Fluorescence resonance energy transfer: FRET studies of ligand binding to cell surface receptors

We describe a simple optical system employing fluorescence resonance energy transfer (FRET) to identify potential binding domains on the macrophage scavenger receptor for the ligand maleylated bovine serum albumin (mal-BSA). Using a plasma membrane vesicle system, we placed donor probes on the ligand and acceptor probes in the membrane to determine the distance of bound ligand from the cell surface. Two donors and three acceptors were employed. Transfer between ligand covalently modified with multiple dansyl molecules and hexadecanoylaminoeosin in the membrane yielded a distance of 46.5 ± 7.5 å; transfer from the same type of donors to octadecylrhodamine B in the membrane gave a distance of 58.5 ± 3.0 å. No transfer was observed between ligand mono-labeled with fluorescein and l,l′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanineperchlorate in the membrane. This suggests that the orientation of mal-BSA bound to the receptor places the fluorescein probe too far from the lipid surface to experience energy transfer. The distance information identifies a potential location for the binding site, which can be compared to structural information about the receptor and used to extract a binding sequence.     

Aromatic interactions impact ligand binding and function at serotonin 5-HT2C G protein-coupled receptors: receptor homology modelling,ligand docking,and molecular dynamics results validated by experimental studies

The serotonin (5-hydroxytryptamine, 5-HT) 5-HT₂ G protein-coupled receptor (GPCR) family consists of types 2A, 2B, and 2C that share ～75% transmembrane (TM) sequence identity. Agonists for 5-HT_2C receptors are under development for psychoses; whereas, at 5-HT_2A receptors, antipsychotic effects are associated with antagonists – in fact, 5-HT_2A agonists can cause hallucinations and 5-HT_2B agonists cause cardiotoxicity. It is known that 5-HT_2A TM6 residues W6.48, F6.51, and F6.52 impact ligand binding and function; however, ligand interactions with these residues at the 5-HT_2C receptor have not been reported. To predict and validate molecular determinants for 5-HT_2C-specific activation, results from receptor homology modelling, ligand docking, and molecular dynamics simulation studies were compared with experimental results for ligand binding and function at wild type and W6.48A, F6.51A, and F6.52A point-mutated 5-HT_2C receptors.     

Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes

A couple of recent applications of intermolecular NOE (INOE) experiments as applied to biomolecular systems involve the (i) saturation transfer difference NMR (STD-NMR) method and (ii) the intermolecular cross-saturation NMR (ICS-NMR) experiment. STD-NMR is a promising tool for rapid screening of a large library of compounds to identify bioactive ligands binding to a target protein. Additionally, it is also useful in mapping the binding epitopes presented by a bioactive ligand to its target protein. In this latter application, the STD-NMR technique is essentially similar to the ICS-NMR experiment, which is used to map protein-protein or protein-nucleic acid contact surfaces in complexes. In this work, we present a complete relaxation and conformational exchange matrix (CORCEMA) theory (H. N. B. Moseley et al., J. Magn. Reson. B 108, 243-261 (1995)) applicable for these two closely related experiments. As in our previous work, we show that when exchange is fast on the relaxation rate scale, a simplified CORCEMA theory can be formulated using a generalized average relaxation rate matrix. Its range of validity is established by comparing its predictions with those of the exact CORCEMA theory which is valid for all exchange rates. Using some ideal model systems we have analyzed the factors that influence the ligand proton intensity changes when the resonances from some protons on the receptor protein are saturated. The results show that the intensity changes in the ligand signals in an intermolecular NOE experiment are very much dependent upon: (1) the saturation time, (2) the location of the saturated receptor protons with respect to the ligand protons, (3) the conformation of the ligand-receptor interface, (4) the rotational correlation times for the molecular species, (5) the kinetics of the reversibly forming complex, and (6) the ligand/receptor ratio. As an example of a typical application of the STD-NMR experiment we have also simulated the STD effects for a hypothetical trisaccharide bound to a protein. The CORCEMA theory for INOE and the associated algorithm are useful in a quantitative interpretation of the intensity changes in the ligand in both the STD-NMR and ICS-NMR, provided the identity of the receptor protons experiencing direct RF saturation is known. The formalism presented here is likely to be useful in the design of bioactive ligands to a specific target protein and in the quantitative mapping of binding epitopes and interfaces between molecules in complexes.     

Influence of the external noise intensity on the kinetics of ligands binding to receptors

The average, variance, correlation function and the spectral density of ligand–receptor complexes in the presence of the external Langevin noise are calculated and their characteristics are defined. The analysis of the experimental data using the formulas derived in this work enables one to obtain a new information on the process of forming of ligand–receptor complex, namely, the constants rates of formation and the decay of the ligand–receptor complex.     

