high-precision-fret-at-single-molecule-level-for-biomolecule

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

A protocol on how to perform high-precision interdye distance measurements using F&#246;rster resonance energy transfer (FRET) at the single-molecule ...

Clemson University

Impedance spectroscopy is a technique that reveals information, such as macromolecular charges and related properties about protein suspensions and other materials. Here we report on impedance measurements over the frequency range of 1 Hz to 1 MHz of alpha-beta tubulin heterodimers suspended in a buffer. These and other polyelectrolyte suspensions show enormous dielectric responses at low frequencies, due both to the motion of charges suspended in the medium and to an electrical double layer that forms at each electrode-medium interface. We propose an equivalent circuit model to minimize electrode polarization effects and extract the intrinsic response of the bulk medium. At megaHertz frequencies, the conductivity increases with concentration below the critical concentration of approximately 1 mg/ml for microtubule polymerization, above which the conductivity decreases. This suggests that such measurements can be used to monitor the dynamics of microtubule polymerization. Finally, we obtain the net charge number per tubulin dimer of /Z/ = 306 in the saline buffer, which, if maintained as the dimers polymerized, would yield a linear charge density of 3.8 e/angstroms for the assembled microtubules. These results are potentially important for fundamental electrostatic processes in biomolecules and suggest the possibility of developing future bioelectronic applications.

Impedance spectroscopy of alpha-beta tubulin heterodimer suspensions.

One of the key questions regarding intracellular diffusion is how the environment affects molecular mobility. Mostly, intracellular diffusion has been described as hindered, and the physical reasons for this behavior are: immobile barriers, molecular crowding, and binding interactions with immobile or mobile molecules. Using results from multi-photon fluorescence correlation spectroscopy, we describe how immobile barriers and crowding agents affect translational mobility. To study the hindrance produced by immobile barriers, we used sol-gels (silica nanostructures) that consist of a continuous solid phase and aqueous phase in which fluorescently tagged molecules diffuse. In the case of molecular crowding, translational mobility was assessed in increasing concentrations of 500 kDa dextran solutions. Diffusion of fluorescent tracers in both sol-gels and dextran solutions shows clear evidence of anomalous subdiffusion. In addition, data from the autocorrelation function were analyzed using the maximum entropy method as adapted to fluorescence correlation spectroscopy data and compared with the standard model that incorporates anomalous diffusion. The maximum entropy method revealed evidence of different diffusion mechanisms that had not been revealed using the anomalous diffusion model. These mechanisms likely correspond to nanostructuring in crowded environments and to the relative dimensions of the crowding agent with respect to the tracer molecule. Analysis with the maximum entropy method also revealed information about the degree of heterogeneity in the environment as reported by the behavior of diffusive molecules.

Multiple diffusion mechanisms due to nanostructuring in crowded environments.

One of the major challenges in electrochemistry is to properly account for polarization of the electrical double layer that forms at an electrode-electrolyte interface, especially when interpreting the impedance spectra of biological molecules, electrolytes, or live cell suspensions. This double layer, which affects the measured impedance, is also known as the electrode polarization effect. Various methods of correcting for its effects on impedance data have been reported, including varying the spacing between electrodes, four-electrode techniques, and electrodeless methods. Here we discuss the use of a constant phase element in a recently proposed circuit model, which can be thought of as a measure of the fractal nature of the interface. We also report on the conductivity spectra of several saline solutions over the frequency range 1 Hz-1 MHz, in which we observe Debye-like relaxation behavior that changes with ion concentration and type. Good agreement is obtained with an alternative model that treats the cations and anions as overdamped oscillators in harmonic restoring potentials.

Relaxation processes due to the electrode-electrolyte interface in ionic solutions.

We derive an analytical model of the potential differences induced across plasma and internal organelle membranes in suspended cells exposed to oscillatory electric fields. Multiple shells are modeled using iterative applications of the single-shell calculation with mobile charges. This work is motivated, in part, by recent results suggesting the ability to use alternating current (ac) fields to noninvasively monitor enzyme activity within internal membranes, particularly the mitochondrial electron transport chain. Previous work, on induced transmembrane voltages in cells subjected to ac fields, has mainly been limited to oscillatory potentials across the plasma membrane. Here we first develop a three-membrane model, consisting of a plasma membrane surrounding inner and outer membranes representing an internal organelle, such as a mitochondrion. Frequency-dependent transmembrane potentials are modeled for spherical, weakly conducting membrane shells enclosing a conductive cytoplasm surrounding an idealized internal organelle. We then use a two-shell model to simulate induced ac membrane potentials of a suspended isolated mitochondrion in which the outer membrane is usually much more permeable than the inner membrane.

