Homology modeling of the receptor binding domain of human thrombopoietin

Platelet production in blood is regulated by a lineage specific humoral factor, thrombopoietin (TPO). The amino terminal domain of TPO (TPO-N) is responsible for the signal transduction mediated by the TPO receptor, c-mpl. From the predicted length of helices we found that TPO-N belongs to the long-chain subfamily of the four-helix bundle cytokine family. We built a three dimensional model of TPO-N by a comparative homology modeling procedure. The four helices of TPO-N with an up-up-down-down topology are stabilized by a tightly packed central hydrophobic core and the extended loop AB makes an additional hydrophobic core with helices B and D outside of the four helix bundle scaffold. An interpretation of the previous site directed mutageneses results in light of the model enabled us to identify two isolated receptor binding sites. The surface made of Lys 136, Lys 138 and Lys 140 in helix D, and Pro 42 and Glu 50 in loop AB forms the first receptor binding site, while the surface of Asp 8, Arg 10 and Lys14 in helix A represents the second binding site for the sequential receptor oligomerization.     

Preparation of the stabilized glycoenzymes by cross-linking their carbohydrate chains

Each of the three high-mannose type glycoproteins studied, acid phosphatase, invertase, and glucose oxidase, could be specifically cross-linked through its carbohydrate chains. The procedure involves periodate oxidation of carbohydrate residues followed by reaction of the generated aldehyde groups with adipic acid dihydrazide as a cross-linker. The amount and size as well as solubility of the formed polymers could be efficiently controlled by varying the reaction conditions, i.e., the oxidation degree and the concentrations of glycoproteins, cross-linker, and hydrogen ions during the cross-linking reaction. It was found that the quantity and size of polymers increased with oxidation degree and protein concentration and by lowering the pH. When the protein concentration was above and pH below certain values, depending on the glycoenzyme, insoluble polymers formed. The soluble cross-linked polymers retained a high level of original activity, and the minor decrease in specific activity noticed was shown to occur during the periodate oxidation step. The cross-linked glycoenzymes are much more resistant to denaturation by high temperature and by changes in pH, demonstrating the usefulness of this method in preparation of the stabilized glycoprotein derivatives.     

AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

E.coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases.Previous crystal structures have revealed N1-methyl adenine(1-meA) recognition by AlkB and a unique base flipping mechanism,but how the AlkB active site can accommodate bulky base adducts is largely unknown.Employing a previously developed chemical cross-linking technique,we crystallized AlkB with a duplex DNA containing a caged thymine base(cagedT).The structure reveal...     

Functionalization of polymeric membranes by impregnation and in situ cross-linking of a PDMS/β-cyclodextrin network

In this paper a new method for the functionalization of porous membranes with β-CD is reported. Porous polypropylene (PP) hollow fibres have been impregnated with a mixture composed by a partially cross-linked polydimethylsiloxane (PDMS) and β-cyclodextrin (β-CD). The prepolymerization of the PDMS components was necessary to avoid their inclusion in the β-CD cavity. The firm heterogenization of the β-CD was obtained by in situ cross-linking of the PDMS/β-CD network in the porous membranes. The presence of the PDMS/β-CD network in the membranes was confirmed by FT-IR-ATR (on the outer and inner surfaces) and EDX analyses (on the cross-section).The effect of the impregnation times on membrane morphology, loading and porosity has been investigated. The binding capacity of the heterogenized β-CDs has been tested using the phenolphthalein as guest molecule.     

Specificity of receptor-ligand interactions and their effect on dimerisation as observed by electrospray mass spectrometry: bile acids form stable adducts to the RXRalpha

