Fluorescence Resonance Energy Transfer Studies Research Articles

Investigating the binding of caffeic acid to human hemoglobin using multispectroscopic and molecular docking approaches

Caffeic acid (CA) is a hydroxycinnamic acid derivative that possess a wide variety of biological properties and is non-toxic to humans. The binding mechanism of CA with human hemoglobin (HHb) was studied for the first time using multispectroscopic and molecular docking methods. The UV–visible absorption spectra showed that CA interacts with HHb through the formation of ground state complex. The fluorescence studies revealed that CA quenches HHb fluorescence by the static mechanism and confirmed the presence of a single CA binding site on the HHb molecule. The negative values of thermodynamics parameters (ΔH,ΔSand ΔG) showed that the binding of CA to HHb is a spontaneous and exothermic process. Hydrogen bonds and van der Waal interactions are the major intermolecular forces that stabilize the HHb-CA complex. Synchronous fluorescence experiments showed that binding of CA altered the microenvironment around tryptophan residues of HHb. Fluorescence resonance energy transfer studies indicated a high propensity of energy transfer from tryptophan residues of HHb to CA. Circular dichroism spectra and catalytic esterase activity confirmed that only minor changes occur in the secondary structure of HHb in the presence of CA. Molecular docking study identified the HHb amino acid residues involved in binding to CA. Analysis of the binding mode of CA with HHb represents an important step in elucidating the molecular mechanism of the protection of HHb from oxidative damage. This will help in understanding the potential role of CA and related antioxidants as therapeutic agents in various blood-related diseases.

A comparative study of conventional FRET and light harvesting properties of Rh-110/Rh-6G and Rh-19/Rh-B organic dye pairs impregnated in sol-gel glasses

Two different pairs of laser dyes, Rhodamine-110 (Rh-110)/Rhodamine-6G (Rh-6G) and Rhodamine-19 (Rh-19)/Rhodamine-B (Rh-B) (the first dye in each pair as a donor and the second as an acceptor) were impregnated in silica samples prepared by the sol-gel method and spectroscopically studied using absorption and steady-state fluorescence techniques. The critical transfer distance (R0), actual distance (r) between the donor and acceptor, overlap integral [J()], FRET (fluorescence resonance energy transfer) efficiency (E), and antenna effect efficiency (AE) were investigated in detail based on the variation in acceptor concentration. The FRET efficiency, antenna effect efficiency, and actual donor-acceptor distance for Rh-110/Rh-6G and Rh-19/Rh-B dye pairs corresponding to acceptor concentration ranges (3.83 to 7.65) × 10−5 M l−1 and (3.71 to 8.34) × 10−5 M l−1, respectively, were found to be in the ranges of 57.38% to 74.89%, 36.97% to 24.13%, 5.44 nm to 4.77 nm, and 77.01%. Furthermore, maximum FRET efficiencies of 85.68% and 87.63% and antenna effect efficiencies of 36.97% and 40.95% for Rh-110/Rh-6G and Rh-19/Rh-B, respectively, were also reported. Our results demonstrate the superior FRET efficiency of Rh-19/Rh-B over Rh-110/Rh-6G dye pair in sol-gel glasses, while the antenna effect efficiency of Rh-110/Rh-6G is higher than that of Rh-19/Rh-B for the same donor to acceptor (D/A) ratio. Finally, Rh-110/Rh-6G is a better energy harvester than the Rh-19/Rh-B dye pair at the common D/A ratio. These results are explained in terms of molecular structure similarity, polarity, and rigidity of donor and acceptor.

