FRET Dyes Significantly Affect SAXS Intensities of Proteins

Structural analyses in biophysics aim at revealing a relationship between a molecule's dynamic structure and its physiological function. Förster resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) are complementary experimental approaches to this. Their concomitant application in combined studies has recently opened a lively debate on how to interpret FRET measurements in the light of SAXS data with the popular example of the radius of gyration, commonly derived from both FRET and SAXS. There still is a lack of understanding in how to mutually relate and interpret quantities equally obtained from FRET or SAXS, and to what extent FRET dyes affect SAXS intensities in combined applications. In the present work, we examine the interplay of FRET and SAXS from a computational simulation perspective. Molecular simulations are a valuable complement to experimental approaches and supply instructive information on dynamics. As FRET depends not only on the mutual separation but also on the relative orientations, the dynamics, and therefore also the shapes of the dyes, we utilize a novel method for simulating FRET-dye-labeled proteins to investigate these aspects in atomic detail. We perform structure-based simulations of four different proteins with and without dyes in both folded and unfolded conformations. In-silico derived radii of gyration are different with and without dyes and depend on the chosen dye pair. The dyes apparently influence the dynamics of unfolded systems. We find that FRET dyes attached to a protein have a significant impact on theoretical SAXS intensities calculated from simulated structures, especially for small proteins. Radii of gyration from FRET and SAXS deviate systematically, which points to further underlying mechanisms beyond prevalent explanation approaches.     

Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach

The varied yet family‐specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH‐family‐specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low‐nanomolar inhibitor that is selective for GH family 47 inverting α‐mannosidases. Here we show, through quantum‐mechanical approaches, that kifunensine is restrained to a “ring‐flipped” ¹C₄ conformation with another accessible, but higher‐energy, region around the ^1,4B conformation. The conformations of kifunensine in complex with a range of GH47 enzymes—including an atomic‐level resolution (1 Å) structure of kifunensine with Caulobacter sp. CkGH47 reported herein and with GH family 38 and 92 α‐mannosidases—were mapped onto the kifunensine free‐energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymes but cannot mimic any conformational states relevant to the reaction coordinate of mannosidases from other families.     

Conformational Landscape of Cytochrome P450 Reductase Interactions

Oxidative reactions catalyzed by Cytochrome P450 enzymes (CYPs), which constitute the most relevant group of drug-metabolizing enzymes, are enabled by their redox partner Cytochrome P450 reductase (CPR). Both proteins are anchored to the membrane of the endoplasmic reticulum and the CPR undergoes a conformational change in order to interact with the respective CYP and transfer electrons. Here, we conducted over 22 microseconds of molecular dynamics (MD) simulations in combination with protein–protein docking to investigate the conformational changes necessary for the formation of the CPR–CYP complex. While some structural features of the CPR and the CPR–CYP2D6 complex that we highlighted confirmed previous observations, our simulations revealed additional mechanisms for the conformational transition of the CPR. Unbiased simulations exposed a movement of the whole protein relative to the membrane, potentially to facilitate interactions with its diverse set of redox partners. Further, we present a structural mechanism for the susceptibility of the CPR to different redox states based on the flip of a glycine residue disrupting the local interaction network that maintains inter-domain proximity. Simulations of the CPR–CYP2D6 complex pointed toward an additional interaction surface of the FAD domain and the proximal side of CYP2D6. Altogether, this study provides novel structural insight into the mechanism of CPR–CYP interactions and underlying conformational changes, improving our understanding of this complex machinery relevant for drug metabolism.     

F?rster Resonance Energy Transfer (FRET) as a Tool for Dissecting the Molecular Mechanisms for Maturation of the Shigella Type III Secretion Needle Tip Complex

Förster resonance energy transfer (FRET) provides a powerful tool for monitoring intermolecular interactions and a sensitive technique for studying Å-level protein conformational changes. One system that has particularly benefited from the sensitivity and diversity of FRET measurements is the maturation of the Shigella type III secretion apparatus (T3SA) needle tip complex. The Shigella T3SA delivers effector proteins into intestinal cells to promote bacterial invasion and spread. The T3SA is comprised of a basal body that spans the bacterial envelope and a needle with an exposed tip complex that matures in response to environmental stimuli. FRET measurements demonstrated bile salt binding by the nascent needle tip protein IpaD and also mapped resulting structural changes which led to the recruitment of the translocator IpaB. At the needle tip IpaB acts as a sensor for host cell contact but prior to secretion, it is stored as a heterodimeric complex with the chaperone IpgC. FRET analyses showed that chaperone binding to IpaB’s N-terminal domain causes a conformational change in the latter. These FRET analyses, with other biophysical methods, have been central to understanding T3SA maturation and will be highlighted, focusing on the details of the FRET measurements and the relevance to this particular system.     