Effects of oscillatory electric fields on internal membranes: an analytical model.

Development of biologically relevant crowding solutions necessitates improved understanding of how the relative size and density of mobile obstacles affect probe diffusion. Both the crowding density and relative size of each co-solute in a mixture will contribute to the measured microviscosity as assessed by altered translational mobility. Using multiphoton fluorescent correlation spectroscopy, this study addresses how excluded volume of dextran polymers from 10 to 500 kDa affect microviscosity quantified by measurements of calmodulin labeled with green fluorescent protein as the diffusing probe. Autocorrelation functions were fit using both a multiple-component model with maximum entropy method (MEMFCS) and an anomalous model. Anomalous diffusion was not detected, but fits of the data with the multiple-component model revealed separable modes of diffusion. When the dominant mode of diffusion from the MEMFCS analysis was used, we observed that increased excluded volume slows probe mobility as a simple exponential with crowder concentration. This behavior can be modeled with a single parameter, beta, which depends on the dextran size composition. Two additional modes of diffusion were observed using MEMFCS and were interpreted as unique microviscosities. The fast mode corresponded to unhindered free diffusion as in buffer, whereas the slower agreed well with the bulk viscosity. At 10% crowder concentration, one finds a microviscosity approximately three times that of water, which mimics that reported for intracellular viscosity.

Macromolecular crowding and size effects on probe microviscosity.

Calmodulin (CaM) is the major pathway that transduces intracellular Ca2+ increases to the activation of a wide variety of downstream signaling enzymes. CaM and its target proteins form an integrated signaling network believed to be tuned spatially and temporally to control CaM's ability to appropriately pass signaling events downstream. Here, we report the spatial diffusivity and availability of CaM labeled with enhanced green fluorescent protein (eGFP)-CaM, at basal and elevated Ca2+,quantified by the novel fluorescent techniques of raster image scanning spectroscopy and number and brightness analysis. Our results show that in basal Ca2+ conditions cytoplasmic eGFP-CaM diffuses at a rate of 10 microm(2)/s, twofold slower than the noninteracting tracer, eGFP, indicating that a significant fraction of CaM is diffusing bound to other partners. The diffusion rate of eGFP-CaM is reduced to 7 microm(2)/s when a large (646 kDa) target protein Ca2+/CaM-dependent protein kinase II is coexpressed in the cells. In addition, the presence of Ca2+/calmodulin-dependent protein kinase II, which can bind up to 12 CaM molecules per holoenzyme, increases the stoichiometry of binding to an average of 3 CaMs per diffusive molecule. Elevating intracellular Ca2+ did not have a major impact on the diffusion of CaM complexes. These results present us with a model whereby CaM is spatially modulated by target proteins and support the hypothesis that CaM availability is a limiting factor in the network of CaM-signaling enzymes.

Spatial diffusivity and availability of intracellular calmodulin.

Ca(2+)-Calmodulin-dependent protein kinase II (CaMKII) is an abundant synaptic protein that was recently shown to regulate the organization of actin filaments leading to structural modifications of synapses. CaMKII is a dodecameric complex with a special architecture that provides it with unique potential for organizing the actin cytoskeleton. We report using biochemical assays that the beta isoform of CaMKII binds to and bundles actin filaments, and the disposition of betaCaMKII within the actin bundles was revealed by cryoelectron tomography. In addition, betaCaMKII was found to inhibit actin polymerization, suggesting that it either serves as a capping protein or binds monomeric actin, reducing the amount of freely available monomers to nucleate polymer assembly. By means of fluorescent cross-correlation spectroscopy, we determined that betaCaMKII does indeed bind to monomeric actin, reaching saturation at a stoichiometry of 12:1 actin monomers per betaCaMKII holoenzyme with a binding constant of 2.4 x 10(5) m(-1). In cells, betaCaMKII has a dual functional role; it can sequester monomeric actin to reduce actin polymerization and can also bundle actin filaments. Together, these effects would impact both the dynamics of actin filament assembly and enhance the rigidity of the filaments once formed, significantly impacting the structure of synapses.

{beta}CaMKII regulates actin assembly and structure.