Protein binding studies and antioxidant activities of two mononuclear dioxomolybdenum(VI) complexes with 2-(3-methyl-5-phenyl pyrazol-1-yl) benzthiazole

Two yellow air-stable mononuclear dioxomolybdenum(VI) complexes, MoO2Cl2L (1) and MoO2Br2L (2) [where L = N,N donor ligand 2-(3-methyl-5-phenyl pyrazol-1-yl) benzthiazole], have been synthesized from their parent oxomolybdenum(V) complexes in dichloromethane. The binding affinity and binding mode of the molybdenum complexes with bovine serum albumin (BSA) have been explored by absorption and fluorescence titrations and time resolved fluorescence measurements. The number of binding sites for the complexes is nearly equal to unity, indicating there is only one binding site per BSA molecule. Molecular docking studies are also carried out to elucidate the binding mechanism, indicating that the complexes could quench the intrinsic fluorescence of BSA in a static quenching manner. Fluorescence resonance energy transfer study reveals that energy transfer takes place from Tryptophan residue of BSA to the synthesized complexes. The anti-oxidative properties of the complexes are examined by ABTS radical scavenging activities and DPPH radical quenching. The complexes exhibit different activities due to the influence of halogen substitution to the metal ion. MoO2Br2L (2) exhibits better activities than MoO2Cl2L (1) according to their EC50 values.

Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics.

Regulation of biological processes by proteins often involves the formation of transient, multimeric complexes whose characterization is mechanistically important but challenging. The bacterial toxin CcdB binds and poisons DNA Gyrase. The corresponding antitoxin CcdA extracts CcdB from its complex with Gyrase through the formation of a transient ternary complex, thus rejuvenating Gyrase. We describe a high throughput methodology called Ter-Seq to stabilize probable ternary complexes and measure associated kinetics using the CcdA-CcdB-GyrA14 ternary complex as a model system. The method involves screening a yeast surface display (YSD) saturation mutagenesis library of one partner (CcdB) for mutants that show enhanced ternary complex formation. We also isolated CcdB mutants that were either resistant or sensitive to rejuvenation, and used surface plasmon resonance (SPR) with purified proteins to validate the kinetics measured using the surface display. Positions, where CcdB mutations lead to slower rejuvenation rates, are largely involved in CcdA-binding, though there were several notable exceptions suggesting allostery. Mutations at these positions reduce the affinity towards CcdA, thereby slowing down the rejuvenation process. Mutations at GyrA14-interacting positions significantly enhanced rejuvenation rates, either due to reduced affinity or complete loss of CcdB binding to GyrA14. We examined the effect of different parameters (CcdA affinity, GyrA14 affinity, surface accessibilities, evolutionary conservation) on the rate of rejuvenation. Finally, we further validated the Ter-Seq results by monitoring the kinetics of ternary complex formation for individual CcdB mutants in solution by fluorescence resonance energy transfer (FRET) studies.

Cis interactions between CD2 and its ligands on T cells are required for T cell activation.

CD2 is largely described to promote T cell activation when engaged by its ligands, CD48 in mice and CD58 in humans, that are present on antigen-presenting cells (APCs). However, both CD48 and CD58 are also expressed on T cells. By generating new knockout mouse strains lacking CD2 or CD48 in the C57BL/6 background, we determined that whereas CD2 was necessary on T cells for T cell activation, its ligand CD48 was not required on APCs. Rather, CD48 was also needed on T cells. One exception was during cytotoxicity, which required CD48 on T cells and APCs. Fluorescence resonance energy transfer (FRET) studies in nonimmune cells provided evidence that cis interactions between CD2 and CD48 existed within individual cells. CD2-CD48 interactions on T cells enabled more robust T cell receptor (TCR) signals, including protein tyrosine phosphorylation. Using T cells from a CD2 knock-in mouse in which a tag was inserted at the carboxyl terminus of CD2, mass spectrometry analyses revealed that the role of CD2 in T cell activation correlated with its ability to interact with components of the TCR complex and the protein tyrosine kinase Lck. CD2-CD58 provided a similar function in human T cells. Thus, our data imply that T cell-intrinsic cis interactions of CD2 with its ligands are required for TCR signaling and T cell activation. Interactions with ligands on APCs contribute during cytotoxicity.

