Lifetimes of intermediates in the beta -sheet to alpha -helix transition of beta -lactoglobulin by using a diffusional IR mixer

Adaptive enzyme-responsive self-assembling multivalent apelin ligands for targeted myocardial infarction therapy

Microvascular dysfunction following myocardial infarction exacerbates coronary flow obstruction and impairs the preservation of ventricular function. The apelinergic system, known for its pleiotropic effects on improving vascular function and repairing ischemic myocardium, has emerged as a promising therapeutic target for myocardial infarction. Despite its potential, the natural apelin peptide has an extremely short circulating half-life. Current apelin analogs have limited receptor binding efficacy and poor targeting, which restricts their clinical applications. In this study, we utilized an enzyme-responsive peptide self-assembly technique to develop an enzyme-responsive small molecule peptide that adapts to the expression levels of matrix metalloproteinases in myocardial infarction lesions. This peptide is engineered to respond to the high concentration of matrix metalloproteinases in the lesion area, allowing for precise and abundant presentation of the apelin motif. The changes in hydrophobicity allow the apelin motif to self-assemble into a supramolecular multivalent peptide ligand-SAMP. This self-assembly behavior not only prolongs the residence time of apelin in the myocardial infarction lesion but also enhances the receptor-ligand interaction through increased receptor binding affinity due to multivalency. Studies have demonstrated that SAMP significantly promotes angiogenesis after ischemia, reduces cardiomyocyte apoptosis, and improves cardiac function. This novel therapeutic strategy offers a new approach to restoring coronary microvascular function and improving damaged myocardium after myocardial infarction.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

Infrared compatible rapid mixer to probe millisecond chemical kinetics

Fast microfluidic mixers are a valuable tool for studying solution-phase chemical reaction kinetics and molecular processes with spectroscopy. However, microfluidic mixers that are compatible with infrared vibrational spectroscopy have seen only limited development due to the poor infrared transparency of the current microfabrication material. We describe the design, fabrication, and characterization of CaF₂-based continuous flow turbulent mixers, which are capable of measuring kinetics in the millisecond time window with infrared spectroscopy, when integrated into an infrared microscope. Kinetics measurements demonstrate the ability to resolve relaxation processes with 1 millisecond time resolution, and straightforward improvements are described that should result in sub-100 µs time-resolution.

Shear-free mixing to achieve accurate temporospatial nanoscale kinetics through scanning-SAXS: ion-induced phase transition of dispersed cellulose nanocrystals

Time-resolved in situ characterization of well-defined mixing processes using small-angle X-ray scattering (SAXS) is usually challenging, especially if the process involves changes of material viscoelasticity. In specific, it can be difficult to create a continuous mixing experiment without shearing the material of interest; a desirable situation since shear flow both affects nanoscale structures and flow stability as well as resulting in unreliable time-resolved data. Here, we demonstrate a flow-focusing mixing device for in situ nanostructural characterization using scanning-SAXS. Given the interfacial tension and viscosity ratio between core and sheath fluids, the core material confined by sheath flows is completely detached from the walls and forms a zero-shear plug flow at the channel center, allowing for a trivial conversion of spatial coordinates to mixing times. With this technique, the time-resolved gel formation of dispersed cellulose nanocrystals (CNCs) was studied by mixing with a sodium chloride solution. It is observed how locally ordered regions, so called tactoids, are disrupted when the added monovalent ions affect the electrostatic interactions, which in turn leads to a loss of CNC alignment through enhanced rotary diffusion. The demonstrated flow-focusing scanning-SAXS technique can be used to unveil important kinetics during structural formation of nanocellulosic materials. However, the same technique is also applicable in many soft matter systems to provide new insights into the nanoscale dynamics during mixing.

Metasurface with metallic nanoantennas and graphene nanoslits for sensing of protein monolayers and sub-monolayers

Biomolecule sensing plays an important role in both fundamental biological studies and medical diagnostic applications. Infrared (IR) spectroscopy presents opportunities for sensing biomolecules as it allows their fingerprints to be determined by directly measuring their absorption spectra. However, the detection of biomolecules at low concentrations is difficult with conventional IR spectroscopy due to signal-to-noise considerations. This has led to recent interest on the use of nanostructured surfaces to boost the signals from biomolecules in a method termed surface enhanced infrared spectroscopy. So far, efforts have largely involved the use of metallic nanoantennas (which produce large field enhancement) or graphene nanostructures (which produce strong field confinement and provide electrical tunability). Here, we propose a nanostructured surface that combines the large field enhancement of metallic nanoantennas with the strong field confinement and electrical tunability of graphene plasmons. Our device consists of an array of plasmonic nanoantennas and graphene nanoslits on a resonant substrate. We perform systematic electromagnetic simulations to quantify the sensing performance of the proposed device and show that it outperforms designs in which only plasmons from metallic nanoantennas or plasmons from graphene are utilized. These investigations consider the model system of a representative protein-goat anti-mouse immunoglobulin G (IgG) - in monolayer or sub-monolayer form. Our findings provide guidance for future biosensors for the sensitive quantification and identification of biomolecules.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Polymeric microfluidic continuous flow mixer combined with hyperspectral FT-IR imaging for studying rapid biomolecular events

