Effects of sequence context on the binding of tryptophan-containing peptides by the cucurbit[8]uril–methyl viologen complex

This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8√MV). The extent of quenching of Trp fluorescence upon binding to Q8√MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity of the amino acid residues at positions adjacent to the Trp-binding site has little if any influence on the binding affinity. This finding suggests that Q8√MV should be effective for the recognition of Trp residues within a broad range of peptide sequences.     

铜离子对水溶液中再生丝素蛋白构象转变的诱导作用

综合外加疏水性荧光探针ANS和荧光猝灭等多种荧光分析手段以及远紫外圆二色(far-UVCD)实验,发现在再生丝素蛋白稀溶液中,Cu(Ⅱ)通过与丝素蛋白疏水区域的直接络合从而诱导蛋白质分子发生构象转变,这一过程与乙醇诱导下的丝素蛋白变性有着相当大的区别.就络合位点而言,除了普遍认为的组氨酸(His)残基外,丝素蛋白分子中的色氨酸(Trp)残基是Cu(Ⅱ)的另一个有效络合点,并且这种络合在一定条件下是可逆的.     

酪氨酸猝灭Eosin Y的荧光

氨基酸残基对探针分子的荧光猝灭行为可以为生物大分子的结构及构象动力学研究提供重要的信息.本文运用飞秒瞬态吸收光谱和时间相关单光子计数实验系统研究了在水(H₂O)和氘代水(D₂O)溶液中乙酰基取代酪氨酸(AcTyr)对Eosin Y的超快荧光猝灭动力学过程.发现导致AcTyr对Eosin Y荧光猝灭的主要原因是由于它们之间形成了短寿命的基态复合物.我们还发现Eosin Y与AcTyr形成的基态复合物的激发态寿命具有明显的动力学同位素效应,表明AcTyr对Eosin Y的荧光猝灭是通过质子耦合电子转移过程发生的.     

Studies on the interaction of salvianolic acid B with human hemoglobin by multi-spectroscopic techniques

The interaction between salvianolic acid B (Sal B) and human hemoglobin (HHb) under physiological conditions was investigated by UV-vis absorption, fluorescence, synchronous fluorescence and circular dichroism spectroscopic techniques. The experimental results indicate that the quenching mechanism of fluorescence of HHb by Sal B is a static quenching procedure, the binding reaction is spontaneous, and the hydrophobic interactions play a major role in binding of Sal B to HHb. Based on F?rster's theory of non-radiative energy transfer, the binding distance between Sal B and the inner tryptophan residues of HHb was determined to be 2.64 nm. The synchronous fluorescence experiment revealed that Sal B can not lead to the microenvironmental changes around the Tyr and Trp residues of HHb, and the binding site of Sal B on HHb is located at α(1)β(2) interface of HHb. Furthermore, the CD spectroscopy indicated the secondary structure of HHb is not changed in the presence of Sal B.     

A highly selective and sensitive fluorescence "turn-on" probe for Ag+ in aqueous solution and live cells

A naphthalimide-based fluorescent probe, NPQ, that contains a novel receptor was successfully developed. NPQ exhibited "turn-on" fluorescence and excellent selectivity toward Ag(+) in the presence of various other metal ions in aqueous solution. A series of control compounds were designed and synthesized in order to explore the photoinduced electron transfer (PET) quenching mechanism of NPQ and binding mode of NPQ with Ag(+). Moreover, with the NPQ-Ag(+) complex, I(-) was easily selectively recognized by a marked fluorescence quenching. The live cell imaging experiments demonstrate that NPQ can be used as a fluorescent probe for monitoring Ag(+) in living cells.     

Synthesis, characterization and theoretical analysis on a oxygen-sensing phosphorescent copper(I) complex

The fluorescence quenching of 9-aminoacridine by certain substituted uracils in water was studied using absorption, steady state and time resolved measurements. The bimolecular quenching rate constants (k_q), binding constant K and number of binding sites (n) were calculated based on the fluorescence quenching data. The free energy change (ΔG_et) for electron transfer process was calculated by Rehm–Weller equation. From lifetime measurement we observed that the quenching was mainly due to static mechanism involving ground state complex formation.     

PROPERTIES OF THE RETINAL BINDING SITE IN BACTERIORHODOPSIN. USE OF RETINOL AND RETINYL MOIETIES AS FLUORESCENT PROBES

Abstract— The fluorescence spectra of various reduced bacteriorhodopsin chromophore species indicate energy transfer from aromatic amino acid side chains of the protein to the retinyl moiety. Binding studies with retinol reveal that energy transfer occurs only when the retinyl moiety is bound in the chromophoric site of the protein. Retroretinol is a fluorescent probe for the binding site.     