Addressing the Superior Drug Delivery Performance of Bilosomes─A Microscopy and Fluorescence Study.

The global health scenario in present times has raised human awareness about drug delivery strategies. Among colloidal drug delivery vehicles, vesicular nanocarriers such as liposomes and niosomes are popular. However, liposomes and niosomes get disrupted in the harsh environment of the gastrointestinal tract. In this context, the drug delivery community has reported the superior performance of vesicles containing bile salts, that is, bilosomes. The present work attempts to examine the structural/morphological aspects underlying the superior performance of bilosomes. Optical microscopy, electron microscopy, and light scattering give a definite proof of the enhanced stability of bilosomes compared to niosomes, both prepared from the same amphiphilic molecule. Fluorescence probing of the vesicles provides detailed insight into the bilayer characteristics and the differences between bilosomes and niosomes. Fluorescence resonance energy transfer studies lend further support to the findings that bilosomes have a more flexible bilayer structure than niosomes. The entrapment efficiency of the vesicles for the well-known antioxidant curcumin (whose bioavailability is a matter of concern due to low water solubility) was also studied. Bilosomes show higher curcumin entrapment efficiency than niosomes. For use in drug delivery, one needs to establish a trade-off between cargo/drug entrapment and release. Thus, a flexible bilayer structure is an advantage.

Dynamic Fluorescent Anti-Counterfeiting Labels Based on Conjugated Polymers Confined in Submicron Fibrous Membranes.

Developing a new anti-counterfeiting strategy is of great significance to combating the global counterfeiting problem. Here we report the construction of a dynamic fluorescence response system for anti-counterfeiting by combining the photochromism induced by the ring-opening of spiropyran (SP) to merocyanine (MC) with the fluorescence resonance energy transfer (FRET) between the conjugated polymer and MC. After elucidating the design principle, a new conjugated polymer, PPETE-SP, consisting of a poly[p-(phenylene ethynylene)-alt-(thienylene-ethynylene)] (PPETE) backbone with pendant SP, was synthesized and characterized. With poly(methyl methacrylate) (PMMA) as the matrix, the PPETE-SP/PMMA fibrous membrane was prepared via electrospinning. Under the irradiation of UV light, the fluorescent color of the membrane dynamically changed from green to light green, then light pink, and finally pink, and this process was reversible under visible light. The fluorescence emission switch was examined for 10 cycles and proved to have good repeatability, indicating that the membrane can be directly used as an anti-counterfeiting label for multiple verifications. The FRET efficiency was found to be about 61% based on the FRET study with confocal laser scanning microscopy. The covalent bonding between PPETE backbone and SP, the confinement of PPETE-SP chains in the fibrous membrane, as well as employing PMMA as the matrix were demonstrated to be crucial in realizing the photochromism and the FRET. Different anti-counterfeiting modes were proposed, providing rich selections for operation of verification. Such facile-to-operate and hard-to-imitate dynamic fluorescent responsive materials are very promising for use in practical anti-counterfeiting applications.

Tailoring Niosomes- Implications for Controlled Cargo Release and Function as Nanoreactors.

Nonionic surfactant vesicles (Niosomes) were prepared using polyoxyethylene alkyl ether (Brij 58).The impact of variation of the Brij: cholesterol molar ratio on the niosomal structure was studied. Fluorescence studies performed with the membrane probe 1,6-Diphenyl-1,3,5-triene (DPH) gave important insight on the bilayer integrity of the niosomes in response to environmental perturbations. The aim of the work being assessment of the efficacy of the niosomes as "drug release vehicles", release studies were performed with a xanthene dye Carboxyfluorescein (CF). Further, the vesicles were used as nanoreactors for the synthesis of gold nanoparticles (GNPs) as it is often useful to house nanoparticles in biological /biomimicking environments. Stable, spherical GNPs of diameter 6-10 nm were formed in these vesicles. As the vesicular bilayer mimics the cell membrane, the present work is relevant to the use of the GNPs for diagnostic and therapeutic purpose. It has also been established that fluorescence resonance energy transfer (FRET) effectively occurs between DPH and CF in the niosomes. The FRET studies provide important insight on the location of dyes within the vesicles thus indicating the prospective applications of this fluorescence technique for tracking the location of probes in biomimicking systems which maybe extrapolated to in vivo biological systems in future.