Early reaction intermediates in protein folding, such as those resulting in β-amyloid formation due to transient misfolding, emerge within a few hundred microseconds. Here, we report a method to obtain sub-millisecond temporal resolution and molecular structural information of protein (mis-)folding events by using a microfluidic continuous-flow mixer (MCFM) in combination with Fourier transform infrared (FT-IR) imaging. The MCFMs are made out of cyclic olefin copolymer (COC) films, because this approach allows for rapid prototyping of different mixer designs. Furthermore, COC offers high IR transparency between 1500 and 2500 cm^-1, thus maximizing the signal to noise ratio of the IR data obtained from a sample of interest. By combining narrow and wide channel widths in MCFM design, the platform provides fast mixing (460 μs) to induce protein (mis-)folding, and it maximizes the residence time in the observing area, so a wide range of reaction timescales can be captured in a single image. We validated the platform for its ability to induce and observe sub-millisecond processes by studying two systems: (i) the mixing of H₂O and D₂O and (ii) the mixing induced deprotonation of carboxylic acid. First, we observed excellent agreement between simulated and experimental data of the on-chip mixing of H₂O and D₂O, which verifies the distance-reaction time relationships based on simulation. Second, deprotonation of carboxylic acid by on-chip mixing with sodium hydroxide solution validates the ability of the platform to induce rapid pH jump that is needed for some biomolecular reactions. Finally, we studied the methanol-induced partial-unfolding of ubiquitin to show that our platform can be used to study biomolecular events 'on-pathway' using FT-IR imaging. We successfully extracted kinetic and structural details of the conformational changes along the channel. Our results are in agreement with prior studies that required more elaborate stopped flow approaches to acquire data for different time points. In summary, the reported method uses an easy-to-fabricate microfluidic mixer platform integrated with hyperspectral FT-IR imaging for rapid acquisition of structural details and kinetic parameters of biomolecular reactions. This approach does not need stopped flow or molecular imaging probes, as required respectively for alternative FT-IR spectroscopy and fluorescence approaches.

Emerin induces nuclear breakage in Xenopus extract and early embryos

Emerin is an inner nuclear membrane protein often mutated in Emery–Dreifuss muscular dystrophy. Because emerin has diverse roles in nuclear mechanics, cytoskeletal organization, and gene expression, it has been difficult to elucidate its contribution to nuclear structure and disease pathology. In this study, we investigated emerin’s impact on nuclei assembled in Xenopus laevis egg extract, a simplified biochemical system that lacks potentially confounding cellular factors and activities. Notably, these extracts are transcriptionally inert and lack endogenous emerin and filamentous actin. Strikingly, emerin caused rupture of egg extract nuclei, dependent on the application of shear force. In egg extract, emerin localized to nonnuclear cytoplasmic membranes, and nuclear rupture was rescued by targeting emerin to the nucleus, disrupting its membrane association, or assembling nuclei with lamin A. Furthermore, emerin induced breakage of nuclei in early-stage X. laevis embryo extracts, and embryos microinjected with emerin were inviable, with ruptured nuclei. We propose that cytoplasmic membrane localization of emerin leads to rupture of nuclei that are more sensitive to mechanical perturbation, findings that may be relevant to early development and certain laminopathies.

Nanomaterial-Based Plasmon-Enhanced Infrared Spectroscopy

Surface-enhanced infrared absorption (SEIRA) has attracted increasing attention due to the potential of infrared spectroscopy in applications such as molecular trace sensing of solids, polymers, and proteins, specifically fueled by recent substantial developments in infrared plasmonic materials and engineered nanostructures. Here, the significant progress achieved in the past decades is reviewed, along with the current state of the art of SEIRA. In particular, the plasmonic properties of a variety of nanomaterials are discussed (e.g., metals, semiconductors, and graphene) along with their use in the design of efficient SEIRA configurations. To conclude, perspectives on potential applications, including single-molecule detection and in vivo bioassays, are presented.

Epigallocatechin-3-gallate and related phenol compounds redirect the amyloidogenic aggregation pathway of ataxin-3 towards non-toxic aggregates and prevent toxicity in neural cells and Caenorhabditis elegans animal model

The protein ataxin-3 (ATX3) triggers an amyloid-related neurodegenerative disease when its polyglutamine stretch is expanded beyond a critical threshold. We formerly demonstrated that the polyphenol epigallocatechin-3-gallate (EGCG) could redirect amyloid aggregation of a full-length, expanded ATX3 (ATX3-Q55) towards non-toxic, soluble, SDS-resistant aggregates. Here, we have characterized other related phenol compounds, although smaller in size, i.e. (-)-epigallocatechin gallate (EGC), and gallic acid (GA). We analysed the aggregation pattern of ATX3-Q55 and of the N-terminal globular Josephin domain (JD) by assessing the time course of the soluble protein, as well its structural features by FTIR and AFM, in the presence and the absence of the mentioned compounds. All of them redirected the aggregation pattern towards soluble, SDS-resistant aggregates. They also prevented the appearance of ordered side-chain hydrogen bonding in ATX3-Q55, which is the hallmark of polyQ-related amyloids. Molecular docking analyses on the JD highlighted three interacting regions, including the central, aggregation-prone one. All three compounds bound to each of them, although with different patterns. This might account for their capability to prevent amyloidogenesis. Saturation transfer difference NMR experiments also confirmed EGCG and EGC binding to monomeric JD. ATX3-Q55 pre-incubation with any of the three compounds prevented its calcium-influx-mediated cytotoxicity towards neural cells. Finally, all the phenols significantly reduced toxicity in a transgenic Caenorhabditis elegans strain expressing an expanded ATX3. Overall, our results show that the three polyphenols act in a substantially similar manner. GA, however, might be more suitable for antiamyloid treatments due to its simpler structure and higher chemical stability.