Electrospray (ES) mass spectrometry data is presented showing that agonist binding to the nuclear receptor (NR), retinoid X receptor alpha (RXRalpha), is competitive. The competitive nature of agonist binding can be used to discriminate between the specific and non-specific binding of small lipophilic molecules to NRs. Further, data is presented which show that high-affinity ligand binding to the RXRalpha ligand-binding domain (LBD) stabilises the domain homodimer. The results indicate that homodimerisation, a functional property of the receptor associated with the binding of agonist ligands, could be used to discriminate between specific and non-specific binding events. Additionally, we report on the remarkable stability of the gas-phase complex between the RXRalpha LBD protein and endogenous bile acids. Protein-bile acid interactions in the gas phase were found to be surprisingly strong, withstanding 'in-source' fragmentation in the ES interface, and, in the case of taurocholic acid (TCA) and lithocholic acid-3-sulphate (LCA-3-sulphate), collision-induced dissociation within the collision cell of a tandem mass spectrometer. Bile acids were found to be inactive towards RXRalpha in transfection assays, and have not been reported to be ligands for the RXRalpha, although lithocholic acid (LCA) has been found to be a competitor in the photoaffinity labelling of RXRbeta with 9-cis-retinoic acid (9-cis-RA). The observation of strong RXRalpha-bile acid non-covalent complexes in ES mass spectrometry highlight the danger of extrapolating gas-phase binding data to the solution phase and further to a possible biological activity, particularly when surface-active compounds such as bile acids are involved. The introduction of a competitive ligand-binding experiment can alleviate this problem and allow the differentiation between specific and non-specific binding.     

An automated method for predicting the positions of hydrogen-bonding atoms in binding sites

Hydrogen bonds are the most specific, and therefore predictable of the intermolecular interactions involved in ligand–protein binding. Given the structure of a molecule, it is possible to estimate the positions at which complementary hydrogen-bonding atoms could be found. Crystal-survey data are used in the design of a program, HBMAP, that generates a hydrogen-bond map for any given ligand, which contains all the feasible positions at which a complementary atom could be found. On superposition of ligands, the overlapping regions of their maps represent positions of receptor atoms to which each molecule can bind. The certainty of these positions is increased by the incorporation of a larger number and diversity of molecules. In this work, superposition is achieved using the program HBMATCH, which uses simulated annealing to generate the correspondence between points from the hydrogen-bonding maps of the two molecules. Equivalent matches are distinguished on the basis of their steric similarity. The strategy is tested on a number of ligands for which ligand–protein complexes have been solved crystallographically, which allows validation of the techniques. The receptor atom positions of thermolysin are successfully predicted when the correct superposition is obtained.     

The measurement of molecular diversity by receptor site interaction simulation

The assembly of large compound libraries for the purpose of screening against various receptor targets to identify chemical leads for drug discovery programs has created a need for methods to measure the molecular diversity of such libraries. The method described here, for which we propose the acronym RESIS (for Receptor Site Interaction Simulation), relates directly to this use. A database is built of three-dimensional representations of the compounds in the library and a set of three-point three-dimensional theoretical receptor sites is generated based on putative hydrophobic and polar interactions. A series of flexible, three-dimensional searches is then performed over the database, using each of the theoretical sites as the basis for one such search. The resulting pattern of hits across the grid of theoretical receptor sites provides a measure of the molecular diversity of the compound library. This can be conveniently displayed as a density map which provides a readily comprehensible visual impression of the library diversity characteristics. A library of 7500 drug compounds derived from the CIPSLINEPC databases was characterized with respect to molecular diversity using the RESIS method. Some specific uses for the information obtained from application of the method are discussed. A comparison was made of the results from the RESIS method with those from a recently published two-dimensional approach for assessing molecular diversity using sets of compounds from the Maybridge database (MAY).     

Analysis of FeII-mediated decomposition of a linoleic acid-derived lipid hydroperoxide by liquid chromatography/mass spectrometry

Intracellular Fe(II), which is up-regulated during oxidative stress and during iron overload, induces the formation of a hydroxyl radical by Fenton chemistry. The hydroxyl radical can convert the prototypic omega-6 polyunsaturated fatty acid, linoleic acid, to 13-hydroperoxy-9,11-(Z,E)-octadecadienoic acid (13-HPODE). Cyclooxygenases can also convert linoleic acid to 13(S)-HPODE during oxidative stress. Subsequent Fe(II)-mediated decomposition to protein- and DNA-reactive bifunctional electrophiles was examined by normal-phase liquid chromatography (LC)/atmospheric pressure chemical ionization (APCI)/mass spectrometry. The potential individual bifunctional electrophiles trans-4,5-epoxy-2(E)-decenal (EDE), cis-EDE, 4-oxo-2(E)-nonenal (ONE) and 4-hydroxy-2(E)-nonenal (HNE) exhibited protonated molecular ions at m/z 169, 169, 155 and 157, respectively. The MH(+) ion at m/z 173 for 4-hydroperoxy-2(E)-nonenal (HPNE) was very weak with an ion corresponding to the loss of OH at m/z 156 as the major ion in the APCI mass spectrum. The bifunctional electrophiles were all separated under normal-phase LC conditions. Interestingly, ions corresponding to ONE and HNE were detected at the same retention time as HPNE, suggesting that it decomposed in the source of the mass spectrometer to ONE and HNE. All five bifunctional electrophiles were formed when 13-HPODE was treated with 50 microM Fe(II). At this concentration of Fe(II), the addition of vitamin C resulted in increased bifunctional electrophile formation. At higher concentrations of Fe(II) (500 microM to 2 mM), no HPNE was detected and there was no additive effect of vitamin C. Additional experiments with synthetic HPNE revealed that it was quantitatively converted to a mixture of ONE and HNE by Fe(II). The HNE is thought to arise from a one-electron reduction of an alkoxy radical derived from HPNE. In contrast, ONE can arise through an alpha-cleavage of the HPNE-derived alkoxy radical or by direct dehydration of HPNE.     

