Mid-infrared spectroscopy for protein analysis: potential and challenges

Cellular and Biophysical Applications of Genetic Code Expansion

Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

Fluorescence in depth: integration of spectroscopy and imaging with Raman, IR, and CD for advanced research

Fluorescence spectroscopy serves as a vital technique for studying the interaction between light and fluorescent molecules. It encompasses a range of methods, each presenting unique advantages and applications. This technique finds utility in various chemical studies. This review discusses Fluorescence spectroscopy, its branches such as Time-Resolved Fluorescence Spectroscopy (TRFS) and Fluorescence Lifetime Imaging Microscopy (FLIM), and their integration with other spectroscopic methods, including Raman, Infrared (IR), and Circular Dichroism (CD) spectroscopies. By delving into these methods, we aim to provide a comprehensive understanding of the capabilities and significance of fluorescence spectroscopy in scientific research, highlighting its diverse applications and the enhanced understanding it brings when combined with other spectroscopic methods. This review looks at each technique's unique features and applications. It discusses the prospects of their combined use in advancing scientific understanding and applications across various domains.

Enhanced properties of the mid-infrared superluminescent emitter with a composite waveguide

This study reports on a composite structure composing tilted taper, and tilted and curved waveguides with the aim of enhancing the spectral width and output power of mid-infrared quantum cascade superluminescent emitters (QC-SLEs). The computational results indicate that a tilt angle of 10° and a curved angle of 20° can avoid the selectivity of a certain wavelength due to interference effects at tilt angles of 6° and 8°, resulting in the minimum reflectivity of 1.3×10-4 and 4.4×10-4 for each wide and narrow cavity surface. Simultaneously, the modes propagating perpendicular to the cavity surface exist the least. The corresponding experimental results show a significant enhancement in the spectral width to 168.5c m -1 and a high power output of 5.1 mW for the device. This study presents what we believe to be a novel concept for the designing of superluminescent emitters with both a broadband and high power output.

Quantifying Bound Proteins on Pegylated Gold Nanoparticles Using Infrared Spectroscopy

Protein-nanoparticle (NP) complexes are nanomaterials that have numerous potential uses ranging from biosensing to biomedical applications such as drug delivery and nanomedicine. Despite their extensive use quantifying the number of bound proteins per NP remains a challenging characterization step that is crucial for further developments of the conjugate, particularly for metal NPs that often interfere with standard protein quantification techniques. In this work, we present a method for quantifying the number of proteins bound to pegylated thiol-capped gold nanoparticles (AuNPs) using an infrared (IR) spectrometer, a readily available instrument. This method takes advantage of the strong IR bands present in proteins and the capping ligands to quantify protein-NP ratios and circumvents the need to degrade the NPs prior to analysis. We show that this method is generalizable where calibration curves made using inexpensive and commercially available proteins such as bovine serum albumin (BSA) can be used to quantify protein-NP ratios for proteins of different sizes and structures.

Surface-acoustic-wave-driven graphene plasmonic sensor for fingerprinting ultrathin biolayers down to the monolayer limit

Surface plasmon polaritons in graphene can enhance the performance of mid-infrared spectroscopy, which is key for the study of both the composition and the conformation of organic molecules via their vibrational resonances. In this paper, a plasmonic biosensor using a graphene-based van der Waals heterostructure on a piezoelectric substrate is theoretically demonstrated, where far-field light is coupled to surface plasmon-phonon polaritons (SPPPs) through a surface acoustic wave (SAW). The SAW creates an electrically-controlled virtual diffraction grating, suppressing the need for patterning the 2D materials, that limits the polariton lifetime, and enabling differential measurement schemes, which increase the signal-to-noise ratio and allow a quick commutation between reference and sample signals. A transfer matrix method has been used for simulating the SPPPs propagating in the system, which are electrically tuned to interact with the vibrational resonances of the analytes. Furthermore, the analysis of the sensor response with a coupled oscillators model has proven its capability of fingerprinting ultrathin biolayers, even when the interaction is too weak to induce a Fano interference pattern, with a sensitivity down to the monolayer limit, as tested with a protein bilayer or a peptide monolayer. The proposed device paves the way for the development of advanced SAW-assisted lab-on-chip systems combining the existing SAW-mediated physical sensing and microfluidic functionalities with the chemical fingerprinting capability of this novel SAW-driven plasmonic approach.

Label-free mid-infrared photothermal live-cell imaging beyond video rate

Advancement in mid-infrared (MIR) technology has led to promising biomedical applications of MIR spectroscopy, such as liquid biopsy or breath diagnosis. On the contrary, MIR microscopy has been rarely used for live biological samples in an aqueous environment due to the lack of spatial resolution and the large water absorption background. Recently, mid-infrared photothermal (MIP) imaging has proven to be applicable to 2D and 3D single-cell imaging with high spatial resolution inherited from visible light. However, the maximum measurement rate has been limited to several frames s^-1, limiting its range of use. Here, we develop a significantly improved wide-field MIP quantitative phase microscope with two orders-of-magnitude higher signal-to-noise ratio than previous MIP imaging techniques and demonstrate live-cell imaging beyond video rate. We first derive optimal system design by numerically simulating thermal conduction following the photothermal effect. Then, we develop the designed system with a homemade nanosecond MIR optical parametric oscillator and a high full-well-capacity image sensor. Our high-speed and high-spatial-resolution MIR microscope has great potential to become a new tool for life science, in particular for live-cell analysis.