In vitro biochemical reactions are most often studied in dilute solution, a poor mimic of the intracellular space of eukaryotic cells, which are crowded with mobile and immobile macromolecules. Such crowded conditions exert volume exclusion and other entropic forces that have the potential to impact chemical equilibria and reaction rates. In this article, we used the well-characterized and ubiquitous molecule calmodulin (CaM) and a combination of theoretical and experimental approaches to address how crowding impacts CaM's conformational plasticity. CaM is a dumbbell-shaped molecule that contains four EF hands (two in the N-lobe and two in the C-lobe) that each could bind Ca(2+), leading to stabilization of certain substates that favor interactions with other target proteins. Using coarse-grained molecular simulations, we explored the distribution of CaM conformations in the presence of crowding agents. These predictions, in which crowding effects enhance the population of compact structures, were then confirmed in experimental measurements using fluorescence resonance energy transfer techniques of donor- and acceptor-labeled CaM under normal and crowded conditions. Using protein reconstruction methods, we further explored the folding-energy landscape and examined the structural characteristics of CaM at free-energy basins. We discovered that crowding stabilizes several different compact conformations, which reflects the inherent plasticity in CaM's structure. From these results, we suggest that the EF hands in the C-lobe are flexible and can be thought of as a switch, while those in the N-lobe are stiff, analogous to a rheostat. New combinatorial signaling properties may arise from the product of the differential plasticity of the two distinct lobes of CaM in the presence of crowding. We discuss the implications of these results for modulating CaM's ability to bind Ca(2+) and target proteins.

Modulation of calmodulin plasticity by the effect of macromolecular crowding.

When signaling molecules diffuse through the cytosol, they encounter a wide variety of obstacles that hinder their mobility in space and time. Some of those factors include, but are not limited to, interactions with mobile and immobile targets or obstacles. Besides finding a crowded environment inside the cell, macromolecules assemble into molecular complexes that drive specific biological functions adding additional complexity to their diffusion. Thus, simple models of diffusion often fail to explain mobility through the cell interior, and new approaches are needed. Here we used fluorescent correlation spectroscopy to measure diffusion of three molecules of similar size with different surface properties diffusing in actin gels. The fluorescent probes were (a) quantum dots, (b) yellow-green fluorescent spheres, and (c) the beta isoform of Ca(2+) calmodulin-dependent protein kinase II tagged with green fluorescent protein. We compared various models for fitting the autocorrelation function (ACF) including single component, two-component, and anomalous diffusion. The two-component and anomalous diffusion models were superior and were largely indistinguishable based on a goodness of fit criteria. To better resolve differences between these two models, we modified the ACF to observe temporal variations in diffusion. We found in both simulated and experimental data a transient anomalous subdiffusion between two freely diffusing regimes produced by binding interactions of the diffusive tracers with actin gels.

Transient anomalous subdiffusion: effects of specific and nonspecific probe binding with actin gels.

Quantifying translational mobility in neurons: comparison between current optical techniques.

An analysis method of lifetime, polarization and spectrally filtered fluorescence correlation spectroscopy, referred to as filtered FCS (fFCS), is introduced. It uses, but is not limited to, multiparameter fluorescence detection to differentiate between molecular species with respect to their fluorescence lifetime, polarization and spectral information. Like the recently introduced fluorescence lifetime correlation spectroscopy (FLCS) [Chem. Phys. Lett. 2002, 353, 439-445], fFCS is based on pulsed laser excitation. However, it uses the species-specific polarization and spectrally resolved fluorescence decays to generate filters. We determined the most efficient method to generate global filters taking into account the anisotropy information. Thus, fFCS is able to distinguish species, even if they have very close or the same fluorescence lifetime, given differences in other fluorescence parameters. fFCS can be applied as a tool to compute species-specific auto- (SACF) and cross- correlation (SCCF) functions from a mixture of different species for accurate and quantitative analysis of their concentration, diffusion and kinetic properties. The computed correlation curves are also free from artifacts caused by unspecific background signal. We tested this methodology by simulating the extreme case of ligand-receptor binding processes monitored only by differences in fluorescence anisotropy. Furthermore, we apply fFCS to an experimental single-molecule FRET study of an open-to-closed conformational transition of the protein Syntaxin-1. In conclusion, fFCS and the global analysis of the SACFs and SCCF is a key tool to investigate binding processes and conformational dynamics of biomolecules in a nanosecond-to-millisecond time range as well as to unravel the involved molecular states.