蛋白受体结合筛选-气质联用法测定动物组织中的氯霉素残留

建立了动物组织中氯霉素残留的蛋白受体结合筛选和GC MS分析方法。受体结合生物筛选的筛选限为0.1μg kg,假阴性率为零,其它常用抗生素的交叉反应率均<0.1%。筛选阳性样本经液液分配萃取、C18SPE固相萃取净化后衍生进行GC MS的NCI选择离子监测分析。其定量检出限为0 1μg kg,样品添加水平0 1～10μg kg时,回收率为76 2%～103 5%,相对标准偏差为7 5%～10 6%。     

Efficient calculation of relative binding free energies by umbrella sampling perturbation

An important task of biomolecular simulation is the calculation of relative binding free energies upon chemical modification of partner molecules in a biomolecular complex. The potential of mean force (PMF) along a reaction coordinate for association or dissociation of the complex can be used to estimate binding affinities. A free energy perturbation approach, termed umbrella sampling (US) perturbation, has been designed that allows an efficient calculation of the change of the PMF upon modification of a binding partner based on the trajectories obtained for the wild type reference complex. The approach was tested on the interaction of modified water molecules in aqueous solution and applied to in silico alanine scanning of a peptide‐protein complex. For the water interaction test case, excellent agreement with an explicit PMF calculation for each modification was obtained as long as no long range electrostatic perturbations were considered. For the alanine scanning, the experimentally determined ranking and binding affinity changes upon alanine substitutions could be reproduced within 0.1–2.0 kcal/mol. In addition, good agreement with explicitly calculated PMFs was obtained mostly within the sampling uncertainty. The combined US and perturbation approach yields, under the condition of sufficiently small system modifications, rigorously derived changes in free energy and is applicable to any PMF calculation. © 2014 Wiley Periodicals, Inc.     

半乳糖修饰人血清白蛋白的质谱分析

研究发现,存在于哺乳动物肝细胞膜上的血浆无唾液酸糖蛋白受体(asialoglycoproteinreceptor,ASGP-R)是一种肝结合蛋白(hepaticbindingprotein,HBP),能专一性识别分子末端带有半乳糖残基的糖蛋白并与之结合,定向转到肝细胞内的溶酶体进行代谢,针对ASGP-R作为靶点的肝靶向药物载体半乳糖化人血白蛋白偶合物(galactosyl-neoglycoalbumin,NGA),已引起药物研究工作者的极大重视。将药物与带有半乳糖残基的蛋白偶合,可提高药物的肝靶向性,提高治疗指数,减少非靶器官的毒副作用。大量研究表明,肝结合蛋白受体介导的肝靶向给药系统是最具研究价值和应用前景的肝靶向给药系统之一。     

Cooperative hydration effect on the binding of organic vapors by a cross-linked polymer and beta-cyclodextrin

A cooperative hydration effect being favorable for the binding of organic vapors by cross-linked poly(N-6-aminohexylacrylamide) and beta-cyclodextrin was observed in ternary systems in the absence of liquid phase. For these systems the vapor sorption isotherms were determined by the static method of headspace gas chromatographic analysis at 298 K. The obtained isotherms show an increase of binding affinity for vapor of hydrophobic sorbates above a threshold value of receptor hydration. Further hydration gives a saturation of this affinity for the studied hydrophilic polyacrylamide derivative, while the affinity of beta-cyclodextrin for the hydrophilic sorbate ethanol even decreases. A similar behavior of this polymer and beta-cyclodextrin at the change of their hydration helps to explain the observed cooperative hydration effect in terms of clathrate formation.     