Rise-Time of FRET-Acceptor Fluorescence Tracks Protein Folding

Uniform labeling of proteins with fluorescent donor and acceptor dyes with an equimolar ratio is paramount for accurate determination of Förster resonance energy transfer (FRET) efficiencies. In practice, however, the labeled protein population contains donor-labeled molecules that have no corresponding acceptor. These FRET-inactive donors contaminate the donor fluorescence signal, which leads to underestimation of FRET efficiencies in conventional fluorescence intensity and lifetime-based FRET experiments. Such contamination is avoided if FRET efficiencies are extracted from the rise time of acceptor fluorescence upon donor excitation. The reciprocal value of the rise time of acceptor fluorescence is equal to the decay rate of the FRET-active donor fluorescence. Here, we have determined rise times of sensitized acceptor fluorescence to study the folding of double-labeled apoflavodoxin molecules and show that this approach tracks the characteristics of apoflavodoxinʼs complex folding pathway.     

Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between ⁴C₁ and ¹C₄ chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.     

Studies of wool keratin by EPR spectroscopy

Electron paramagnetic resonance (EPR) tests were conducted on four kinds of interrelated samples—natural undyed wool fibers (SW3, SW5), fibers dyed with model direct dyes (1W, 5W), fibers treated destructively with formic acid for descaling and dyed with the same dyes (K1W, K5W), and the dyes themselves (1%). For all samples, a radical signal of g = 2.007 was detected. The presence of Mn²⁺ and Fe³⁺ ions in the wool fiber structure was postulated. Modifications of disulfide regions of fiber matrix were also analyzed. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 1459–1465, 2006     

Practical Significance,Theory and Determination of Compatibility of Dyes on Synthetic-polymer Fibres

The compatibility of dyes is particularly important in regard to the time, reproducibility and levelness of dyeing. For basic dyes on acrylic fibres and anionic dyes on nylon, a characteristic of the dye—the compatibility value K— is valuable in determining whether it can be used in the same bath as others. Dyes having the same K-value are compatible under most dyeing conditions. For disperse dyes, K-values do not exist. In selecting such dyes for use together, other properties of the dyes and the concentrations to be used in the particular combination must be considered.     

Monitoring Biosensor Activity in Living Cells with Fluorescence Lifetime Imaging Microscopy

Live-cell microscopy is now routinely used to monitor the activities of the genetically encoded biosensor proteins that are designed to directly measure specific cell signaling events inside cells, tissues, or organisms. Most fluorescent biosensor proteins rely on Förster resonance energy transfer (FRET) to report conformational changes in the protein that occur in response to signaling events, and this is commonly measured with intensity-based ratiometric imaging methods. An alternative method for monitoring the activities of the FRET-based biosensor proteins is fluorescence lifetime imaging microscopy (FLIM). FLIM measurements are made in the time domain, and are not affected by factors that commonly limit intensity measurements. In this review, we describe the use of the digital frequency domain (FD) FLIM method for the analysis of FRET signals. We illustrate the methods necessary for the calibration of the FD FLIM system, and demonstrate the analysis of data obtained from cells expressing “FRET standard” fusion proteins. We then use the FLIM-FRET approach to monitor the changes in activities of two different biosensor proteins in specific regions of single living cells. Importantly, the factors required for the accurate determination and reproducibility of lifetime measurements are described in detail.     