Influence of intraparticle cross-linking on polymer diffusion in latex films prepared from secondary dispersions

In this work, we synthesized surfactant-free latex dispersions of nanoparticles (NPs) based upon emulsification of a preformed proprietary BASF polymer (MnGPC = 5000 g/mol, Ð = 3, denoted as Pol), in which the —COOH groups were partially neutralized by ammonia. To obtain useful coatings with polymers of such low molecular weight (MW), we approached this problem through the reaction of carboxylated polymer dispersions with neopentyl glycol diglycidyl ether (NGDE, 20 to 60 mol% based on carboxyl groups) to increase the MW and to introduce gel content. We employed AFM to monitor the influence of cross-link density on the surface roughness and found the presence of cross-links increases the resistance of particles to deformation. Fluorescence resonance energy transfer (FRET) measurements were carried out to determine the extent of polymer mixing upon film formation. Our most important finding is that the gel content substantially limited the extent of molecular mixing at long annealing times or in corresponding solvent-cast films. In parallel, we carried out a series of similar reactions on the secondary dispersion particles with a monoepoxide, consisting of a mixture of dodecyl and tetradecyl glycidyl ether. This reaction maintained the size and size distribution of the latex particles. These polymers had no gel content, but the reaction with the epoxide lowered the Tg of the polymer. FRET studies showed a pronounced influence of Tg on the rates of polymer diffusion in these films.

Abstract 10: MANP Activation of the Cyclic GMP/PDE2/CYP11B2 Pathway Inhibits Aldosterone In Vitro and In Vivo

Aldosterone is a critical driver for cardiovascular disease (CVD). We recently discovered that MANP, a novel atrial natriuretic peptide (ANP) analog, possessed more potent aldosterone inhibitory action than ANP. MANP is currently entering clinical trials for hypertension and thus understanding its aldosterone suppressing mechanism is important. The mechanism of aldosterone inhibition by natriuretic peptides (NPs) remains to be clearly defined. Conflicting results were reported on the roles of particulate guanylyl cyclase A receptor (pGC-A) and NP clearance receptor (NPRC) in aldosterone inhibition. Furthermore, the functions of protein kinase G (PKG) and phosphodiesterases (PDE) on aldosterone regulation are not clear. Herein, we investigated the molecular mechanism of aldosterone regulation in the human adrenocortical cell line H295R and in mice. We firstly showed that pGC-A mediates aldosterone inhibition. In contrast, with NPRC agonist and antagonist, we showed that NPRC did not inhibit aldosterone. Next, we confirmed that MANP inhibits aldosterone via PDE2, not PKG, with specific agonists, antagonists, siRNA silencing, and fluorescence resonance energy transfer (FRET) experiments. Specifically, MANP suppressed ANGII mediated activation of aldosterone (fold change) MANP+ANGII 3.2±0.1* vs. ANGII 3.8±0.1 (*p<0.05) with IBMX, a PDEs inhibitor and the PDE2 antagonist Bay 60-7550 reversed MANP-mediated aldosterone suppression (IBMX+MANP+ANGII 3.9±0.2 and Bay+MANP+ANGII 4.1±0.1). With PKG agonists and inhibitors, aldosterone levels were not changed. In PDE2 activity FRET studies, aldosterone control was 3.7±0.4 and with MANP 0.9±0.2* supporting PDE2 activation by MANP. Further, the inhibitory effect of PDE2 is mediated by a reduction of intracellular Ca2+ concentration (~22%). We then showed that MANP directly reduced aldosterone synthase CYP11B2 expression in vitro. Lastly, in PDE2 knockout mice (embryonic lethal), embryonic adrenal CYP11B2 expression is markedly increased (wild type: 1±0.2, KO: 2.8±0.5*). Our findings innovatively elucidate the pGC-A/cGMP/PDE2 pathway in aldosterone inhibition by MANP in vitro and in vivo. Additionally, our data also support the development of MANP as a novel ANP analog drug for CVD.