Insights into Insulin Fibril Assembly at Physiological and Acidic pH and Related Amyloid Intrinsic Fluorescence

Human insulin is a widely used model protein for the study of amyloid formation as both associated to insulin injection amyloidosis in type II diabetes and highly prone to form amyloid fibrils in vitro. In this study, we aim to gain new structural insights into insulin fibril formation under two different aggregating conditions at neutral and acidic pH, using a combination of fluorescence, circular dichroism, Fourier-transform infrared spectroscopy, and transmission electron miscroscopy. We reveal that fibrils formed at neutral pH are morphologically different from those obtained at lower pH. Moreover, differences in FTIR spectra were also detected. In addition, only insulin fibrils formed at neutral pH showed the characteristic blue-green fluorescence generally associated to amyloid fibrils. So far, the molecular origin of this fluorescence phenomenon has not been clarified and different hypotheses have been proposed. In this respect, our data provide experimental evidence that allow identifying the molecular origin of such intrinsic property.

Combining microfluidics and FT-IR spectroscopy: towards spatially resolved information on chemical processes

This review outlines the combination of infrared spectroscopy and continuous microfluidic processes.

Extraordinary stability of hemocyanins from L. polyphemus and E. californicum studied using infrared spectroscopy from 294 to 20 K

Infrared spectroscopic evidence of a high stability towards exposure to sub-zero temperatures for hemocyanins from the arthropods Limulus polyphemus and Eurypelma californicum.

Sandwich-format 3D printed microfluidic mixers: a flexible platform for multi-probe analysis

We report on a microfluidic mixer fabrication platform that increases the versatility and flexibility of mixers for biomolecular applications. A sandwich-format design allows the application of multiple spectroscopic probes to the same mixer. A polymer spacer is 'sandwiched' between two transparent windows, creating a closed microfluidic system. The channels of the mixer are defined by regions in the polymer spacer that lack material and therefore the polymer need not be transparent in the spectral region of interest. Suitable window materials such as CaF₂ make the device accessible to a wide range of optical probe wavelengths, from the deep UV to the mid-IR. In this study, we use a commercially available 3D printer to print the polymer spacers to apply three different channel designs into the passive, continuous-flow mixer, and integrated them with three different spectroscopic probes. All three spectroscopic probes are applicable to each mixer without further changes. The sandwich-format mixer coupled with cost-effective 3D printed fabrication techniques could increase the applicability and accessibility of microfluidic mixing to intricate kinetic schemes and monitoring chemical synthesis in cases where only one probe technique proves insufficient.

Insoluble protein assemblies characterized by fourier transform infrared spectroscopy

Fourier transform infrared (FTIR) spectroscopy is a useful tool for the structural characterization of insoluble protein assemblies, as it allows to obtain information on the protein secondary structures and on their intermolecular interactions. The protocols for FTIR spectroscopy and microspectroscopy measurements in transmission and attenuated total reflection modes will be presented and illustrated in the following examples: bacterial inclusion bodies, self-assembling peptides, thermal aggregates, and amyloid fibrils.

Shedding light on protein folding, structural and functional dynamics by single molecule studies

The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

Physiological intermolecular modification spectroscopy for the prediction of response to anti-tumor necrosis factor therapy in patients with inflammatory bowel diseases

BACKGROUND/AIMS

Anti-tumor necrosis factor (TNF) antibodies have clinical efficiency only in a subgroup of patients with inflammatory bowel diseases (IBD). Prediction of clinical response is a critical clinical problem. Physiological intermolecular modification spectroscopy (PIMS) is a label-free technology performed in physiological conditions. PIMS enables real-time monitoring of dynamic molecular resonance of entire proteins and macromolecules of an individual. The aim of this study was to explore the capacity of PIMS to discriminate IBD patients regarding response to anti-TNF treatment.

METHODS

Protein extracts of peripheral blood mononuclear cells (PBMC) from 30 outpatients diagnosed with ulcerative colitis (UC) or Crohn's disease (CD) and treated with infliximab were subjected to PIMS analysis in a blinded transversal study. Total protein from each patient's PBMCs was challenged with infliximab. Dynamic changes in macromolecular interaction were registered while the temperature rose from -37 to 37°C. Individual macromolecular volume and molecular elasticity were determined for each patient.

RESULTS

Clinical data revealed that 67% of UC and 79% of CD patients responded to infliximab therapy during the 3-month study period based on their respective clinical activity score. These results confirm that PIMS data predicted response to anti-TNF therapy with an accuracy of 96%.

CONCLUSION

PIMS stratified IBD patients into two groups, responders and nonresponders, which correlated with the clinical efficacy of anti-TNF therapy. PIMS seems to be a powerful technology to adapt IBD treatment to the individual patient. Further studies with PIMS might enable to predict clinical response to biological treatment in IBD patients before the therapy is initiated.

Binding interaction of a prospective chemotherapeutic antibacterial drug with β-lactoglobulin: results and challenges

This Article reports a detailed characterization of the binding interaction of a potential chemotherapeutic antibacterial drug, norfloxacin (NOF), with the mammalian milk protein β-lactoglobulin (βLG). The thermodynamic parameters, ΔH, ΔS, and ΔG, for the binding phenomenon as-evaluated on the basis of van't Hoff relationship reveal the predominance of electrostatic/ionic interactions underlying the binding process. However, the drug-induced quenching of the intrinsic tryptophanyl fluorescence of the protein exhibits intriguing characteristics on Stern-Volmer analysis (displays an upward curvature instead of conforming to a linear regression). Thus, an extensive time-resolved fluorescence spectroscopic characterization of the quenching process has been undertaken in conjugation with temperature-dependent fluorescence quenching studies to unveil the actual quenching mechanism. The invariance of the fluorescence decay behavior of βLG as a function of the quencher (here NOF) concentration coupled with the commensurate dependence of the drug-protein binding constant (K) on temperature, the drug-induced fluorescence quenching of βLG is argued to proceed through static mechanism. This postulate is aided further support from absorption, fluorescence, and circular dichroism (CD) spectral studies. The present study also throws light on the important issue of drug-induced modification in the native protein conformation on the lexicon of CD, excitation-emission matrix spectroscopic techniques. Concurrently, the drug-protein interaction kinetics and the energy of activation of the process are also explored from stopped-flow fluorescence technique. The probable binding locus of NOF in βLG is investigated from AutoDock-based blind docking simulation.