Green-Emitting Rhodamine Dyes for Vital Labeling of Cell Organelles Using STED Super-Resolution Microscopy

Fluorescence microscopy reveals the localization, spatial distribution, and temporal dynamics of the specifically labeled organelles in living cells. Labeling with exogenous conjugates prepared from fluorescent dyes and small molecules (ligands) is an attractive alternative to the use of fluorescent proteins, but proved to be challenging due to insufficient cell-permeability of the probes, unspecific staining, or low dye brightness. We evaluated four green-emitting rhodamine dyes and their conjugates intended for the specific labeling of lysosomes, mitochondria, tubulin, and actin in living cells. The imaging performance of the probes in living human fibroblasts has been studied by using confocal and stimulated emission depletion (STED) super-resolution microscopy with a commercial 595 nm STED laser. Two bright and photostable dyes (LIVE 510 and LIVE 515) provide specific and versatile staining.     

Multilevel Changes in Protein Dynamics upon Complex Formation of the Calcium‐Loaded S100A4 with a Nonmuscle Myosin IIA Tail Fragment

Dysregulation of Ca²⁺‐binding S100 proteins plays important role in various diseases. The asymmetric complex of Ca²⁺‐bound S100A4 with nonmuscle myosin IIA has high stability and highly increased Ca²⁺ affinity. Here we investigated the possible causes of this allosteric effect by NMR spectroscopy. Chemical shift‐based secondary‐structure analysis did not show substantial changes for the complex. Backbone dynamics revealed slow‐timescale local motions in the H1 helices of homodimeric S100A4; these were less pronounced in the complex form and might be accompanied by an increase in dimer stability. Different mobilities in the Ca²⁺‐coordinating EF‐hand sites indicate that they communicate by an allosteric mechanism operating through changes in protein dynamics; this must be responsible for the elevated Ca²⁺ affinity. These multilevel changes in protein dynamics as conformational adaptation allow S100A4 fine‐tuning of its protein–protein interactions inside the cell during Ca²⁺ signaling.     

One‐pot preparation of multicolor polymeric nanoparticles with high brightness by single wavelength excitation

Fluorescent nanoparticles with multiplex distinct emission signatures and high brightness by a single wavelength excitation are substantially needed in multiplex bioassays and imaging. In this study, we synthesized fluorescent polymeric nanoparticles incorporated with three polymerizable organic dyes via a one‐pot miniemulsion. By altering the doping ratio of three tandem dyes, the nanoparticles display abundant multiple fluorescence such as blue, cyan, green, orange, pink, red etc., together with distinguishable emission signatures under a single wavelength excitation, which were arising from the effective fluorescence resonance energy transfer (FRET) between the three energy‐matched dyes. Meanwhile, a large Stokes shift (up to 250 nm) can be generated by taking place multiple FRET cascade mechanism between donor and acceptor fluorophores in nanoparticles, which also suggests broad applications in biological labeling and imaging. Moreover, these nanoparticles are uniform in size, highly bright, excellently photostable, and shown prominent longterm stability. Overall, the novel multicolor fluorescent polymeric nanoparticles augur well for their potential applications in multiplexed bioanalysis and emitting displays. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 41492.     

Site‐Specific Labelling of Native Mammalian Proteins for Single‐Molecule FRET Measurements

Human cells are complex entities in which molecular recognition and selection are critical for cellular processes often driven by structural changes and dynamic interactions. Biomolecules appear in different chemical states, and modifications, such as phosphorylation, affect their function. Hence, using proteins in their chemically native state in biochemical and biophysical assays is essential. Single‐molecule FRET measurements allow exploration of the structure, function and dynamics of biomolecules but cannot be fully exploited for the human proteome, as a method for the site‐specific coupling of organic dyes into native, non‐recombinant mammalian proteins is lacking. We address this issue showing the site‐specific engineering of fluorescent dyes into human proteins on the basis of bioorthogonal reactions. We show the applicability of the method to study functional and post‐translationally modified proteins on the single‐molecule level, among them the hitherto inaccessible human Argonaute 2.     

Intrinsic Tryptophan Fluorescence in the Detection and Analysis of Proteins: A Focus on F?rster Resonance Energy Transfer Techniques

Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λ_EX ∼ 280 nm, λ_EM ∼ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the protein’s) local environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.     