Film Formation of Waterborne 2K Polyurethanes: Effect of Polyols Containing Different Carboxylic Acid Content

While the interaction of NCO with carboxylic acids has been documented, a comprehensive knowledge of its effect on the film formation in a two-component waterborne polyurethane (2K-WPU) system is lacking. In this work, we synthesized a series of carboxyl-functional acrylic polyols (Mn ≈ 5000 g/mol, Đ ≈ 2.7, Tg ≈ 15 °C) of uniform diameter (120 nm) with varying amounts of methacrylic acid introduced into the latex. For 2K-WPU dispersions with a molar NCO/OH ratio of 1.3:1, we monitored particle size by dynamic light scattering and NCO consumption by FTIR. In the dispersion, we found that the particle size remained nearly constant, and the NCO was almost completely consumed after 2 days. Incorporating COOH in the polyol latex accelerated the consumption of NCO. We synthesized polyol samples labeled with donor and acceptor dyes for fluorescence resonance energy transfer (FRET) studies of polymer diffusion and molecular mixing. In films formed from the polyol latex in the absence of hmPIC, the COOH content of the polyols had no significant effect on the rate or extent of polymer diffusion. In contrast, in films formed from the 2K-WPU dispersions with a stoichiometric NCO/OH ratio (1.3:1), the extent of ET rapidly increased to the maximum value, showing that the full extent of molecular mixing of the two components can be accomplished in films. Thus, the hmPIC acts as a reactive plasticizer. In parallel experiments in which the hmPIC was labeled with the donor dye, we found evidence for partial mixing of the PIC and polyol in the dispersed state. We also showed that the rate of mixing of the hmPIC and the polyol in the films cast from these dispersions was accelerated by −COOH groups in the polyol.

Conformational Dynamics of the Dengue Virus Protease Revealed by Fluorescence Correlation and Single-Molecule FRET Studies.

The dengue virus protease (DENV-PR) represents an attractive target for counteracting DENV infections. It is generally assumed that DENV-PR can exist in an open and a closed conformation and that active site directed ligands stabilize the closed state. While crystal structures of both the open and the closed conformation were successfully resolved, information about the prevalence of these conformations in solution remains elusive. Herein, we address the question of whether there is an equilibrium between different conformations in solution which can be influenced by addition of a competitive inhibitor. To this end, DENV-PR was statistically labeled by two dye molecules constituting a FRET (fluorescence resonance energy transfer) couple. Fluorescence correlation spectroscopy and photon-burst detection were employed to examine FRET pair labeled DENV-PRs freely diffusing in solution. The measurements were performed with two double mutants and with two dye couples. The data provide strong evidence that an equilibrium of at least two conformations of DENV-PR exists in solution. The competitive inhibitor stabilizes the closed state. Because the open and closed conformations appear to coexist in solution, our results support the picture of a conformational selection rather than that of an induced fit mechanism with respect to the inhibitor-induced formation of the closed state.