Filtered FCS: species auto- and cross-correlation functions highlight binding and dynamics in biomolecules.

Fluorescence correlation spectroscopy (FCS) in combination with Förster resonance energy transfer (FRET) has been developed to a powerful statistical tool, which allows for the analysis of FRET fluctuations in the huge time of nanoseconds to seconds. FRET-FCS utilizes the strong distance dependence of the FRET efficiency on the donor (D)-acceptor (A) distance so that it developed to a perfect method for studying structural fluctuation in biomolecules involved in conformational flexibility, structural dynamics, complex formation, folding, and catalysis. Structural fluctuations thereby result in anticorrelated donor and acceptor signals, which are analyzed by FRET-FCS in order to characterize underlying structural dynamics. Simulated and experimental examples are discussed. First, we review experimental implementations of FRET-FCS and present theory for a two-state interconverting system. Additionally, we consider a very common case of FRET dynamics in the presence of donor-only labeled species. We demonstrate that the mean relaxation time for the structural dynamics can be easily obtained in most of cases, whereas extracting meaningful information from correlation amplitudes can be challenging. We present a strategy to avoid a fit with an underdetermined model function by restraining the D and A brightnesses of the at least one involved state, so that both FRET efficiencies and both rate constants (i.e., the equilibrium constant) can be determined. For samples containing several fluorescent species, the use of pulsed polarized excitation with multiparameter fluorescence detection allows for filtered FCS (fFCS), where species-specific correlation functions can be obtained, which can be directly interpreted. The species selection is achieved by filtering using fluorescence decays of individual species. Analytical functions for species auto- and cross-correlation functions are given. Moreover, fFCS is less affected by photophysical artifacts and often offers higher contrast, which effectively increases its time resolution and significantly enhances its capability to resolve multistate kinetics. fFCS can also differentiate between species even when their brightnesses are the same and thus opens up new possibilities to characterize complex dynamics. Alternative fluctuation algorithms to study FRET dynamics are also briefly reviewed.

Analyzing Förster resonance energy transfer with fluctuation algorithms.

Protein signaling occurs in crowded intracellular environments, and while high concentrations of macromolecules are postulated to modulate protein-protein interactions, analysis of their impact at each step of the reaction pathway has not been systematically addressed. Potential cosolute-induced alterations in target association are particularly important for a signaling molecule like calmodulin (CaM), where competition among >300 targets governs which pathways are selectively activated. To explore how high concentrations of cosolutes influence CaM-target affinity and kinetics, we methodically investigated each step of the CaM-target binding mechanism under crowded or osmolyte-rich environments mimicked by ficoll-70, dextran-10, and sucrose. All cosolutes stabilized compact conformers of CaM and modulated association kinetics by affecting diffusion and rates of conformational change; however, the results showed that differently sized molecules had variable effects to enhance or impede unique steps of the association pathway. On- and off-rates were modulated by all cosolutes in a compensatory fashion, producing little change in steady-state affinity. From this work insights were gained on how high concentrations of inert crowding agents and osmolytes fit into a kinetic framework to describe protein-protein interactions relevant for cellular signaling.

Relative Cosolute Size Influences the Kinetics of Protein-Protein Interactions.

Hyperglycemia is associated with an increased risk of cardiovascular disease, and the consequences of intensive therapy may depend on the mechanism of the anti-diabetic agent(s) used to achieve a tight control. In animal models, stable analogues of glucagon-like peptide-1 (GLP-1) were able to reduce body weight and blood pressure and also had favorable effects on ischemia following coronary reperfusion. In a similar way, dipeptidyl peptidase IV (DPP-IV) showed to have favorable effects in animal models of ischemia/reperfusion. This could be due to the fact that DPP-IV inhibitors were able to prevent the breakdown of GLP-1 and glucose-dependent insulinotropic polypeptide, but they also decreased the degradation of several vasoactive peptides. Preclinical data for GLP-1, its derivatives and inhibitors of the DPP-IV enzyme degradation suggests that these agents may be able to, besides controlling glycaemia, induce cardio-protective and vasodilator effects. Notwithstanding the many favorable cardiovascular effects of GLP-1/incretins reported in different studies, many questions remain unanswered due the limited number of studies in human beings that aim to examine the effects of GLP-1 on cardiovascular endpoints. For this reason, long-term trials searching for positive cardiovascular effects are now in process, such as the CAROLINA and CARMELINA trials, which are supported by small pilot studies performed in humans (and many more animal studies) with incretin-based therapies. On the other hand, selective renal sodium-glucose co-transporter 2 inhibitors were also evaluated in the prevention of cardiovascular outcomes in type 2 diabetes. However, it is quite early to draw conclusions, since data on cardiovascular outcomes and cardiovascular death are limited and long-term studies are still ongoing. In this review, we will analyze the mechanisms underlying the cardiovascular effects of incretins and, at the same time, we will present a critical position about the real value of these compounds in the cardiovascular system and its protection.

