Monitor Protein Conformational Changes Research Articles

NRhFluors: Quantitative Revealing the Interaction between Protein Homeostasis and Mitochondria Dysfunction via Fluorescence Lifetime Imaging.

Degenerative diseases are closely related to the changes of protein conformation beyond the steady state. The development of feasible tools for quantitative detection of changes in the cellular environment is crucial for investigating the process of protein conformational variations. Here, we have developed a near-infrared AIE probe based on the rhodamine fluorophore, which exhibits dual responses of fluorescence intensity and lifetime to local viscosity changes. Notably, computational analysis reveals that NRhFluors fluorescence activation is due to inhibition of the RACI mechanism in viscous environment. In the chemical regulation of rhodamine fluorophores, we found that variations of electron density distribution can effectively regulate CI states and achieve fluorescence sensitivity of NRhFluors. In addition, combined with the AggTag method, the lifetime of probe A9-Halo exhibits a positive correlation with viscosity changes. This analytical capacity allows us to quantitatively monitor protein conformational changes using fluorescence lifetime imaging (FLIM) and demonstrate that mitochondrial dysfunction leads to reduced protein expression in HEK293 cells. In summary, this work developed a set of near-infrared AIE probes activated by the RACI mechanism, which can quantitatively detect cell viscosity and protein aggregation formation, providing a versatile tool for exploring disease-related biological processes and therapeutic approaches.

Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells.

Acridonylalanine (Acd) is a fluorescent amino acid that is highly photostable, with a high quantum yield and long fluorescence lifetime in water. These properties make it superior to existing genetically encodable fluorescent amino acids for monitoring protein interactions and conformational changes through fluorescence polarization or lifetime experiments, including fluorescence lifetime imaging microscopy (FLIM). Here, we report the genetic incorporation of Acd using engineered pyrrolysine tRNA synthetase (RS) mutants that allow for efficient Acd incorporation in both E. coli and mammalian cells. We compare protein yields and amino acid specificity for these Acd RSs to identify an optimal construct. We also demonstrate the use of Acd in FLIM, where its long lifetime provides strong contrast compared to endogenous fluorophores and engineered fluorescent proteins, which have lifetimes less than 5 ns.

Biophysical and Spectroscopic Methods for Monitoring Protein Misfolding and Amyloid Aggregation.

Proteins exhibit a remarkable structural plasticity and may undergo conformational changes resulting in protein misfolding both in a biological context and upon perturbing physiopathological conditions. Such nonfunctional protein conformers, including misfolded states and aggregates, are often associated to protein folding diseases. Understanding the biology of protein folding diseases thus requires tools that allow the structural characterization of nonnative conformations of proteins and their interconversions. Here we present detailed procedures to monitor protein conformational changes and aggregation based on spectroscopic and biophysical methods that include circular dichroism, ATR-Fourier-transformed infrared spectroscopy, fluorescence spectroscopy and dynamic light scattering. To illustrate the application of these methods we report to our previous studies on misfolding, aggregation and amyloid fibril formation by superoxide dismutase 1 (SOD1), a protein whose toxic deposition is implicated in the neurodegenerative disease amyotrophic lateral sclerosis (ALS).

Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies.

We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded "heavy" and "light" GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the "heavy" and "light" peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules.

Likely due to conformational rearrangements, small molecule inhibitors may stabilize the active conformation of protein kinases and paradoxically promote tumorigenesis. We combined limited proteolysis with stable isotope labeling MS to monitor protein conformational changes upon binding of small molecules. Applying this method to the human serine/threonine kinase B-Raf, frequently mutated in cancer, we found that binding of ATP or its nonhydrolyzable analogue AMP-PNP, but not ADP, stabilized the structure of both B-Raf(WT) and B-Raf(V600E). The ATP-competitive type I B-Raf inhibitor vemurafenib and the type II inhibitor sorafenib stabilized the kinase domain (KD) but had distinct effects on the Ras-binding domain. Stabilization of the B-Raf(WT) KD was confirmed by hydrogen/deuterium exchange MS and molecular dynamics simulations. Our results are further supported by cellular assays in which we assessed cell viability and phosphorylation profiles in cells expressing B-Raf(WT) or B-Raf(V600E) in response to vemurafenib or sorafenib. Our data indicate that an overall stabilization of the B-Raf structure by specific inhibitors activates MAPK signaling and increases cell survival, helping to explain clinical treatment failure. We also applied our method to monitor conformational changes upon nucleotide binding of the pseudokinase KSR1, which holds high potential for inhibition in human diseases.

Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck

Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.

Pyrene: A Probe to Study Protein Conformation and Conformational Changes

The review focuses on the unique spectral features of pyrene that can be utilized to investigate protein structure and conformation. Pyrene is a fluorescent probe that can be attached covalently to protein side chains, such as sulfhydryl groups. The spectral features of pyrene are exquisitely sensitive to the microenvironment of the probe: it exhibits an ensemble of monomer fluorescence emission peaks that report on the polarity of the probe microenvironment, and an additional band at longer wavelengths, the appearance of which reflects the presence of another pyrene molecule in spatial proximity (~10 Å). Its high extinction coefficient allows us to study labeled proteins in solution at physiologically relevant concentrations. The environmentally- and spatially-sensitive features of pyrene allow monitoring protein conformation, conformational changes, protein folding and unfolding, protein-protein, protein-lipid and protein-membrane interactions.

Structural characteristics of the hydrophobic patch of azurin and its interaction with p53: a site-directed spin labeling study

Site-directed spin labeling (SDSL) is a powerful tool for monitoring protein structure, dynamics and conformational changes. In this study, the domain-specific properties of azurin and its interaction with p53 were studied using this technique. Mutations of six residues, that are located in the hydrophobic patch of azurin, were prepared and spin labeled. Spectra of the six azurin mutants in solution showed that spin labeled residues 45 and 63 are in a very restricted environment, residues 59 and 65 are in a spacious environment and have free movement, and residues 49 and 51 are located in a relatively closed pocket. Polarity experiments confirmed these results. The changes observed in the spectra of spin labeled azurin upon interaction with p53 indicate that the hydrophobic patch is involved in this interaction. Our results provide valuable insight into the topographic structure of the hydrophobic domain of azurin, as well as direct evidence of its interaction with p53 in solution via the hydrophobic patch. Cytotoxicity studies of azurin mutants showed that residues along the hydrophobic patch are important for its cytotoxicity.

Interaction of gold nanoparticles with protein: A spectroscopic study to monitor protein conformational changes

Gold nanoparticles (GNPs) conjugated with biomolecules are promising building blocks for assembly into nanostructured functional materials for developing biomarker platforms because of their size dependent optical and electrical properties. Biocompatible GNPs were synthesized using glutamic acid as a reducing agent and the interaction between bovine serum albumin (BSA) and GNPs was investigated using fluorescence and circular dichroism (CD) spectroscopies. The binding constant (Kb) of protein (BSA) to GNPs was determined by measuring the quenching of the fluorescence intensity of tryptophan residues of the protein molecules after conjugation. The conformational change in BSA at its native form after conjugation with GNPs confirmed that protein undergoes a more flexible conformational state on the boundary surface of GNPs after bioconjugation. The CD studies further showed a decrease in the α-helical content after conjugation. The results confirmed that the change in conformation was larger at higher concentrations of GNPs.

Microtiter plate monoclonal antibody epitope analysis of Ca 2+- and Mg 2+-induced conformational changes in troponin C

Spectroscopic methods such as circular dichroism and Förster resonance energy transfer are current approaches for monitoring protein conformational changes. Those analyses require special equipment and expertise. The need for fluorescence labeling of the protein may interfere with the native structure. We have developed a microtiter plate-based monoclonal antibody (mAb) epitope analysis to detect protein conformational changes in a high throughput manner. This method is based on the concept that the affinity of the antigen-binding site of an antibody for the specific antigenic epitope will change when the 3-D structure of the epitope changes. The effectiveness of this approach was demonstrated in the present study on troponin C (TnC), an allosteric protein in the Ca 2+ regulatory system of striated muscle. Using TnC purified by a highly effective rapid procedure and mAbs developed against epitopes in the N- and C-domains of TnC enzyme-linked immunosorbant assay (ELISA) clearly detected Ca 2+-induced conformational changes in both the N-terminal regulatory domain and the C-terminal structural domain of TnC. On the other hand, Mg 2+-binding to the C-domain of TnC resulted in a long-range effect on the N-domain conformation, indicating a functional significance of Ca 2+–Mg 2+ exchange at the C-domain metal ion-binding sites. In addition to further understanding of the structure–function relationship of TnC, the data demonstrate that the mAb epitope analysis provides a simple high throughput method for monitoring 3-D structural changes in native proteins under physiological condition and has broad applications in protein structure–function relationship studies.