Binding study of florfenicol with DNA by multi-spectroscopy and molecular docking techniques

The investigation on the binding interaction mechanism of florfenicol with DNA in vitro was reported via multi-spectroscopy measurements and molecular docking approach in the present work. The static fluorescence quenching process accompanied with non-radiation energy transfer between florfenicol and DNA was confirmed by Stern-Volmer analysis, lifetime measurement and fluorescence resonance energy transfer study. Florfenicol was the A-T rich minor groove binding agent of DNA. Various experiments including site marker competitive experiments, viscosity measurements, helix melting studies, ionic strength measurements, thermal denaturation experiments, circular dichroism (CD) spectra measurements and UV–vis spectra characteristics were carried out to disclose the interaction mode. In addition, molecular docking stimulated appropriate binding orientation to further prove above experimental results. The binding constants were 6.92 × 103, 6.21 × 103 and 5.61 × 103 M−1 at 291, 301 and 311 K respectively and the binding distance r0 was 5.30 nm. Thermodynamic parameters, such as ΔHӨ =−7.90 kJ mol−1 and ΔSӨ = 46.39 J mol−1 K−1, showed that electrostatic attraction was the key force in the binding.

Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations

Single-molecule force spectroscopy is a powerful tool for studying protein folding. Over the last decade, a key question has emerged: how are changes in intrinsic biomolecular dynamics altered by attachment to μm-scale force probes via flexible linkers? Here, we studied the folding/unfolding of α3D using atomic force microscopy (AFM)-based force spectroscopy. α3D offers an unusual opportunity as a prior single-molecule fluorescence resonance energy transfer (smFRET) study showed α3D's configurational diffusion constant within the context of Kramers theory varies with pH. The resulting pH dependence provides a test for AFM-based force spectroscopy's ability to track intrinsic changes in protein folding dynamics. Experimentally, however, α3D is challenging. It unfolds at low force (<15 pN) and exhibits fast-folding kinetics. We therefore used focused ion beam-modified cantilevers that combine exceptional force precision, stability, and temporal resolution to detect state occupancies as brief as 1 ms. Notably, equilibrium and nonequilibrium force spectroscopy data recapitulated the pH dependence measured using smFRET, despite differences in destabilization mechanism. We reconstructed a one-dimensional free-energy landscape from dynamic data via an inverse Weierstrass transform. At both neutral and low pH, the resulting constant-force landscapes showed minimal differences (∼0.2 to 0.5 kBT) in transition state height. These landscapes were essentially equal to the predicted entropic barrier and symmetric. In contrast, force-dependent rates showed that the distance to the unfolding transition state increased as pH decreased and thereby contributed to the accelerated kinetics at low pH. More broadly, this precise characterization of a fast-folding, mechanically labile protein enables future AFM-based studies of subtle transitions in mechanoresponsive proteins.

Structural and molecular aspects of flavonoids as ligands for serum transferrin

Human serum transferrin (HST) acts as a carrier for Fe3+ and other ions. Binding of flavonoids to HST produces changes in the protein structure with direct implication on iron delivery into cells. We investigate the binding mechanism and affinity towards HST of three flavonoids: rutin, luteolin, and apigenin by different techniques: UV–Vis, fluorescence, fluorescence resonance energy transfer (FRET) combined with molecular docking. UV–Vis results indicate an interaction between flavonoids and HST. It was observed that HST fluorescence was quenched by these three flavonoids via a static process. All the interactions were moderate and the main driving forces are hydrophobic (ΔH > 0 and ΔS > 0) for rutin and luteolin binding or electrostatic (ΔH < 0 and ΔS > 0) for apigenin binding. FRET and molecular docking studies confirm the fluorescence static quenching mechanism by flavonoid binding. The binding of all three flavonoids increases HST stability. These results present the potential use of HST in target-oriented delivery of flavonoids and possibly other drugs into cells.