Theoretical analysis of the inter-ligand overhauser effect: a new approach for mapping structural relationships of macromolecular ligands

A theoretical framework has been developed for the evaluation of inter-ligand Overhauser effects (ILOE), predicted when pairs of ligands are observed in the presence of a macromolecular receptor which can form a ternary complex such that some of the protons on the two ligands are in close proximity with each other (generally less than approximately 5 A). Simulations for a pair of ligands with three spins each have been performed for a variety of geometric and rate parameters. Analogous to previously described calculations of TRNOE behavior, theoretical behavior of each of the nine cross peaks, A(ij), in a NOESY experiment involving ligands which can exist in the free, binary, or ternary complex states can be calculated. However, for exchange which is sufficiently rapid on the relaxation and chemical shift time scales, use of a collapsed matrix, C, corresponding to sums of sets of nine elements, will often be appropriate and generally simplifies the analysis. In order to generate inter-ligand Overhauser effects, it is optimal for the fraction of receptor involved in the ternary complex to be reasonably large; i.e., concentrations of both ligands should be near saturation. Based on a model assuming random binding order of the ligands, the dependence of ILOE resonance intensities on kinetic rate constants roughly parallels the dependence of transferred NOE (TRNOE) intensities. For diffusion controlled binding, i.e., k(on) approximately 10(8) M(-1) s(-1), the method is best suited for equilibrium dissociation constants in the micromolar-millimolar range (k(off) approximately 10(2)-10(5) s(-1)). Toward the slower dissociation rate constant end of this range, TRNOE and ILOE effects are still predicted, but the initial build-up curves become markedly nonlinear. For a kinetic binding scheme which assumes ordered binding of the ligands, the inherent asymmetry of the ligand binding process leads to more complex kinetics and alters the dependence of the ILOE on the kinetic parameters. In this case, the binding of the second ligand effectively reduces the exchange rate of the first ligand, reducing the transfer of NOE and ILOE information. The reduction in TRNOE and ILOE information which is prediced for the ordered ligand binding model is overcome at larger dissociation rate constants for either ligand 1 or ligand 2. In addition to the structural information available from ILOE data, the strong dependence of TRNOE and ILOE curves on ordered ligand binding suggests that such measurements could be useful for the characterization of ligand binding kinetics.     

Photophysical properties of tris-methoxycoumarin derivative of a cryptand

The paper reports the photophysical studies of a macrobicyclic cryptand where the three secondary amino nitrogen have been derivatized with methoxy coumarin in various solvents at room temperature and at 77 K. The system having (F-S)₃-R configuration (where F is fluorophore, S is CH₂ spacer and R is receptor unit) shows intramolecular PET from the receptor nitrogen atoms of the cryptand moiety to the coumarin units reducing the fluorescence quantum yield and lifetime of coumarin in the ligand. However, the fluorescence intensity is enhanced in presence of protons and Zn⁺² ion in dry THF medium. Metal ions like Cu(II) and Co(II) quench the fluorescence. Presence of protons induces a greater enhancement of emission intensity implying all the nitrogen lone pairs responsible for PET are protonated. Another interesting feature of this ligand is that it exhibits room temperature phosphorescence (RTP) apart from exhibiting PET. The observation of RTP has not been reported earlier for any other coumarin derivative.     

傅里叶变换红外光谱研究鲤鱼雌激素受体与邻苯二甲酸酯的相互作用

通过电泳结合电洗脱(SDS-PAGE)的方法分离纯化鲤鱼体内的雌激素受体,得到高纯度的受体;再通过傅里叶变换红外光谱探讨雌激素受体与邻苯二甲酸二正丁酯(DBP)结合后其结构的变化,通过实验发现,配体DBP能与雌激素受体结合并对雌激素受体的结构产生了明显的影响。     

Multiple Ligand and Cell-Dependent States of Lateral Mobility of Plasmalemmal G Protein-Coupled Cholecystokinin Receptors