The Interaction Between Crystal Violet and Bovine Serum Albumin: Spectroscopic and Molecular Docking Investigations

The present work reported the investigations on the interaction between a triphenylmethane industrial dye—crystal violet (CV)—and bovine serum albumin (BSA) by spectroscopic methods and molecular docking calculation. The static quenching mechanism of the intrinsic fluorescence of BSA by CV was deduced by the fluorescence measurements and the ground-state complex formation was confirmed from the UV-vis spectra. The site maker competition binding experiments together with the molecular docking showed that the CV molecule specifically bound on the subdomain IIA of BSA. The obtained values of thermodynamic properties of binding suggested that the hydrophobic interaction was dominated as suggested by molecular docking results that the CV molecule was surrounded by hydrophobic amino acid residues. The conformation change of BSA in the binding process was detected by circular dichroism spectra and Fourier-transform infrared (FTIR) spectra and also reflected by the size change of BSA from the measurements by dynamic light scattering (DLS).     

Study of the Binding of Herbacetin to Bovine Serum Albumin by Fluorescence Spectroscopy

In this paper, the interaction between herbacetin and BSA was investigated by fluorescence and three-dimensional fluorescence spectroscopy under simulated physiological conditions. It was proved that the fluorescence quenching of BSA by herbacetin was mainly the result of the formation of a herbacetin–BSA complex. The modified Stern–Volmer quenching constant and the corresponding thermodynamic parameters ΔH ⁰, ΔG ⁰ and ΔS ⁰ were calculated at different temperatures. The results indicated that electrostatic interactions were the predominant intermolecular forces in stabilizing the complex. The distance r=3.23 nm between the donor (BSA) and acceptor (herbacetin) was obtained according to Förster’s nonradioactive energy transfer theory. The synchronous fluorescence and three-dimensional fluorescence spectra results showed that the hydrophobity of amino acid residues increased in the presence of herbacetin. These results revealed that the microenvironment and conformation of BSA changed during the binding reaction.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

单宁酸与牛血红蛋白相互作用的光谱研究

利用荧光光谱技术研究了单宁酸与牛血红蛋白分子的相互作用。实验结果表明:单宁酸分子与BHb发生反应生成基态复合物,导致BHb内源荧光的猝灭,该猝灭属于静态猝灭。测定了不同温度下该反应的表观结合常数、结合位点数及结合热力学参数,热力学参数的变化表明上述作用过程是一个熵增加、自由能降低的自发分子间作用过程,单宁酸与BHb之间以疏水和氢键作用力为主;根据Frster能量转移理论,测得供体与受体间结合距离r和能量转移效率E;并用同步荧光光谱法探讨了单宁酸对BHb构象的影响。     

铱(IV)离子与人血丙种球蛋白的作用研究

在0.1 mol•L^－1醋酸-醋酸钠(pH 5.0)体系中, 采用紫外吸收光谱、荧光光谱及同步荧光光谱法研究了人血丙种球蛋白(gamma seroglobulinum humanum, 简称GSH)与铱(IV)离子的相互作用. 结果表明, Ir(IV)离子使人血丙种球蛋白的构象发生了改变, α-螺旋含量减少, 并且用同步荧光光谱发现Ir(IV)离子与人血丙种球蛋白的作用位点更接近于色氨酸, 从而使色氨酸残基的疏水性略有减小. 荧光光谱结果表明Ir(IV)对人血丙种球蛋白内源荧光(342 nm)产生了较强的荧光猝灭作用, 根据不同温度下Ir(IV)对人血丙种球蛋白的荧光猝灭作用, 证明了这种荧光猝灭为静态猝灭机制, 计算了其结合常数和结合位点数, 从而得出了静电作用力为其主要的作用力.     

Two-dimensional fluorescence correlation spectroscopy IV: resolution of fluorescence of tryptophan residues in alcohol dehydrogenase and lysozyme

