GST-BiP, were subcloned in E. coli, expressed and purified. The fusion proteins were restrictively digested by Factor Xa (FaXa) to obtain the free cloned proteins FKBP23 and BiP. With the assay of adsorption of free FKBP23 or BiP with GST-BiP or GST-FKBP23 attached to the Glutathione-Sepharose 4B, the adsorbed FKBP23 or BiP could be detected by Immunoblot. It means that FKBP23 binds to BiP. Furthermore, BiP in leukocyte ER-extract can be adsorbed with GST-FKBP23 attached to the glutathione-Sepharose 4B. It shows that FKBP23 binds to natural BiP in ER, too. These experiments show that a PPIase binds to a molecular chaperone of the Hsp70 family.     

Surface-imprinted polymers in microfluidic devices

Molecularly imprinted polymers are generated by curing a cross-linked polymer in the presence of a template. During the curing process, noncovalent bonds form between the polymer and the template. The interaction sites for the noncovalent bonds become "frozen" in the cross-linking polymer and maintain their shape even after the template is removed. The resulting cavities reproduce the size and shape of the template and can selectively reincorporate the template when a mixture containing it flows over the imprinted surface. In the last few decades the field of molecular imprinting has evolved from being able to selectively capture only small molecules to dealing with all kinds of samples. Molecularly imprinted polymers (MIPs) have been generated for analytes as diverse as metal ions, drug molecules, environmental pollutants, proteins and viruses to entire cells. We review here the relatively new field of surface imprinting, which creates imprints of large, biologically relevant templates. The traditional bulk imprinting, where a template is simply added to a prepolymer before curing, cannot be applied if the analyte is too large to diffuse from the cured polymer. Special methods must be used to generate binding sites only on a surface. Those techniques have solved crucial problems in separation science as well as chemical and biochemical sensing. The implementation of imprinted polymers into microfluidic chips has greatly improved the applicability of microfluidics. We present the latest advances and different approaches of surface imprinting and their applications for microfluidic devices.     

Aβ-binding molecules: Possible application as imaging probes and as anti-aggregation agents

As amyloid β (Aβ) is at the centre of pathogenesis of Alzheimer's disease (AD), Aβ aggregate-specific probes for in vivo studies of Aβ are potentially important for the early diagnosis and the assessment of new treatment strategies in the AD brain by noninvasive imaging. Several series of compounds derived from Congo red (CR) and Thioflavin T (ThT) have been evaluated as potential probes for the Aβ imaging. They include a diversity of core structures contributing to their affinities to Aβ. Small-molecule inhibi- tors were known to inhibit the formation of Aβ oligomers and fibrils. This inhibition has to be performed in such a way that these inhibitors bind to Aβ in the binding channel where Aβ-binding probes should sit. Therefore, several of them were used as novel core structures to develop Aβ probes, with their de- rivatives exhibiting good Aβ affinities. This approach will facilitate the design of a variety of candidates for Aβ probe molecules and anti-aggregation-therapeutic drugs. Moreover, the finding of Aβ probes with diverse core structures recognized by binding sites on Aβs will likely provide a promising per- spective for the design of 99mTc-labeled probe-derived molecules.     

Studies on β2-Glycoprotein Ⅰ Recognizing Molecules from a Phage Peptide Library

β2-Glycoprotein I(β2-GPI) has been identified as a cofactor in the recognition of phospholipid Ag cardiolipin (CL) by anticardiolipin Ab(aCL) purified from patients' serum with autoimmune disease. However, there is a considerable controversy as to the anti-β2-GPI -antibodies occurred in aCL. In order to select β2-GPI recognizing molecules, β2-GPI was used as a probe to screen affinity phage clones panned from a phage peptide library. After four cycles of selection, the phage recovery increased from 2.4×10-5% to 1.1×10-3%, indicating that a specific enrichment had been achieved. In order to characterize these phage clones, we investigated their specific binding to β2-GPI and their inhibition of β2-GPI binding to anti-β2-GPI antibodies. Almost 40 percent of clones reflected considerable binding abilities and inhibitory activities towards anti-β2-GPI antibodies. A group of related peptides were identified by DNA sequencing, in which there were seven related peptide sequences, with four of them representing more than once. These peptide sequences display similarities at several positions. Sequence motif (-F-S-L-) was evident in most of the peptides. It suggests that these peptides may specifically block the anti-β2-GPI antibodies binding to β2-GPI. Our result supports the idea that β2-GPI acts as a Ag for these anti-β2-GPI antibodies occurred in the aCL.     