Lateral movement of receptor molecules in the plane of the plasmalemma has important implications for signal transduction and receptor regulation, yet mechanisms affecting such movement are not well understood. We have studied the lateral mobility of the G protein-coupled cholecystokinin (CCK) receptor expressed in the natural milieu of the rat pancreatic acinar cell and in a model cell system, the CHO-CCKR cell, after occupation with fluorescent agonist and antagonist. Lateral diffusion characteristics were distinct in each type of cell and for receptors occupied by each type of ligand, fluorescent agonist, rhodamine-Gly-[(Nle^28,31)CCK-26-33], and fluorescent antagonist, rhodamine-Gly-[(D-Trp³⁰,Nle^28,31)CCK-26-32]-phenethyl ester. Multiple states of mobility were detected for CCK receptors. The slowest population of mobile receptors on the CHO-CCKR cells moved at similar rates when occupied by both antagonist and agonist, while the faster-moving populations moved at a faster rate when occupied with antagonist than with agonist. The fastest component of mobile receptors may reflect unconstrained interactions of the antagonist-occupied receptors with signaling or anchoring structures, while the slowest component may represent the fraction of ligand-occupied receptors that ultimately undergo internalization. The intermediate mobility states may reflect receptor interactions with signal transduction and regulatory machinery. While only a single population of mobile receptors was demonstrable on the acinar cells, increased ligand concentrations (agonist and antagonist) resulted in increased percentages of mobile receptors, suggesting a stoichiometric limitation of immobilizing molecular constraints. Inhibition of protein kinase C had no significant effect on the lateral mobility of agonist-occupied CCK receptors.     

叶酸修饰的AgInS2量子点在体外癌细胞成像上的应用

成功制备出高品质的三元AgInS₂量子点。通过配体交换法将油溶性AgInS₂量子点转为水溶性量子点, 通过dBSA修饰水溶性量子点形成配位体壳, 使量子点具有更好的稳定性(4周)。从透射电子显微镜(TEM)观察到dBSA修饰后的量子点的粒径增加, 分散性较好, 并且在可见光区域有明显的光致发光。用叶酸对dBSA-MPA量子点进行修饰, 并通过傅立叶变换红外光谱进行了验证。将得到的FA-dBSA-MPA纳米复合材料应用于能与叶酸受体特异性结合的乳腺癌细胞中, 并在荧光倒置显微镜中检测到量子点成功对乳腺癌细胞进行了标记。与dBSA-MPA量子点相比, 表面被叶酸修饰后的量子点与癌细胞的结合效率显著提高。     

Vitamin D and bone: — How does vitamin D regulate bone formation and resorption? —

Vitamin D was discovered as an anti-rachitic agent, but even at present, there is no direct evidence to support the concept that vitamin D directly stimulates osteoblastic bone formation and mineralization. It appears to be paradoxical, but vitamin D functions in the process of osteoclastic bone resorption. Osteoclasts, the only cells responsible for bone resorption, develop from hematopoietic cells of the monocyte-macrophage lineage. In 1992, we hypothesized that a membrane-bound factor, designated as “osteoclast differentiation factor (ODF)”, is expressed on the plasma membrane of osteoblasts/stromal cells in response to osteotropic factors including the active form of vitamin D₃, 1α,25-dihydroxyvitamin D₃ [1α,25(OH)₂D₃]. Recently, four research groups including ours independently identified three key molecules (RANKL, RANK, and OPG) responsible for osteoclastogenesis. A long-sought-after ligand, ODF, was identical to RANKL. RANKL was a member of the membrane-associated TNF ligand family, which induced differentiation of spleen cells (osteoclast progenitors) into osteoclasts in the presence of M-CSF. RANK, a member of the TNF receptor family, was a signaling receptor essential for the RANKL-mediated osteoclastogenesis. OPG, a secreted member of the TNF receptor family, was a decoy receptor for RANKL. The discovery of RANKL, RANK and OPG opens a new era in the study of bone biology and the therapy of several metabolic bone diseases such as osteoporosis, rheumatoid arthritis, and periodontal diseases.     

Reverse depletion effects and the determination of ligand density on some spherical bioparticles

In cell environments crowded with macromolecules, the depletion effects act and assist in the assembly of a wide range of cellular structures, from the cytoskeleton to the chromatin loop, which are well accepted. But a recent quantum dot experiment indicated that the dimensions of the receptor–ligand complex have strong effects on the size-dependent exclusion of proteins in cell environments. In this article, a continuum elastic model is constructed to resolve the competition between the dimension of the receptor–ligand complex and depletion effects in the endocytosis of a spherical virus-like bioparticle. Our results show that the depletion effects do not always assist endocytosis of a spherical virus-like bioparticle; while the dimension of the ligand–receptor complex is larger than the size of a small bioparticle in cell environments, the depletion effects do not work and reverse effects appear. The ligand density covered on the virus can be identified quantitatively.     

Membrane Organization and Dynamics of the G-Protein-Coupled Serotonin<Subscript>1A</Subscript> Receptor Monitored Using Fluorescence-Based Approaches

The G-protein-coupled receptor (GPCR) superfamily represents one of the largest classes of molecules involved in signal transduction across the plasma membrane. Fluorescence-based approaches have provided valuable insights into GPCR functions such as receptor–receptor and receptor–ligand interactions, real-time assessment of signal transduction, receptor dynamics on the plasma membrane, and intracellular trafficking of receptors. This has largely been possible with the use of fluorescent probes such as the green fluorescent protein (GFP) from the jellyfish Aequoria victoria and its variants. We discuss the potential of fluorescence-based approaches in providing novel information on the membrane organization and dynamics of the G-protein-coupled serotonin_1A receptor tagged to the enhanced yellow fluorescent protein (EYFP). These authors contributed equally to the work.     