Designing unconventional Fmoc-peptide-based biomaterials: structure and related properties

We have recently employed L-amino acids in the lipase-catalyzed biofabrication of a class of self-assembling Fmoc-peptides that form 3-dimensional nanofiber scaffolds. Here we report that using d-amino acids, the homochiral self-assembling peptide Fmoc-D-Phe3 (Fmoc-F*F*F*) also forms a 3-dimensional nanofiber scaffold that is substantially distinguishable from its L-peptide and heterochiral peptide (F*FF and FF*F*) counterparts on the basis of their physico-chemical properties. Such chiral peptides self-assemble into ordered nanofibers with well defined fibrillar motifs. Circular dichroism and atomic force microscopy have been employed to study in depth such fibrillar peptide structures. Dexamethasone release kinetics from PLGA and CS-PLGA nanoparticles entrapped within the peptidic hydrogel matrix encourage its use for applications in drug controlled release.

Submillisecond mixing in a continuous-flow, microfluidic mixer utilizing mid-infrared hyperspectral imaging detection

We report a continuous-flow, microfluidic mixer utilizing mid-infrared hyperspectral imaging detection, with an experimentally determined, submillisecond mixing time. The simple and robust mixer design has the microfluidic channels cut through a polymer spacer that is sandwiched between two IR transparent windows. The mixer hydrodynamically focuses the sample stream with two side flow channels, squeezing it into a thin jet and initiating mixing through diffusion and advection. The detection system generates a mid-infrared hyperspectral absorbance image of the microfluidic sample stream. Calibration of the hyperspectral image yields the mid-IR absorbance spectrum of the sample versus time. A mixing time of 269 μs was measured for a pD jump from 3.2 to above 4.5 in a D2O sample solution of adenosine monophosphate (AMP), which acts as an infrared pD indicator. The mixer was further characterized by comparing experimental results with a simulation of the mixing of an H2O sample stream with a D2O sheath flow, showing good agreement between the two. The IR microfluidic mixer eliminates the need for fluorescence labeling of proteins with bulky, interfering dyes, because it uses the intrinsic IR absorbance of the molecules of interest, and the structural specificity of IR spectroscopy to follow specific chemical changes such as the protonation state of AMP.

In-situ ultra-sensitive infrared absorption spectroscopy of biomolecule interactions in real time with plasmonic nanoantennas

Infrared absorption spectroscopy is a powerful biochemical analysis tool as it extracts detailed molecular structural information in a label-free fashion. Its molecular specificity renders the technique sensitive to the subtle conformational changes exhibited by proteins in response to a variety of stimuli. Yet, sensitivity limitations and the extremely strong absorption bands of liquid water severely limit infrared spectroscopy in performing kinetic measurements in biomolecules’ native, aqueous environments. Here we demonstrate a plasmonic chip-based technology that overcomes these challenges, enabling the in-situ monitoring of protein and nanoparticle interactions at high sensitivity in real time, even allowing the observation of minute volumes of water displacement during binding events. Our approach leverages the plasmonic enhancement of absorption bands in conjunction with a non-classical form of internal reflection. These features not only expand the reach of infrared spectroscopy to a new class of biological interactions but also additionally enable a unique chip-based technology.

Infrared absorption spectroscopy provides important information about molecules, but is hampered by the absorption of water. Adato and Altug exploit the plasmonic enhancement from nanoantennas to overcome this, enabling chip-based monitoring of biological samples in aqueous environments.

Taylor dispersion and the position-to-time conversion in microfluidic mixing devices

Microfluidic mixing devices are increasingly popular tools for probing the non-equilibrium dynamics of biomolecular systems. Commonly, hydrodynamic focusing is used to reduce the length scales that limit the time of diffusive mixing in the laminar flow regime, such that even sub-millisecond dead times for triggering a reaction have been achieved. Detection of a suitable signal at different points along the channel downstream of the mixing region, corresponding to different times after mixing, then allows the kinetics of the reaction to be obtained. However, the requisite accurate conversion of the positions in the channel to times after mixing is complicated by Taylor dispersion, the combined effect of diffusion and shear flow on the dispersion of the molecules in the microfluidic device. As a result, an accurate position-to-time conversion has only been possible in the limiting regimes, i.e. for very early times, where sample diffusion can be neglected, and for very long times, where the molecules have uniformly sampled the entire channel cross-section. Here, we use detailed three-dimensional, time-dependent finite-element calculations to obtain an accurate position-to-time conversion that bridges these two limits and allows us to quantify the effects of Taylor dispersion on the time resolution of a representative mixing device optimized for single-molecule fluorescence detection. The accuracy of the calculations is confirmed by direct comparison of the calculated velocity field with dual-focus fluorescence correlation spectroscopy measurements.