Generalized two-dimensional (2D) fluorescence correlation spectroscopy has been used to resolve the fluorescence spectra of two tryptophan (Trp) residues in alcohol dehydrogenase and lysozyme. In each protein, one Trp residue is buried in a hydrophobic domain of the protein matrix and the other Trp residue is located at a hydrophilic domain close to the protein-water interface. Fluorescence quenching by iodide ion, a hydrophilic quencher, was employed as a perturbation to induce the intensity change in the spectra. The Trp residue which is located at the hydrophilic domain is effectively quenched by the quencher, while the Trp residue located at the hydrophobic domain is protected from the quenching. Therefore, the fluorescence of these two Trp residues have a different sensitivity to the quenching, showing a different response to the concentration of the quencher. Fluorescence spectra of the two Trp residues in alcohol dehydrogenase, which are heavily overlapped in conventional one-dimensional spectra, have been successfully resolved by the 2D correlation technique. From the asynchronous correlation map, it was revealed that the quenching of Trp located at the hydrophobic part was brought about after that of Trp located at the hydrophilic part. In contrast, the fluorescence spectra of the two Trp residues could not be resolved after the alcohol dehydrogenase was denatured with guanidine hydrochloride. These results are consistent with the well-known structure of alcohol dehydrogenase. Furthermore, it was elucidated that the present 2D analysis is not interfered by Raman bands of the solvent, which sometimes bring difficulty into the conventional fluorescence analysis. Fluorescence spectra of the Trp residues in lysozyme could not be resolved by the 2D correlation technique. The differences between the two proteins are attributed to the fact that the Trp residue in the hydrophobic site of lysozyme is not sufficiently protected from the quenching.     

Photoinduced Electron Transfer in Dry Gelatin Containing Bound Methylene Blue

Excited states of methylene blue bound to dry gelatin undergo electron-transfer quenching reactions with neighboring amino acid residues to give reduced, methylene blue-free radicals. At the low loadings of methylene blue bound to gelatin used in this work, the absorption spectra indicated that the methylene blue existed principally in its monomeric form. The rates of methylene blue fluorescence quenching depended on the temperature at which the gelatin was dried. There was no detectable fluorescence characteristic of the localized excited singlet state of methylene blue when the dye is bound to gelatin dried at 15°C, where a significant proportion of the protein exists in its a -helical form. Instead, weak emission with a maximum at 645 nm is observed. It is inferred from this that the rate of quenching of any localized excited singlet states of the dye bound to a -helical gelatin is very fast thereby competing efficiently with radiative relaxation. The weak emission at 645 nm is ascribed to a fluorescent exciplex formed between bound methylene blue and a neighboring electron/proton donor residue of the gelatin. While fluorescence characteristic of the localized methylene blue singlet state was observed from dyed gelatin dried at 50°C, i.e. in its random coil form, the triplet state is subject to rapid quenching by electron/proton transfer with protein moieties.     

Enantioselective fluorescent recognition of chiral acids by cyclohexane-1,2-diamine-based bisbinaphthyl molecules

The cyclohexane-1,2-diamine-based bisbinaphthyl macrocycles (S)-/(R)-5 and their cyclic and acyclic analogues are synthesized. The interactions of these compounds with various chiral acids are studied. Compounds (S)-/(R)-5 exhibit highly enantioselective fluorescent responses and high fluorescent sensitivity toward alpha-hydroxycarboxylic acids and N-protected amino acids. Among these interactions, (S)-mandelic acid (10(-3) M) led to over 20-fold fluorescence enhancement of (S)-5 (1.0 x 10(-5) M in benzene/0.05% DME) at the monomer emission, and (S)-hexahydromandelic acid (10(-3) M) led to over 80-fold fluorescence enhancement. These results demonstrate that (S)-5 is useful as an enantioselective fluorescent sensor for the recognition of the chiral acids. On the basis of the study of the structures of (S)-5 and the previously reported 1,2-diphenylethylenediamine-based bisbinaphthyl macrocycle (S)-4, the large fluorescence enhancement of (S)-5 with a chirality-matched alpha-hydroxycarboxylic acid is attributed to the formation of a structurally rigidified host-guest complex and the further interaction of this complex with the acid to suppress the photoinduced electron-transfer fluorescent quenching caused by the nitrogens in (S)-5.     

Studies on the interaction of cinnamic acid with bovine serum albumin

The interaction between cinnamic acid and bovine serum albumin (BSA) have been studied at three temperatures, 296, 303 and 310 K. Fluorescence quenching spectra in combination with Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy was used to investigate the drug-binding mode, the binding constant and the protein structure changes in the presence of cinnamic acid in aqueous solution at pH 7.40. The fluorescence quenching constant K(q), K(sv) and the binding constant K were calculated according to Stern-Volmer equation based on the quenching of the fluorescence of BSA in the presence of cinnamic acid. The thermodynamic parameters, the enthalpy (DeltaH) and the entropy change (DeltaS) were estimated to be -16.457 kJ mol(-1) and 38.028 J mol(-1) K(-1) according to the van't Hoff equation. The displacement experiment shows that cinnamic acid can bind to the subdomain IIA (corresponding to Sudlow's drug binding site I). The distance between the tryptophan residues in BSA and cinnamic acid bound to site I was estimated to be 1.63 nm using F?ster's equation on the basis of fluorescence energy transfer. The decreased binding constant in the presence of common ions indicates that common ions have effect on drug-BSA system.     