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     

Exploring the binding mechanism of thioflavin-T to the β-amyloid peptide by blind docking method

Using blind dock method,we find that thioflavin-T(ThT) can bind to both monomers and fibrils of the full-length β-amyloid peptide(Aβ1-42) and has a higher binding affinity to the fibrils.It is shown that the hydrophobic interaction between the ligand(ThT) and substrate(Aβ1-42) are stronger than hydrogen bonds.Furthermore,ThT tends to be located near the C-terminus of Aβ monomer through hydrophobic and electrostatic interactions,while it tends to contact the residues Met35 and Gly27 of the fibril surface mainly through hydrophobic interaction.Finally,according to the docking results and ThT fluorescence assay,a kinetic equation is proposed to deduce the aggregation rate coefficient of Aβ1-42.     

ROLE OF THIOL-DISULFIDE EXCHANGE IN INSULIN BINDING TO ITS RECEPTOR

The effects of reduction by DTT, oxidation by DTNB and treatment with NEM on the thiol contents and insulin binding to its receptor in mice liver membranes were studied. Reduction with DTT leads to a parallel increase in the thiol content and the speciflc binding of insulin to the membrane. Scatchard analysis of the results shows little change in the number of binding sites but a twofold increase of the binding constant. Washing the membrane with bound insulin by a DTT containing buffer results in a more marked increase in the release of bound insulin than washing with buffer alone, suggesting that part of the insulin is bound to its receptor by covalent disulfide linkages through a thIol-disulfide exchange reaction and reduction with DTT leads to a marked increase in this "disulfide-linked" insulin. Treatment with DTNB or NEM of the DTT-reduced membrane seems to reverse the effect of DTT reduction, although the reaction of the untreated membrane with DTNB or NEM had little or no effect on the specific     

A LINEARIZATION CRITERION FOR THE ANALYSIS OF ALLOSTERIC PROTEIN-LIGAND SYSTEMS

A linear criterion testing the applicability of the Monod-Wyman-Changeux(MWC) mechanism characterizing,at a single effector con-centration,concerted allosteric transitions plots log {[α-v_r(1 α)]/[v_r(1 cα)-cα]} against log[(1 cα)/(1 α)],with a slope of (n-1)andintercept of log L.(Here v_r is the relative velocity or,in bind-ing experiments,the fractional binding,α the substrate concentra-tion relative to the smallest conformational dissociation constantK_R,L the constant for the conformational equilibrium,c=K_R/K_Tthe ratio of conformational dissociation constants,and n the de-gree of the rate or binding function).The plot is applied to theexperiments of Roughton and Lyster [Hvalradets Skrifter,48,185-198,(1965)] on the binding of oxggen to human hemoglobin.At pH7.0 the data are in agreement with the predictions of the MWC-mechanism.This conclusion is confirmed by weighted nonlinear re-gression analysis which yields a statistically not significantlack of fit,random weighted residuals,and parameters which agreeclosely with those obtained from the graphical analysis.At pH 9.1the MWC-mechanism is not applicable.At either pH the experimentsdo not support the suitability of the sequential binding mechanismeither with square or tetrahedral geometry.     

[~3H] TYROSINE BINDING TO PLASMA MEMBRANE PREPARATION OF RAT CORPORA LUTEA

Plasma membrane preparations of rat corpora lutea have been incubated with [~3H]tyrosine. [~3H]-tyrosine binding sites are demonstrated and Scatchard analysis shows that there exist two types of binding sites, one with high affinity and low capacity, the other with low affinity and high capacity. The kinetics studies demonstrate that the [~3H]tyrosine binding to the two types of binding sites is reversible and the speed of binding to the high affinity type is faster than that to the low affinity type. The analysis of the chemical structure of tyrosine analogues and related compounds with respect to the specificity of the binding sites reveal that both types of binding sites show specificity, but the specificity of the high affinity sites is higher than that of the low affinity sites. The relations of tyrosine structure to binding processing and to tyrosine inhibitory action on hCG-induced progesterone production are discussed. It is suggested that the high affinity binding sites might be regarded as "ty     

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.     

A Novel Toxicological Evaluation of TiO2 Nanoparticles on DNA Structure0

TiO2 has been tested to be toxic to DNA under the photo-irradiation of ultraviolet A （UVA）. However, in the dark conditions, after several days of treatment with TiO2 in aqueous solution, the interaction between TiO2 and two types of DNA was detected and the mechanisms were studied by the methods of gel-electrophoresis, IR spectroscopy and TEM. The results showed that the DNA would be bound to TiO2; the ratio of binding was related to the concentration and the treating time; the mechanism of binding is related to phosphate groups of DNA. Besides, DNA with different structure showed different degree of binding. These findings showed a new possible way through which the TiO2 nanoparticles interact with DNA.     