Monitoring protein-ligand interactions by time-resolved FTIR difference spectroscopy

Time-resolved FTIR difference spectroscopy is a valuable tool to monitor the dynamics and exact molecular details of protein-ligand interactions. FTIR difference spectroscopy selects, out of the background absorbance of the whole sample, the absorbance bands of the protein groups and of the ligands that are involved in the protein reaction. The absorbance changes can be monitored with time-resolutions down to nanoseconds and followed for time periods ranging over nine orders of magnitude even in membrane proteins with a size of 100,000 Da. Here, we discuss the various experimental setups. The rapid scan technique allows a time resolution in the millisecond regime, whereas the step scan technique allows nanosecond time resolution. We show appropriate sample cells and how to trigger a reaction within these cells. The kinetic analysis of the data is discussed. A crucial step in the data analysis is the reliable assignment of bands to chemical groups of the protein and the ligand. This is done either by site directed mutagenesis, where the absorbance bands of the exchanged amino acids disappear or by isotopically labeling, where the band of the labelled group is frequency shifted.

Ionic liquid-induced formation of the α-helical structure of β-lactoglobulin

Structural modification of bovine milk β-lactoglobulin (β-LG) in aqueous 1-butyl-3-methylimidazolium nitrate ([bmim][NO3]) and ethylammonium nitrate ([EAN][NO3]) solutions has been investigated by Fourier transform infrared and circular dichroism spectroscopy. Remarkably, high ionic liquid (IL) concentrations (>15 mol %IL) caused formation of a non-native α-helical structure of β-LG and disruption of its tertiary structure. Furthermore, while [bmim][NO3] promoted protein aggregation, [EAN][NO3] inhibited it probably owing to differences in the unique solution structure (nanoheterogeneity) of the ILs by the different cationic species. The IL-induced α-helical formation of β-LG shows a behavior similar to the alcohol denaturation, but a disordered structure-rich state was observed in the β-α transition process by adding IL, in contrast to the case of an aqueous alcohol solution of protein. We propose that the molten salt-like property of aqueous IL solutions strongly support α-helical formation of proteins.

Biophysical characterization of two different stable misfolded monomeric polypeptides that are chaperone-amenable substrates

Misfolded polypeptide monomers may be regarded as the initial species of many protein aggregation pathways, which could accordingly serve as primary targets for molecular chaperones. It is therefore of paramount importance to study the cellular mechanisms that can prevent misfolded monomers from entering the toxic aggregation pathway and moreover rehabilitate them into active proteins. Here, we produced two stable misfolded monomers of luciferase and rhodanese, which we found to be differently processed by the Hsp70 chaperone machinery and whose conformational properties were investigated by biophysical approaches. In spite of their monomeric nature, they displayed enhanced thioflavin T fluorescence, non-native β-sheets, and tertiary structures with surface-accessible hydrophobic patches, but differed in their conformational stability and aggregation propensity. Interestingly, minor structural differences between the two misfolded species could account for their markedly different behavior in chaperone-mediated unfolding/refolding assays. Indeed, only a single DnaK molecule was sufficient to unfold by direct clamping a misfolded luciferase monomer, while, by contrast, several DnaK molecules were necessary to unfold the more resistant misfolded rhodanese monomer by a combination of direct clamping and cooperative entropic pulling.

The acidic pH-induced structural changes in Pin1 as revealed by spectral methodologies

Pin1 is closely associated with the pathogenesis of cancers and Alzheimer's disease (AD). Previously, we have shown the characteristics of the thermal denaturation of Pin1. Herein, the acid-induced denaturation of Pin1 was determined by means of fluorescence emission, synchronous fluorescence, far-UV CD, ANS fluorescence and RLS spectroscopies. The fluorescence emission spectra and the synchronous fluorescence spectra suggested the partially reversible unfolding (approximately from pH 7.0 to 4.0) and refolding (approximately from pH 4.0 to 1.0) of the structures around the chromophores in Pin1, apparently with an intermediate state at about pH 4.0-4.5. The far-UV CD spectra indicated that acidic pH (below pH 4.0) induced the structural transition from α-helix and random coils to β-sheet in Pin1. The ANS fluorescence and the RLS spectra further suggested the exposure of the hydrophobic side-chains of Pin1 and the aggregation of it especially below pH 2.3, and the aggregation possibly resulted in the formation of extra intermolecular β-sheet. The present work primarily shows that acidic pH can induce kinds of irreversible structural changes in Pin1, such as the exposure of the hydrophobic side-chains, the transition from α-helix to β-sheet and the aggregation of Pin1, and also explains why Pin1 loses most of its activity below pH 5.0. The results emphasize the important role of decreased pH in the pathogenesis of some Pin1-related diseases, and support the therapeutic approach for them by targeting acidosis and modifying the intracellular pH gradients.

Adsorption of diblock polypeptides on polystyrene latex

The adsorption of peptides at solid/liquid interfaces is affected by peptide/surface and peptide/peptide hydrophobic and electrostatic forces. Three diblock copolypeptides and two homopeptides were adsorbed on poly(styrene) nanospheres from water, water/methanol, and water/glycerol mixtures at different pH's to study both of these effects. Peptides with one hydrophilic (glutamic acid or lysine) and one nonpolar block (alanine) or with both hydrophilic blocks with opposite charges (glutamic acid and lysine) were chemically synthesized and used as adsorbates in this study. The amount adsorbed was determined, and dynamic light scattering (DLS) was used to measure the adsorbed layer thickness. It was found that peptide/surface and peptide/peptide electrostatic interactions dominate the adsorption process. Hydrophobic forces also play a role, but secondary to electrostatic forces. Positively charged blocks show high affinity for the surface, whereas negatively charged blocks were excluded from it. Poly(Lys) has the highest affinity by the surface, while (Glu)(14)-b-(Ala)(5) has the lowest. Adsorption of all peptides was inhibited by methanol and promoted by glycerol. The adsorption for (Lys)(5)-b-(Glu)(6) was extremely sensitive to pH, irrespective of cosolvent, whereas the thickness for (Lys)(30)-b-(Ala)(41) was sensitive to pH as well as cosolvent. Aggregation was observed in the presence of the nanosurfaces but not in the bulk peptides under some pH and solvent conditions.