用分子对接方法预测HIV-1整合酶与金精三羧酸抑制剂的相互作用

用分子对接方法 (Docking)研究了HIV 1整合酶与其抑制剂金精三羧酸的结合过程 .为弄清金属离子在结合中所起的作用 ,选择含有一个Mg+ 2 或不含Mg+ 2 的两种不同的整合酶受体分别与金精三羧酸对接 .结果表明 ,Mg+ 2 对稳定配体与受体的结合起了重要作用 .金精三羧酸配体与含有一个金属Mg+ 2 的整合酶受体对接 ,最优结合自由能为 - 4 5 .19kJ/mol.当Mg+ 2 失去后 ,整合酶的活性中心构象将发生变化 ,使金精三羧酸抑制剂与整合酶的结合自由能 (- 2 4 .35kJ/mol)明显增加 .预测了未知的HIV 1整合酶与其抑制剂金精三羧酸的复合物结构 ,并可对基于结构的抗HIV 1整合酶的药物设计提供重要信息     

Role of fluctuations in ligand binding cooperativity of membrane receptors

Signal transduction upon binding of a ligand to a membrane protein can occur not only via allosteric conformational changes but also through fluctuations. We report a numerical study on the influence of conformational fluctuations on the cooperativity of a binding reaction in a simple model of an integral membrane receptor consisting of transmembrane helices. We find that small fluctuations lateral as well as perpendicular to the membrane can increase the cooperativity, with the former more dominant. Moreover, too much fluctuation induces negative cooperativity. Proteins with fewer than four helices do not show positive cooperativity under any circumstances. This behavior is rather robust, and independent of the receptor topology or ligand size. Fluctuations measured in all-atom molecular dynamics simulations of a G-protein coupled receptor fall within the predicted region of maximum cooperativity.     

Nanostructure Empowers Active Tumor Targeting in Ligand‐Based Molecular Delivery

Cell‐selective targeting is expected to enhance effectiveness and minimize side effects of cytotoxic agents. Functionalization of drugs or drug nanoconjugates with specific cell ligands allows receptor‐mediated selective cell delivery. However, it is unclear whether the incorporation of an efficient ligand into a drug vehicle is sufficient to ensure proper biodistribution upon systemic administration, and also at which extent biophysical properties of the vehicle may contribute to the accumulation in target tissues during active targeting. To approach this issue, structural robustness of self‐assembling, protein‐only nanoparticles targeted to the tumoral marker CXCR4 is compromised by reducing the number of histidine residues (from six to five) in a histidine‐based architectonic tag. Thus, the structure of the resulting nanoparticles, but not of building blocks, is weakened. Upon intravenous injection in animal models of human CXCR4⁺ colorectal cancer, the administered material loses the ability to accumulate in tumor tissue, where it is only transiently found. It instead deposits in kidney and liver. Therefore, precise cell‐targeted delivery requires not only the incorporation of a proper ligand that promotes receptor‐mediated internalization, but also, unexpectedly, its maintenance of a stable multimeric nanostructure that ensures high ligand exposure and long residence time in tumor tissue.     

Computational analysis of the binding ability of heterocyclic and conformationally constrained epibatidine analogs in the neuronal nicotinic acetylcholine receptor

One of the most critical issues on the study of ligand–receptor interactions in drug design is the knowledge of the bioactive conformation of the ligand. In this study, we describe a computational approach aimed at estimating the binding ability of epibatidine analogs to interact with the neuronal nicotinic acetylcholine receptor (nAChR) and get insights into the bioactive conformation. The protocol followed consists of a docking analysis and evaluation of pharmacophore parameters of the docked structures. On the basis of the biological data, the results have revealed that the docking analysis is able to predict active ligands, whereas further efforts are needed to develop a suitable and solid pharmacophore model.     

Mechanism of smell: Electrochemistry,receptors and cell signaling

This report presents in four main parts a novel approach based on electrochemistry, receptors and cell signaling. In Part A, there is limited correlation between dipole moments (DMs), associated electrostatic fields (EFs), and odor. For Part B, binding of the odorant to the receptor results in interaction of the ligand EF with those of the protein receptor, resulting in alteration. Part C addresses passage of the message by the altered EF to the olfactory neurons. Part D represents the final step in which the electrical signal is converted to perceived odor in the cerebral olfactory cortex.