The study of growth inhibitive protein factor by various mode of HPLC and estimation of its binding with drugs

The protein fraction of the brain of white rat inhibiting the proliferation of homological cells was studied by hydrophobic interaction and reversed-phase liquid chromatography. The hybrid modification of hydrophobic interaction and biopartitional micellar chromatography was also applied for the elution of hydrophobic component of brain protein fraction. It was established that this protein fraction represents a hydrophilic-hydrophobic complex. The binding of pharmacological preparations with the brain protein fraction in the model system was also investigated. The separation of free and protein bound fractions of drugs was carried out by cloud-point extraction. It was shown that the degree of binding of phenobarbital with the mentioned protein fraction exceeds the same values for carbamazepine and chlorpromazine.     

Analysis of volatiles emitted by potato plants by means of a Colorado beetle electroantennographic detector

An electroantennographic detector based on the antenna of the Colorado potato beetle (Leptinotarsa decemlineata Say, 1824) was used to investigate volatile organic compounds emitted by injured potato plants (Solanum tuberosum L., 1753). Samples were collected on charcoal traps using the CLSA method. Analyses were performed with a GC-EAD-FID setup as well as a GC-MS system. The experiments revealed that several groups of compounds are perceptible to the Colorado potato beetle. The ability of the Colorado potato beetle to detect green leaf odours (e.g. (Z)-3-hexen-1-ol and (E)-2-hexenal), linalool and some terpenes has been noticed before [Visser et al., J. Chem. Ecol. 5 (1979) 13]. In this work the presence of (Z)-3-hexen-1-ol, (E)-2-hexenal and linalool in the potato odour could be confirmed. Moreover, β-myrcene, benzeneethanol, and several sesquiterpenes (e.g. caryophyllene and germacrene-D) were identified. The GC-EAD experiments reveal that apart from the green leaf odours and linalool prominent reactions of the Colorado bettle antenna are induced by benzeneethanol and the sesquiterpene fraction.     

Multiplex binding modes of toluidine blue with calf thymus DNA and conformational transition of DNA revealed by spectroscopic studies

It is noteworthy to understand the details of interactions between antitumor drugs and DNA because the binding modes and affinities affect their antitumor activities. Here, The interaction of toluidine blue (TB), a potential antitumor drug for photodynamic therapy of tumor, with calf thymus DNA (ctDNA) was explored by UV–vis, fluorescence, circular dichroism (CD) spectroscopy, UV-melting method and surface-enhance Raman spectroscopy (SERS). The experimental results suggest that TB could bind to ctDNA via both electrostatic interaction and partial intercalation. The fluorescence quenching of TB by ctDNA was static and due to electron transfer from bases to the excited singlet state of TB. At low [TB]/[DNA] ratio, TB mainly partially intercalated into ctDNA resulting in the slight increase of base stacking degree; at high [TB]/[DNA] ratio, excessive TB externally stacked along the helix surface via coupling with partially intercalated ones, thereby inducing B-A transition of ctDNA. The conformational transition of DNA was confirmed by the obvious improvement of the thermal stability of ctDNA. The SERS spectra suggest that TB could partially intercalate into DNA basepairs with its ring C₁NC_1′ side buried.     

Theoretical studies on opioid receptors and ligands. I. Molecular modeling and QSAR studies on the interaction mechanism of fentanyl analogs binding to μ‐opioid receptor

Based on our previous result of the three‐dimensional model of the μ‐opioid receptor, binding conformations of 13 fentanyl analogs and three‐dimensional structures for the complexs of these analogs with μ‐opioid receptor were constructed employing the molecular modeling method and our binding conformation search program for ligands (BCSPL). Energetic calculation and quantitative structure–activity relationship (QSAR) analysis indicated a good correlation between the calculated binding energies of fentanyl analogs and their binding affinities, pK_i's and pK's, and analgesic activities, − log ED₅₀'s. Based on the three‐dimensional models, the possible interaction mechanism of fentanyl analogs with μ‐opioid receptor can be illustrated and the available structure–activity relationship of these analgesic agents can be explained reasonably. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 285–293, 2000