Simple Estimation of F?rster Resonance Energy Transfer (FRET) Orientation Factor Distribution in Membranes

Because of its acute sensitivity to distance in the nanometer scale, Förster resonance energy transfer (FRET) has found a large variety of applications in many fields of chemistry, physics, and biology. One important issue regarding the correct usage of FRET is its dependence on the donor-acceptor relative orientation, expressed as the orientation factor κ². Different donor/acceptor conformations can lead to κ² values in the 0 ≤ κ² ≤ 4 range. Because the characteristic distance for FRET, R₀, is proportional to (κ²)^1/6, uncertainties in the orientation factor are reflected in the quality of information that can be retrieved from a FRET experiment. In most cases, the average value of κ² corresponding to the dynamic isotropic limit (<κ²> = 2/3) is used for computation of R₀ and hence donor-acceptor distances and acceptor concentrations. However, this can lead to significant error in unfavorable cases. This issue is more critical in membrane systems, because of their intrinsically anisotropic nature and their reduced fluidity in comparison to most common solvents. Here, a simple numerical simulation method for estimation of the probability density function of κ² for membrane-embedded donor and acceptor fluorophores in the dynamic regime is presented. In the simplest form, the proposed procedure uses as input the most probable orientations of the donor and acceptor transition dipoles, obtained by experimental (including linear dichroism) or theoretical (such as molecular dynamics simulation) techniques. Optionally, information about the widths of the donor and/or acceptor angular distributions may be incorporated. The methodology is illustrated for special limiting cases and common membrane FRET pairs.     

Insights from NMR Spectroscopy into the Conformational Properties of Man‐9 and Its Recognition by Two HIV Binding Proteins

Man₉GlcNAc₂ (Man‐9) present at the surface of HIV makes up the binding sites of several HIV‐neutralizing agents and the mammalian lectin DC‐SIGN, which is involved in cellular immunity and trans‐infections. We describe the conformational properties of Man‐9 in its free state and when bound by the HIV entry‐inhibitor protein microvirin (MVN), and define the minimum epitopes of both MVN and DC‐SIGN by using NMR spectroscopy. To facilitate the implementation of 3D ¹³C‐edited spectra to deconvolute spectral overlap and to determine the solution structure of Man‐9, we developed a robust expression system for the production of ¹³C,¹⁵N‐labeled glycans in mammalian cells. The studies reveal that Man‐9 interacts with HIV‐binding proteins through distinct epitopes and adopts diverse conformations in the bound state. In combination with molecular dynamics simulations we observed receptor‐bound conformations to be sampled by Man‐9 in the free state, thus suggesting a conformational selection mechanism for diverse recognition.     

Model of a polymer chain twisted inside a statistical segment. Poly(3‐hexylthiophene) in chloroform solutions

A set of hydrodynamic methods in extremely dilute solutions (determination of intrinsic viscosity [η ], translational diffusion D and flotation in a centrifugal field s ) was used in the studies of conformational properties, dimensions and equilibrium rigidity of individual molecules of a series of samples of poly(3‐hexylthiophene). Absolute molecular masses M _sD were determined. The Mark–Kuhn–Houwink equations for the range of M _sD from 2240 to 15 300 g mol^?1 are given. For the first time, an analysis of conformational properties and equilibrium flexibility of poly(3‐hexylthiophene) molecules was carried out using the model of a statistical segment containing a twisted polymer chain. © 2017 Society of Chemical Industry     

Ionic-liquid-assisted mixed alkali system for reactive dye fixation in a batch process – optimisation through response surface methodology

An ionic liquid, choline hydroxide, was synthesised and used in a mixed alkali system for fixation of homobifunctional reactive dyes. Its molecular structure was confirmed using FTIR, ¹H NMR, and ¹³C NMR spectroscopy. Response surface methodology was employed to optimise the dyeing conditions for reactive dyes using a sodium carbonate–choline hydroxide mixed alkali system. A Box–Behnken design with three variables, namely sodium carbonate concentration, choline hydroxide concentration, and fixation time, was used to design the experimental runs. Analysis of variance was used to estimate the statistical parameters and to evaluate the quality of the statistical model fit. The quality and model terms were evaluated using Fisher's F-test, the coefficient of determination, and probability values. The interactive effect of operating variables on the response (K/S) was studied using three-dimensional response surface plots. The results obtained from the solutions of highest desirability were found to be comparable with conventionally used alkali systems, namely sodium carbonate alone and sodium carbonate–sodium hydroxide mixed alkali. The ionic liquid choline hydroxide could be effectively used along with sodium carbonate for fixation of reactive dyes, with the advantage of reductions in pollution load, total dissolved solids, and chemical oxygen demand.