Fluorescence Spectroscopic Studies on the Interaction of Oleanolic Acid and its Triterpenoid Saponins Derivatives with Two Serum Albumins

The interaction of oleanolic acid (OA) and its glycosylated derivatives (LL-2 and LL-4) with human and bovine serum albumins were investigated using the methods of fluorescence spectroscopy. The spectroscopic analysis of the fluorescence quenching that occurs when OA and its derivatives interact with serum albumin indicates that these quenching constants are inversely correlated with temperature and the quenching process involves static interactions. The binding affinity of OA and OA-derived compounds to bovine serum albumin (BSA) and human serum albumin (HSA) follow the trend LL-4 > LL-2 > OA, suggesting that glycosylation of OA can facilitate its binding to serum albumins. Additionally, the binding affinity of these compounds to HSA is stronger than it is to BSA. The calculated thermodynamic parameters suggest that hydrophobic interactions dominate these interaction processes. We also found that only a single type of binding site exists for OA and its derivatives to HSA and BSA. Synchronous fluorescence results indicate that the binding of OA, LL-2 and LL-4 to BSA and HSA can lead to the conformational changes around the tryptophan residues of the two serum albumins. These results provided valuable clues to the pharmacokinetics and the pharmacologic activities of OA and its types of triterpenoid saponins derivatives.     

Interaction between natural organic matter (NOM) and polycyclic aromatic compounds (PAC) – comparison of fluorescence quenching and solid phase micro extraction (SPME)

The interaction of phenanthrene and 9-aminophenanthrene with natural organic matter (NOM) of different origin was investigated using the fluorescence quenching approach and the solid phase micro extraction method. The results of both methods are compared in terms of the influence of the concentration of the polycyclic aromatic compounds (PAC) as well as the concentration of the NOM on the observed binding constant. Due to the combination of steady-state and time-resolved fluorescence techniques it could be concluded that the observed fluorescence quenching was caused by a static interaction like a complex formation. While for phenanthrene both analytical methods showed no long term effects and the reaction equilibrium between NOM and phenanthrene was established within the first hour, for 9-aminophenanthrene a slow reaction kinetics (within days) was found indicating specific interactions between NOM and the amino group.     

Carbon nanotube-quenched fluorescent oligonucleotides: probes that fluoresce upon hybridization

We report an effective, novel self-assembled single-wall carbon nanotube (SWNT) complex with an oligonucleotide and demonstrate its feasibility in recognizing and detecting specific DNA sequences in a single step in a homogeneous solution. The key component of this complex is the hairpin-structured fluorescent oligonucleotide that allows the SWNT to function as both a "nanoscaffold" for the oligonucleotide and a "nanoquencher" of the fluorophore. Given this functionality, this carbon nanotube complex represents a new class of universal fluorescence quenchers that are substantially different from organic quenchers and should therefore have many applications in molecular engineering and biosensor development. Competitive binding of a DNA target and SWNTs with the oligonucleotide results in fluorescence signal increments relative to the fluorescence without a target as well as in marked fluorescence quenching. In contrast to the common loop-and-stem configuration of molecular beacons (MBs), this novel fluorescent oligonucleotide needs only one labeled fluorophore, yet the emission can be measured with little or no background interference. This property greatly improves the signal-to-background ratio compared with those for conventional MBs, while the DNA-binding specificity is still maintained by the MB. To test the interaction mechanisms of the fluorescent oligonucleotide with SWNTs and target DNA, thermodynamic analysis and fluorescence anisotropy measurements, respectively, were applied. Our results show that MB/SWNT probes can be an excellent platform for nucleic acid studies and molecular sensing.     

"Quenchbodies": quench-based antibody probes that show antigen-dependent fluorescence

Here, we describe a novel reagentless fluorescent biosensor strategy based on the antigen-dependent removal of a quenching effect on a fluorophore attached to antibody domains. Using a cell-free translation-mediated position-specific protein labeling system, we found that an antibody single chain variable region (scFv) that had been fluorolabeled at the N-terminal region showed a significant antigen-dependent fluorescence enhancement. Investigation of the enhancement mechanism by mutagenesis of the carboxytetramethylrhodamine (TAMRA)-labeled anti-osteocalcin scFv showed that antigen-dependency was dependent on semiconserved tryptophan residues near the V(H)/V(L) interface. This suggested that the binding of the antigen led to the interruption of a quenching effect caused by the proximity of tryptophan residues to the linker-tagged fluorophore. Using TAMRA-scFv, many targets including peptides, proteins, and haptens including morphine-related drugs could be quantified. Similar or higher sensitivities to those observed in competitive ELISA were obtained, even in human plasma. Because of its versatility, this "quenchbody" is expected to have a range of applications, from in vitro diagnostics, to imaging of various targets in situ.