Bovine β-lactoglobulin is dimeric under imitative physiological conditions: dissociation equilibrium and rate constants over the pH range of 2.5-7.5

The oligomerization of β-lactoglobulin (βLg) has been studied extensively, but with somewhat contradictory results. Using analytical ultracentrifugation in both sedimentation equilibrium and sedimentation velocity modes, we studied the oligomerization of βLg variants A and B over a pH range of 2.5-7.5 in 100 mM NaCl at 25°C. For the first time, to our knowledge, we were able to estimate rate constants (k(off)) for βLg dimer dissociation. At pH 2.5 k(off) is low (0.008 and 0.009 s(-1)), but at higher pH (6.5 and 7.5) k(off) is considerably greater (>0.1 s(-1)). We analyzed the sedimentation velocity data using the van Holde-Weischet method, and the results were consistent with a monomer-dimer reversible self-association at pH 2.5, 3.5, 6.5, and 7.5. Dimer dissociation constants K(D)(2-1) fell close to or within the protein concentration range of ∼5 to ∼45 μM, and at ∼45 μM the dimer predominated. No species larger than the dimer could be detected. The K(D)(2-1) increased as |pH-pI| increased, indicating that the hydrophobic effect is the major factor stabilizing the dimer, and suggesting that, especially at low pH, electrostatic repulsion destabilizes the dimer. Therefore, through Poisson-Boltzmann calculations, we determined the electrostatic dimerization energy and the ionic charge distribution as a function of ionic strength at pH above (pH 7.5) and below (pH 2.5) the isoelectric point (pI∼5.3). We propose a mechanism for dimer stabilization whereby the added ionic species screen and neutralize charges in the vicinity of the dimer interface. The electrostatic forces of the ion cloud surrounding βLg play a key role in the thermodynamics and kinetics of dimer association/dissociation.

Studying enzymatic bioreactions in a millisecond microfluidic flow mixer

In this study, the pre-steady state development of enzymatic bioreactions using a microfluidic mixer is presented. To follow such reactions fast mixing of reagents (enzyme and substrate) is crucial. By using a highly efficient passive micromixer based on multilaminar flow, mixing times in the low millisecond range are reached. Four lamination layers in a shallow channel reduce the diffusion lengths to a few micrometers only, enabling very fast mixing. This was proven by confocal fluorescence measurements in the channel's cross sectional area. Adjusting the overall flow rate in the 200 μm wide and 900 μm long mixing and observation channel makes it possible to investigate enzyme reactions over several seconds. Further, the device enables changing the enzyme/substrate ratio from 1:1 up to 3:1, while still providing high mixing efficiency, as shown for the enzymatic hydrolysis using β-galactosidase. This way, the early kinetics of the enzyme reaction at multiple enzyme/substrate concentrations can be collected in a very short time (minutes). The fast and easy handling of the mixing device makes it a very powerful and convenient instrument for millisecond temporal analysis of bioreactions.

Analysis of a laminar-flow diffusional mixer for directed self-assembly of liposomes

The present work describes the operation and simulation of a microfluidic laminar-flow mixer. Diffusive mixing takes place between a core solution containing lipids in ethanol and a sheath solution containing aqueous buffer, leading to self assembly of liposomes. Present device architecture hydrodynamically focuses the lipid solution into a cylindrical core positioned at the center of a microfluidic channel of 125 × 125-μm(2) cross-section. Use of the device produces liposomes in the size range of 100-300 nm, with larger liposomes forming at greater ionic strength in the sheath solution and at lower lipid concentration in the core solution. Finite element simulations compute the concentration distributions of solutes at axial distances of greater than 100 channel widths. These simulations reduce computation time and enable computation at long axial distances by utilizing long hexahedral elements in the axial flow region and fine tetrahedral elements in the hydrodynamic focusing region. Present meshing technique is generally useful for simulation of long microfluidic channels and is fully implementable using comsol Multiphysics. Confocal microscopy provides experimental validation of the simulations using fluorescent solutions containing fluorescein or enhanced green fluorescent protein.

Fano-resonant asymmetric metamaterials for ultrasensitive spectroscopy and identification of molecular monolayers

Engineered optical metamaterials present a unique platform for biosensing applications owing to their ability to confine light to nanoscale regions and to their spectral selectivity. Infrared plasmonic metamaterials are especially attractive because their resonant response can be accurately tuned to that of the vibrational modes of the target biomolecules. Here we introduce an infrared plasmonic surface based on a Fano-resonant asymmetric metamaterial exhibiting sharp resonances caused by the interference between subradiant and superradiant plasmonic resonances. Owing to the metamaterial's asymmetry, the frequency of the subradiant resonance can be precisely determined and matched to the molecule's vibrational fingerprints. A multipixel array of Fano-resonant asymmetric metamaterials is used as a platform for multispectral biosensing of nanometre-scale monolayers of recognition proteins and their surface orientation, as well as for detecting chemical binding of target antibodies to recognition proteins.