Site-Specific Incorporation of a 19F-Amino Acid into Proteins as an NMR Probe for Characterizing Protein Structure and Reactivity

19F NMR is a powerful tool for monitoring protein conformational changes and interactions; however, the inability to site-specifically introduce fluorine labels into proteins of biological interest severely limits its applicability. Using methods for genetically directing incorporation of unnatural amino acids, we have inserted trifluoromethyl-l-phenylalanine (tfm-Phe) into proteins in vivo at TAG nonsense codons with high translational efficiency and fidelity. The binding of substrates, inhibitors, and cofactors, as well as reactions in enzymes, were studied by selective introduction of tfm-Phe and subsequent monitoring of the 19F NMR chemical shifts. Subtle protein conformational changes were detected near the active site and at long distances (25 Angstrom). 19F signal sensitivity and resolution was also sufficient to differentiate protein environments in vivo. Since there has been interest in using 19F-labeled proteins in solid-state membrane protein studies, folding studies, and in vivo studies, this general method for genetically incorporating a 19F-label into proteins of any size in Escherichia coli should have broad application beyond that of monitoring protein conformational changes.

Electrochemical quartz crystal nanobalance to detect solvent displacement by pH-induced conformational changes of proteins at Pt.

The electrochemical quartz crystal nanobalance (EQCN) techniques of simultaneous measurements of frequency and cyclic voltammetry (CV) were used to investigate protein adsorption behavior resulting from pH-induced conformational changes at the Pt electrode at 298 K. The adsorption behavior of holo- and apo-alpha-lactalbumin was studied in electrolyte solutions of pH < 2, 7.4, and 11. The EQCN frequency measurements did not directly monitor the mass of the adsorbed protein at anodic potentials, but instead, at a potential characteristic of the double layer for platinum, gave a measure of the extent of solvent displacement by the adsorbed protein (i.e., a "footprint"), which correlated well with known pH-induced conformational changes of the protein. Simultaneous CV charge transfer measurements provided information on the number of layers of protein adsorbed to the surface. This ability of the EQCN to detect solvent displacement by protein adsorption is potentially useful for biosensors to detect and to monitor protein conformational changes in the bulk and during the adsorption process. The Langmuir adsorption isotherm provided the Gibbs energy of adsorption, DeltaG(ADS), and showed excellent agreement between the CV and EQCN frequency measurements.

Limited proteolysis combined with isotope labeling and quantitative LC-MALDI MS for monitoring protein conformational changes: a study on calcium-binding sites of cardiac Troponin C

Studies of protein–protein and protein–ligand interactions are important for understanding biological functions of proteins. A new technique based on the partial proteolysis of proteins combined with quantitative mass spectrometry is developed as a means of tracking structural changes after the formation of a protein–ligand complex. In this technique, a protein of interest with and without the binding of a ligand is digested with an enzyme to generate a set of peptides, followed by separation of the peptides by liquid chromatography. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) is used to identify chromatographically separated peptides, and locate their sequence alignments in the parent protein. Using an isotopically labeled protein as a sample against an unlabeled protein standard, quantitative information can be gathered. This overcomes the inherent lack of quantitative capability of MALDI MS. The utility of the technique to investigate protein–ligand interactions is demonstrated in a model system involving calcium binding to cardiac Troponin C (cTnC). Using this technique, the general location of the three calcium-binding sites of cTnC can be determined by using several different enzymes to generate overlapping peptide maps of cTnC.

Adsorption of a Formulated Protein on a Drug Delivery Device Surface

The interactions between therapeutic proteins and delivery device surfaces may have a significant impact on the efficacy of a recombinant protein-based biological therapy program. Protein–surface interactions may induce conformational changes and aggregation, resulting in the inactivation of the protein therapeutic and even malfunction of the delivery device itself. Protein adsorption phenomena may compromise the intended therapeutic benefit, drive up dosage levels, and increase treatment costs. We studied the interactions of formulated recombinant interleukin-2 (IL-2) with silicone rubber tubing, a commonly used catheter material, in a recirculating system at 37°C over a 24-h period. Bulk solution protein concentration and bioactivity assays were performed at intervals in order to quantify the impact of time of exposure of the protein to the tubing. Attenuated total reflectance Fourier transform infrared spectroscopy was used to monitor protein conformational changes upon adsorption as well as to quantify protein deposition rates. Adsorption onto the tubing walls resulted in a 7 to 20% reduction in the concentration of IL-2 after 24 h of exposure relative to the initial concentration. At the same time, the residual IL-2 bioactivity levels decreased by 97 to 99.5% of initial activity levels. These activity losses, which far exceed the adsorptive losses, are a direct consequence of the protein–surface interactions. A simple mathematical model was constructed in order to project the impact of IL-2–surface interactions on treatment bioefficacy.