Cooperativity between the orthosteric and allosteric ligand binding sites of RORγt

Cooperative ligand binding is an important phenomenon in biological systems where ligand binding influences the binding of another ligand at an alternative site of the protein via an intramolecular network of interactions. The underlying mechanisms behind cooperative binding remain poorly understood, primarily due to the lack of structural data of these ternary complexes. Using time-resolved fluorescence resonance energy transfer (TR-FRET) studies, we show that cooperative ligand binding occurs for RORγt, a nuclear receptor associated with the pathogenesis of autoimmune diseases. To provide the crucial structural insights, we solved 12 crystal structures of RORγt simultaneously bound to various orthosteric and allosteric ligands. The presence of the orthosteric ligand induces a clamping motion of the allosteric pocket via helices 4 to 5. Additional molecular dynamics simulations revealed the unusual mechanism behind this clamping motion, with Ala355 shifting between helix 4 and 5. The orthosteric RORγt agonists regulate the conformation of Ala355, thereby stabilizing the conformation of the allosteric pocket and cooperatively enhancing the affinity of the allosteric inverse agonists.

Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6.

DNA mismatch repair (MMR) is an important postreplication process that eliminates mispaired or unpaired nucleotides to ensure genomic replication fidelity. In humans, Msh2-Msh6 and Msh2-Msh3 are the two mismatch repair initiation factors that recognize DNA lesions. While X-ray crystal structures exist for these proteins in complex with DNA lesions, little is known about their structures during the initial search along nonspecific double-stranded DNA, because they are short-lived and difficult to determine experimentally. In this study, various computational approaches were used to sidestep these difficulties. All-atom and coarse-grained simulations based on the crystal structures of Msh2-Msh3 and Msh2-Msh6 showed no translation along the DNA, suggesting that the initial search conformation differs from the lesion-bound crystal structure. We modeled probable search-mode structures of MSH proteins and showed, using coarse-grained molecular dynamics simulations, that they can perform rotation-coupled diffusion on DNA, which is a suitable and efficient search mechanism for their function and one predicted earlier by fluorescence resonance energy transfer and fluorescence microscopy studies. This search mechanism is implemented by electrostatic interactions among the mismatch-binding domain (MBD), the clamp domains, and the DNA backbone. During simulations, their diffusion rate did not change significantly with an increasing salt concentration, which is consistent with observations from experimental studies. When the gap between their DNA-binding clamps was increased, Msh2-Msh3 diffused mostly via the clamp domains while Msh2-Msh6 still diffused using the MBD, reproducing the experimentally measured lower diffusion coefficient of Msh2-Msh6. Interestingly, Msh2-Msh3 was capable of dissociating from the DNA, whereas Msh2-Msh6 always diffused on the DNA duplex. This is consistent with the experimental observation that Msh2-Msh3, unlike Msh2-Msh6, can overcome obstacles such as nucleosomes. Our models provide a molecular picture of the different mismatch search mechanisms undertaken by Msh2-Msh6 and Msh2-Msh3, despite the similarity of their structures.

Interaction of a hydrophilic molecule with bovine serum albumin: A combined multi-spectroscopic, microscopic and isothermal calorimetric study in the presence of graphene oxide