Existence of different structural intermediates and aggregates on the folding pathway of ovalbumin

Structural modifications of ovalbumin in presence of different concentration of guanidine hydrochloride (Gdn HCl) and glucose were investigated by using intrinsic fluorescence, Fourier transform infra-red spectroscopy, circular dichroism and 8-anilino-1-naphthalene-sulphonic acid, to confirm that partially folded intermediates of ovalbumin lead to aggregation. The two partially folded intermediates of ovalbumin were observed one at 1 M Gdn HCl and another in the presence of 20 mM glucose at 3 M Gdn HCl. Both intermediates exist as compact states with altered intrinsic fluorescence, prominent β-sheet secondary structure and enhanced ANS binding. Ovalbumin in the presence of glucose required more concentration of Gdn HCl (3 M) to exist as an intermediate state than control (1 M). Such alpha-helix/beta-sheet transition of proteins is a crucial step in amyloidogenic diseases and represents an internal rearrangement of local contacts in an already folded protein. Further, incubation for 24 h resulted in the formation of aggregates as detected by thioflavin T-assay. On further increasing the concentration of glucose to 50 mM and incubation time for various days resulted in the formation of molten globule state of ovalbumin at 6th day. Later on, at 10th day advanced glycated end products were observed.

Time-resolved mid-IR spectroscopy of (bio)chemical reactions in solution utilizing a new generation of continuous-flow micro-mixers

A specially designed micro-mixer made of silicon, calcium fluoride, and silicone with an optical transmission path of 8 μm has been used for mid-IR spectroscopy monitoring of mixing-induced chemical reactions in the low millisecond time regime. The basic principle of the proposed continuous-flow technique is to mix two liquids introduced in two times two alternatingly stacked layers through diffusion at the entrance of a 200 μm wide, 1 cm long micro-fluidic channel also serving as measurement area. By using this special, dedicated arrangement, diffusion lengths and hence the mixing times can be significantly shortened and the overall performance improved in comparison to previous systems and alternative methods. Measurements were carried out in transmission mode using an Fourier transform infrared (FTIR) microscope, recording spectra with spot sizes of 180 × 100 μm(2) each at defined spots along this channel. Each of these spots corresponds to a specific reaction time: moving the measurement spot towards the entry yields shorter reaction times, moving it towards the channel's end gives longer reaction times. This principle is generic in nature and provides a solution for accurate, chemically induced triggering of reactions requiring the mixing of two liquid reagents or reagent solutions. A typical experiment thus yields up to 85 time-coded data points, covering a time span from 1 to 80 ms at a total reagent consumption of only about 125 μL. Using the fast neutralization reaction of acetic acid with sodium hydroxide as a model, the time required for 90% mixing was determined to be around 4 ms. Additionally, first experiments on ubiquitin changing its secondary structure from native to "A-state" were carried out, illustrating the potential for time-resolved measurements of proteins in aqueous solutions.

Changes in beta-lactoglobulin conformation at the oil/water interface of emulsions studied by synchrotron radiation circular dichroism spectroscopy

The structure of proteins at interfaces is a key factor determining the stability as well as organoleptic properties of food emulsions. While it is widely believed that proteins undergo conformational changes at interfaces, the measurement of these structural changes remains a significant challenge. In this study, the conformational changes of beta-lactoglobulin (beta-Lg) upon adsorption to the interface of hexadecane oil-in-water emulsions were investigated using synchrotron radiation circular dichroism (SRCD) spectroscopy. Far-UV SRCD spectra showed that adsorption of beta-Lg to the O/W interface caused a significant increase in non-native alpha-helix structure, accompanied by a concomitant loss of beta-sheet structure. Near-UV SRCD spectra revealed that a considerable disruption of beta-Lg tertiary structure occurred upon adsorption. Moreover, heat-induced changes to the non-native beta-Lg conformation at the oil/water interface were very small compared to the dramatic loss of beta-Lg secondary structure that occurred during heating in solution, suggesting that the interface has a stabilizing effect on the structure of non-native beta-Lg. Overall, our findings provide insight into the conformational behavior of proteins at oil/water interfaces and demonstrate the applicability of SRCD spectroscopy for measuring the conformation of adsorbed proteins in optically turbid emulsions.

Continuous-flow multi-analyte biosensor cartridge with controllable linear response range

This article presents the design and fabrication of a microfluidic biosensor cartridge for the continuous and simultaneous measurement of biologically relevant analytes in a sample solution. The biosensor principle is based on the amperometric detection of hydrogen peroxide using enzyme-modified electrodes. The low-integrated and disposable cartridge is fabricated in PDMS and SU-8 by rapid prototyping. The device is designed in such a way that it addresses two major challenges of biosensors using microfluidics approaches. Firstly, the enzymatic membrane is deposited on top of the platinum electrodes via a microfluidic deposition channel from outside the cartridge. This decouples the membrane deposition from the cartridge fabrication and enables the user to decide when and with what mixture he wants to modify the electrode. Secondly, by using laminar sheath-flow of the sample and a buffer solution, a dynamic diffusion layer is created. The analyte has to diffuse through the buffer solution layer before it can reach the immobilized enzyme membrane on the electrode. Controlling of the thickness of the diffusion layer by variation of the flow-rate of the two layers enables the user to adjust the sensitivity and the linear region of the sensor. The point where the buffer and sample stream join proved critical in creating the laminar sheath-flow. Results of computational simulations considering fluid dynamics and diffusion are presented. The consistency of the device was investigated through detection of glucose and lactate and are in accordance with the CFD simulations. A sensitivity of 157+/-28 nA/mM for the glucose sensor and 79+/-12 nA/mM for the lactate sensor was obtained. The linear response range of these biosensors could be increased from initially 2 mM up to 15 mM with a limit of detection of 0.2 mM.