Incretins and selective renal sodium-glucose co-transporter 2 inhibitors in hypertension and coronary heart disease.

The aim of this study was to determine the association between preoperative medium-term (60-90 days) glycemic control, as reflected by glycosylated hemoglobin levels (HbA1c), and the incidence of major complications (mediastinitis, perioperative infarction, heart failure, stroke and kidney failure dialysis) and mortality in diabetic patients undergoing elective coronary artery by-pass graft surgery (CABG). This study suggests that aggressive glycemic control three months before surgery, achieving HbA1c=7% improvement results with less postoperative morbidity and mortality.

Medium-term glycemic control in diabetics before coronary bypass surgery.

The N-methyl-d-aspartate (NMDA) receptors are heteromeric non-selective cation channels that require the binding of glycine and glutamate for gating. Based on crystal structures, the mechanism of partial agonism at the glycine-binding site is thought to be mediated by a shift in the conformational equilibrium between an open clamshell and a closed clamshell-like structure of the bilobed ligand-binding domain (LBD). Using single-molecule Förster resonance energy transfer (smFRET) and multiparameter fluorescence detection, which allows us to study the conformational states and dynamics in the submillisecond time scale, we show that there are at least three conformational states explored by the LBD: the low FRET, medium FRET, and high FRET states. The distance of the medium and low FRET states corresponds to what has been observed in crystallography structures. We show that the high FRET state, which would represent a more closed clamshell conformation than that observed in the crystal structure, is most likely the state initiating activation, as evidenced by the fact that the fraction of the protein in this state correlates well with the extent of activation. Furthermore, full agonist bound LBDs show faster dynamic motions between the medium and high FRET states, whereas they show slower dynamics when bound to weaker agonists or to antagonists.

Conformational Selection and Submillisecond Dynamics of the Ligand-binding Domain of the N-Methyl-d-aspartate Receptor.

Ca(2+)-calmodulin-dependent protein kinase II (CaMKII) is highly abundant in neurons, where its concentration reaches that typically found for cytoskeletal proteins. Functional reasons for such a high concentration are not known, but given the multitude of known binding partners for CaMKII, a role as a scaffolding molecule has been proposed. In this report, we provide experimental evidence that demonstrates a novel structural role for CaMKII. We discovered that CaMKII forms filaments that can extend for several micrometers in the presence of certain divalent cations (Zn(2+), Cd(2+), and Cu(2+)) but not with others (Ca(2+), Mg(2+), Co(2+), and Ni(2+)). Once formed, depleting the divalent ion concentration with chelators completely dissociated the filaments, and this process could be repeated by cyclic addition and removal of divalent ions. Using the crystal structure of the CaMKII holoenzyme, we computed an electrostatic potential map of the dodecameric complex to predict divalent ion binding sites. This analysis revealed a potential surface-exposed divalent ion binding site involving amino acids that also participate in calmodulin (CaM) binding and suggested CaM binding might inhibit formation of the filaments. As predicted, Ca(2+)/CaM binding both inhibited divalent ion-induced filament formation and could disassemble preformed filaments. Interestingly, CaMKII within the filaments retains the capacity to autophosphorylate; however, activity toward exogenous substrates is significantly decreased. Activity is restored upon filament disassembly. We compile our results with structural and mechanistic data from the literature to propose a model of Zn(2+)-mediated CaMKII filament formation, in which assembly and activity are further regulated by Ca(2+)/CaM.

Hugo Sanabria

Department of Physics and Astronomy

Clemson University

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

Hugo Sanabria

.css-o250i3{font-size:18px;font-family:Open Sans,sans-serif;line-height:21.6px;}Department of Physics and Astronomy

Clemson University

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

Department of Physics and Astronomy