One of the most widely studied plasma protein is bovine serum albumin (BSA), and it plays a crucial role in the binding and transportation of many exogenous and endogenous drugs. Coumarin derivatives play a crucial role as an analgesic, anticancer, and anticoagulant agent. Here in this report, we have studied the binding interaction between a 7-amino coumarin derivative, namely 7-(N, N′-diethylamino)coumarin-3-carboxylic acid (7-DCCA) with BSA and also have found out the effect of graphene oxide (GO) on the binding interaction. The binding interaction was probed by employing various spectroscopic, microscopic, isothermal titration calorimetric (ITC), and by using molecular docking studies. The change in absorption and emission maxima position of BSA and 7-DCCA in the absence and presence of GO along with the change in absorbance and emission intensity when we titrated by 7-DCCA or BSA respectively indicates the strong complexation between 7-DCCA and BSA. From the fluorescence resonance energy transfer study, the average distance between tryptophan 213 of the BSA (donor), and the 7-DCCA (acceptor) is found ~50 Ǻ. From excited-state lifetime and fluorescence lifetime imaging (FLIM) studies, we observed that the average lifetime of 7-DCCA is much higher in the presence of BSA compared to buffer medium and in the presence of BSA a heterogeneous environment was created around 7-DCCA. Again in the presence of GO, the formation of a complex of 7-DCCA with a low concentration of BSA shows greater binding interaction as compared to that in the absence of GO. Time-resolved fluorescence anisotropy measurement shows that the addition of GO provides a restricted environment surrounding the 7-DCCA molecule in the presence of both low and high concentrations of BSA. CD study demonstrates the same extent of reduction of α-helical content of BSA protein on binding with 7-DCCA in the absence and presence of GO. ITC study revealed that the interaction between 7-DCCA and BSA is favoured by negative enthalpy change and positive entropy change. Also, from the ITC study, we find out that GO doesn't inflict significant change in the overall global binding interaction pattern, rather it inflicts changes in the mechanistic pathways of binding between 7-DCCA and BSA. Step-scan FTIR studies show the modification of amide I and amide II bonds with time when complexation occurs between BSA and 7-DCCA in the absence and presence of GO. The docking result reveals that the deprotonated form of 7-DCCA has positioned at a distance of ~3.7 nm from Trp 213. Thus these interactions play a central role in the development of coumarin derivative based small molecules to be used for both academic and industrial purposes.

Fluorescent Peptide Dendrimers for siRNA Transfection: Tracking pH Responsive Aggregation, siRNA Binding, and Cell Penetration.

Transfecting nucleic acids into various cells is a key procedure in biological research also envisioned for therapeutic applications. In our effort to obtain simple reagents that would be readily accessible from commercial building blocks, we recently reported peptide dendrimers as single component siRNA transfection reagents accessible in pure form by solid-phase peptide synthesis. Here, we extend our studies of these dendrimers by identifying analogs bearing a coumarin or BODIPY fluorescent label in their core and displaying comparable siRNA transfection efficiencies, pH dependent aggregation, siRNA binding, and secondary structures. Fluorescence resonance energy transfer (FRET) studies show that the dendrimers are tightly associated with siRNA within the formed nanoparticles at pH 7.4 but are released into solution at pH 5.0 and can participate in endosome escape by destabilizing the membrane at this pH value. Colocalization studies furthermore suggest that peptide dendrimers and siRNA remain tightly associated throughout the transfection process.

Effects of vanadium(IV) compounds on plasma membrane lipids lead to G protein-coupled receptor signal transduction

Luteinizing hormone receptors (LHR), expressed at physiological numbers <30,000 receptors per cell, translocate to and signal within membrane rafts following binding of human chorionic gonadotropin (hCG). Similarly LHR signal in cells when treated with bis(maltolato)oxovanadium(IV) (BMOV), bis(ethylmaltolato)oxovanadium(IV) (BEOV) or VOSO4, which decrease membrane lipid packing. Overexpressed LHR (>85,000 receptors per cell) are found in larger clusters in polarized homo-transfer fluorescence resonance energy transfer (homo-FRET) studies that were not affected by either hCG or vanadium compounds. Intracellular cyclic adenylate monophosphate (cAMP) levels indicate that only clustered LHR are active and produce the intracellular second messenger, cAMP. When LHR are over-expressed, cell signaling is unaffected by binding of hCG or vanadium compounds. To confirm the existence of intact complex, the EPR spectra of vanadium compounds in cell media were obtained using 1 mM BMOV, BEOV or VOSO4. These data were used to determine intact complex in a 10 μM solution and verified by speciation calculations. Effects of BMOV and BEOV samples were about two-fold greater than those of aqueous vanadium(IV) making it likely that intact vanadium complex are responsible for effects of LHR function. This represents a new mechanism for activation of a G protein-coupled receptor; perturbations in the lipid bilayer by vanadium compounds lead to aggregation and accumulation of physiological numbers of LHR in membrane raft domains where they initiate signal transduction and production of cAMP, a second messenger involved in signaling.