Ultrafast microfluidic mixer with three-dimensional flow focusing for studies of biochemical kinetics

Studies of the kinetics of biochemical reactions, especially of folding of proteins and RNA, are important for understanding the function of biomolecules and processes in live cells. Many biochemical reactions occur rapidly and thus need to be triggered on very short time scales for their kinetics to be studied, which is often accomplished by mixing in a turbulent flow. More rapid and sample-efficient mixing is achieved in laminar flow in a microfluidic device, in which the sample is two-dimensionally (2D) focused to a thin sheet. Here we describe the design and operation of an ultrafast microfluidic mixer with three-dimensional (3D) flow focusing. The confinement of a 3D-focused sample to a narrow stream near the middle of a microchannel renders its velocity nearly uniform and makes it possible to monitor the reaction kinetics without exclusion of any parts of the sample. Hence, the sample consumption is substantially reduced and the fluorescence of the sample can be monitored without a confocal setup. Moreover, the 3D-focusing allows facile measurements of velocity of the sample with a high spatial resolution using a specially developed technique based on epi-fluorescence imaging. The data on the velocity vs. position are used to precisely calibrate the conversion between position and the reaction time, which is essential for accurate kinetic measurements. The device performs mixing on a 10 micros scale, which is comparable to that of the laminar mixers with 2D focusing. Unlike previous ultrafast laminar mixers, which were machined in hard materials, the present microfluidic device is made of a single cast of poly(dimethylsiloxane), PDMS, and is thus simpler and less expensive to manufacture.

Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function

Single-molecule fluorescence microscopy experiments on RNA molecules brought to light the highly complex dynamics of key biological processes, including RNA folding, catalysis of ribozymes, ligand sensing of riboswitches and aptamers, and protein synthesis in the ribosome. By using highly advanced biophysical spectroscopy techniques in combination with sophisticated biochemical synthesis approaches, molecular dynamics of individual RNA molecules can be observed in real time and under physiological conditions in unprecedented detail that cannot be achieved with bulk experiments. Here, we review recent advances in RNA folding and functional studies of RNA and RNA-protein complexes addressed by using single-molecule Förster (fluorescence) resonance energy transfer (smFRET) technique.

Microfluidic mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy

We have developed a microfluidic mixer optimized for rapid measurements of protein folding kinetics using synchrotron radiation circular dichroism (SRCD) spectroscopy. The combination of fabrication in fused silica and synchrotron radiation allows measurements at wavelengths below 220 nm, the typical limit of commercial instrumentation. At these wavelengths, the discrimination between the different types of protein secondary structure increases sharply. The device was optimized for rapid mixing at moderate sample consumption by employing a serpentine channel design, resulting in a dead time of less than 200 micros. Here, we discuss the design and fabrication of the mixer and quantify the mixing efficiency using wide-field and confocal epi-fluorescence microscopy. We demonstrate the performance of the device in SRCD measurements of the folding kinetics of cytochrome c, a small, fast-folding protein. Our results show that the combination of SRCD with microfluidic mixing opens new possibilities for investigating rapid conformational changes in biological macromolecules that have previously been inaccessible.

Multiscale characterization of individualized beta-lactoglobulin microgels formed upon heat treatment under narrow pH range conditions

Aqueous dispersions of demineralized beta-lactoglobulin (beta-lg) were held at 85 degrees C for 15 min at a constant protein concentration of 1 wt % in the pH range of 3.0-7.0. This led to denatured protein content ranging from 20% (pH 3.0) to 90% (pH 5.0). The protein aggregates formed were characterized as to their stability to sedimentation (turbidity), morphology, size, surface charge, ANS surface hydrophobicity, and content in accessible thiol groups. Additionally, the changes in secondary structures of the protein upon heating were followed by Fourier transform infrared spectroscopy (FTIR). Stable dispersions (no sedimentation for 10 min) of individualized beta-lg microgels were obtained at specific pH 4.6 and 5.8, corresponding to an aggregation yield of about 80%. The width of the pH region leading to these microgels was 0.3 pH unit below or above the two specific pH values. Microgels were characterized by a spherical shape and remarkably low polydispersity in size (<0.2). Their z-average hydrodynamic diameter determined by dynamic light scattering (DLS) was between 160 and 220 nm, and their zeta-potential was +30 or -40 mV, depending on the initial pH before heating. Microgels obtained at pH 4.6 displayed a lower binding capacity for ANS and a lower content of accessible thiol groups as compared to those obtained at pH 5.8. Both types of microgels might therefore differ in their internal and interfacial structures. Between pH 4.6 and 5.8, large sedimenting protein particulates were obtained, whereas soluble aggregates were formed at pH <4.6 or >5.8. Interestingly, DLS experiments showed that before heating, beta-lg was mainly present in an oligomeric state at pH 4.6 and 5.8. This result was confirmed by FTIR measurements indicating the stronger contribution of the 1616-1624 cm(-1) spectral band corresponding to intermolecular beta-sheets in the pH range of 4.0-6.0. Upon heating, FTIR spectroscopy revealed that individualized microgels were obtained under pH conditions where a balance between attractive forces arising from protein unfolding leading to the formation of intermolecular beta-sheets (1616-1624 cm(-1 )band) and the repulsive electrostatic forces due to the initial protein net charge was achieved.