A Peptide Binder of E3 Ligase Adaptor SPOP Disrupts Oncogenic SPOP-Protein Interactions in Kidney Cancer Cells

The E3 ligase adaptor SPOP,overexpressed in the nucleus but frequently dislocated into the cytoplasm in all clear cell Renal Cell Carcinomas(ccRCC),serves as a regulatory hub to promote kidney cancer through the ubiquitination and degradation of multiple downstream cancer proteins.Recently,our identification of a selective small-molecule inhibitor of the SPOP-phosphatase and tensin homolog(PTEN)interaction has demonstrated that the oncogenic SPOP-protein interaction would be a druggable target specific to ccRCC therapy.To our knowledge,this is the first time such a small-molecule inhibitor has been developed.Herein,we have identified a peptide binder for the SPOP-MATH domain that disrupts the oncogenic SPOP-protein interactions in kidney cancer cells.Computational design and biophysical characterization yielded peptide Pep38 that binds to the MATH domain of SPOP and competes on PTEN-binding to SPOP in vitro.The X-ray complex structure reveals that the peptide binder features the following combination:one,a mimic of the native peptide binder and two,an additionalβ-strand motif in sequence,which could contribute to increased binding affinity.In order to improve cellular permeability,we fused Pep38 with the delivery peptide TAT to prepare peptide TAT38,which inhibits the endogenous substrate binding to SPOP and suppresses the proliferation of the ccRCC cells.Our identification of the peptide inhibitors for SPOP-protein interactions provides further validation that the oncogenic SPOP-signaling pathway in ccRCC could be a druggable target specifically applicable to the therapy of kidney cancers.     

An introduction to molecular spintronics

We review the progress and future possibilities in the emerging area of molecular spintronics. We first provide an overview of the different transport regimes in which electronic nanodevices can operate, then briefly overview the important characteristics of molecular magnetic materials that can be useful for application in spintronics and we eventually present several schemes to include such systems into spintronic nanodevices. We hightlight the importance of a chemical approach to the area, and in the last section we showcase some approaches to the creation of hybrids made of carbon nanostructures and molecular magnets, which are gaining increasing attention.     

Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.     

氟胞嘧啶与牛血清白蛋白结合反应研究

The binding of flucytosine to bovine serum albumin （BSA） was studied by means of fluorescence and absorption spectra under the conditions of simulant clay physiology. It showed a powerful ability to quench the fluorescence launching from BSA. After analyzing the fluorescence quenching data by Stem-Volmer equation and Lineweaver-Burk double-reciprocal equation, it was found that they matched the latter better and so they belonged to static quenching. The binding constant was calculated to be 5.710 × 10^3 L·mol^-1 at 297 K. The binding locality was a distance 2.49 nm away from tryptophan residue-212 based on Foster＇s non-radiation energy transfer mechanism. The binding power is mainly the hydrogen bond and van der Waals force according to the thermodynamic parameters. The information of BSA conformation was acquired by synchronous fluorescence spectrum and three-dimensional fluorescence spectrum.     

INTERACTION BETWEEN ADENOSINE-5′-MONOPHOSPHATE AND FRUCTOSE 1,6-BISPHOSPHATASE AND MECHANISM OF ALLOSTERIC INHIBITION——ULTRAVIOLET SPECTROSCOPIC STUDIES

Ultraviolet difference spectroscopic studies of AMP and dAMP upon binding to snake muscle fructose 1, 6-bisphosphatase showed that both of the ligands interacting with the enzyme generated three positive peaks located at 270 nm, 280 nm and 288 nm. The binding constants calculated from the titration curve of difference spactra by the successive addition of nueleotides were 2.0×10~6M~(-1) and 1.2×10~6M~(-1) respectively. The fact of the same binding constants for the two ligands indicated that the unique inhibition behavior of dAMP differing from AMP was not due to the difference of binding between AMP and dAMP, but due to the absence of 2'-OH group on the ribose of dAMP. In contrast to the difference spectra of AMP binding, the U. V. difference spectra produced by tryptic digestion of fructose 1, 6-bisphosphatase gave two negative bands at 280 nm and 288 nm and had a close resemblance to that of the enzyme in urea. The opposite signs of the two kinds of difference U. V. spectra produced by AMP binding