6] Monitoring protein conformational changes during membrane fusion

This chapter discusses on the various procedures for detection of protein conformational change and exposure of hydrophobic regions during membrane fusion. These procedures can be roughly classified into biophysical, biochemical, and immunological methods. Procedures for the detection of the penetration of hydrophobic segments of proteins into bilayer membranes occurring through conformational changes are also outlined. Protein conformational changes and membrane insertion are usually detected under conditions that trigger membrane fusion. Protein conformational changes are reflected most directly by circular dichroism (CD) spectra: CD spectra in the far- and near-ultraviolet regions are sensitive to changes in peptide backbone structure and the conformation around aromatic groups. Ultraviolet spectra in the near-ultraviolet regions are also sensitive to conformational changes around aromatic amino acid residues: red and blue spectral shifts are observed on perturbation of tyrosine and/or tryptophan residues by a solvent, and on their exposure to a more polar environment.

Monitoring protein conformational changes by quenching of intrinsic fluorescence

The quenching of intrinsic flourecence of human serum albumin and pigeon liver malic enzyme by acrylamide was studied after the proteins were denaturated to different stages. The progress of protein denaturation induced by guanidine was accompanied by increasing of effective dynamic quenching constant which provides a convenient parameter for monitoring protein conformational change.

A new differential spectrofluoromotor

A differential fluorometer has been designed and built using the principle of two synchronously rotating mirrors. This is an advanced model of a previously published instrument [Bablouzian, B., Grourke, M., and Fasman, G. D. (1970) J. Biol. Chem. 245, 2081–2085] The instrument measures the fluorescence difference spectrum of two samples which share a common light source, monochromators, and photomultiplier. The excitation beam is chopped by a rotating mirror, and the fluorescence signals are recombined by a second mirror rotating synchronously with the chopping mirror. These signals are synchronously detected by a pair of lock-in voltmeters. Provision is made to measure the ratio of the fluorescence signals as well as their difference simultancously. Difference fluorescence spectroscopy provides an exceptionally sensitive probe to monitor protein conformational changes. These changes can involve either the intrinsic aromatic amino acids or added extrinsic fluorescent probes. Used concurrently with solvent perturbation, or quenching moeities, it can be used to probe the topology of the surface to evaluate the accessibility of aromatics residues. It should have wide utility in systems such as: enzyme-substrate interactions, receptor-receptor site interactions, etc. The extreme sensitivity of the method (e.g., measurement of δ F ± 0.001 at ∼ 10 −9 m added hormone to a cell surface) allows studies to be conducted at concentrations which simulate in vivo conditions.

Exposure of tryptophanyl residues in proteins. Quantitative determination by fluorescence quenching studies.

Acrylamide is an efficient quencher of tryptophanyl fluorescence which we report to be very discriminating in sensing the degree of exposure of this residue in proteins. The quenching reaction involves physical contact between the quencher and an excited indole ring, and can be kinetically described in terms of a collisional and a static component. The rate constant for the collisional component is a kinetic measure of the exposure of a residue in a protein, and values ranging from 4 X 10(9) M-1 S-1 for the fully exposed tryptophan in the polypeptide, adrenocorticotropin, to less than 5 X 10(8) M-1 S-1 for the buried residue in azurin have been found. Static quenching is readily detected in proteins that are denatured, or contain only a single fluorophor. Quenching patterns for most multi-tryptophan containing proteins are difficult to analyze precisely, but qualitative information can, nevertheless, be extracted. Applications of this probing technique for monitoring protein conformational changes, such as the acid-induced expansion of human serum albumin, and inhibitor binding to enzymes, are presented. The value of this method lies in its ability to sense not only the steady-state exposure of a residue in a protein, but also its dynamic exposure.