Quantum Cascade Laser Based Infrared Spectroscopy: A New Paradigm for Protein Secondary Structure Measurement

Mid-infrared spectroscopy is one of the major analytical techniques employed for measurements of protein structure in solution. Traditional Fourier Transform-Infrared (FT-IR) measurement is limited by its blackbody light source that is inherently spatially incoherent and has low optical power output. This limitation is pronounced when working with proteins in aqueous solutions. Strong absorbance of water in protein amide I region 1600-1700 cm-1 restricts light path length to <10 μm and imposes significant experimental challenges in sample and flow cell handling. Emerging laser spectroscopic techniques use high-power coherent laser as light source that overcomes the limitation in FT-IR measurement. In this study, we employed an innovative infrared spectrometer that uses quantum cascade laser (QCL) as light source. Continuous infrared radiation from this laser source can be swiftly swept within the amide I region (1600-1700 cm-1) and amide II region (1500-1600 cm-1), which makes this technique ideal for protein secondary structure study. Protein solutions as low as 0.5 mg/mL were measured rapidly without any sample preparation. Infrared spectra of model proteins were thus collected, and a chemometric model based on partial least squares regression was developed to quantify α-helix and β-strand motifs in protein secondary structure. The model was applied to measurement of the native secondary structure of commercial therapeutic proteins and bovine serum albumin (BSA) and in thermal degradation studies.

Breath analysis by ultra-sensitive broadband laser spectroscopy detects SARS-CoV-2 infection

Rapid testing is essential to fighting pandemics such as coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Exhaled human breath contains multiple volatile molecules providing powerful potential for non-invasive diagnosis of diverse medical conditions. We investigated breath detection of SARS-CoV-2 infection using cavity-enhanced direct frequency comb spectroscopy (CE-DFCS), a state-of-the-art laser spectroscopic technique capable of a real-time massive collection of broadband molecular absorption features at ro-vibrational quantum state resolution and at parts-per-trillion volume detection sensitivity. Using a total of 170 individual breath samples (83 positive and 87 negative with SARS-CoV-2 based on reverse transcription polymerase chain reaction tests), we report excellent discrimination capability for SARS-CoV-2 infection with an area under the receiver-operating-characteristics curve of 0.849(4). Our results support the development of CE-DFCS as an alternative, rapid, non-invasive test for COVID-19 and highlight its remarkable potential for optical diagnoses of diverse biological conditions and disease states.

Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble

Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.

The Convergence of FTIR and EVs: Emergence Strategy for Non-Invasive Cancer Markers Discovery

In conjunction with imaging analysis, pathology-based assessments of biopsied tissue are the gold standard for diagnosing solid tumors. However, the disadvantages of tissue biopsies, such as being invasive, time-consuming, and labor-intensive, have urged the development of an alternate method, liquid biopsy, that involves sampling and clinical assessment of various bodily fluids for cancer diagnosis. Meanwhile, extracellular vesicles (EVs) are circulating biomarkers that carry molecular profiles of their cell or tissue origins and have emerged as one of the most promising biomarkers for cancer. Owing to the biological information that can be obtained through EVs' membrane surface markers and their cargo loaded with biomolecules such as nucleic acids, proteins, and lipids, EVs have become useful in cancer diagnosis and therapeutic applications. Fourier-transform infrared spectroscopy (FTIR) allows rapid, non-destructive, label-free molecular profiling of EVs with minimal sample preparation. Since the heterogeneity of EV subpopulations may result in complicated FTIR spectra that are highly diverse, computational-assisted FTIR spectroscopy is employed in many studies to provide fingerprint spectra of malignant and non-malignant samples, allowing classification with high accuracy, specificity, and sensitivity. In view of this, FTIR-EV approach carries a great potential in cancer detection. The progression of FTIR-based biomarker identification in EV research, the rationale of the integration of a computationally assisted approach, along with the challenges of clinical translation are the focus of this review.

Assessing Tissue Fixation Time and Quality with Label-free Mid Infrared Spectroscopy and Machine Learning

Objectives: This work investigates whether changes in a biospecimen's molecular composition from formaldehyde fixation drive changes in the mid infrared (MID-IR) spectrum. Our ultimate goal was to develop an analytical metrology that could be used to accurately determine the fixation time of a tissue sample as a surrogate to overall tissue quality. Methods: Multiple unstained formalin-fixed paraffin-embedded tissue samples were scanned with an MID-IR microscope to identify a molecular fingerprint of formaldehyde fixation. The fixation specific patterns were then mined to develop a predictive model. A multiple tissue experiment using greater than 100 samples was designed to train the algorithm and validate the accuracy of predicting fixation status. Results: We present data that formaldehyde crosslinking results in alterations to multiple bands of the MID-IR spectra. The impact was most dramatic in the Amide I band, which is sensitive to the conformational state of proteins. The spectroscopic fixation signature was used to train a machine-learning model that could predict fixation time of unknown tissues with an average accuracy of 1.4 hours. Results were validated by histological stain quality for bcl-2, FOXP3, and ki-67. Further, two-dimensional imaging was used to visualize the spatial dependence of fixation, as demonstrated by multiple features in the tissue's vibrational spectra. Conclusions: This work demonstrates that it is possible to predict the fixation status of tissues for which the preanalytics are unknown. This novel capability could help standardize clinical tissue diagnostics and ensure every patient gets the absolutely best treatment based on the highest quality tissue sample.

Plasmonic bound states in the continuum to tailor light-matter coupling

Plasmon resonances play a pivotal role in enhancing light-matter interactions in nanophotonics, but their low-quality factors have hindered applications demanding high spectral selectivity. Here, we demonstrate the design and 3D laser nanoprinting of plasmonic nanofin metasurfaces, which support symmetry-protected bound states in the continuum up to the fourth order. By breaking the nanofins' out-of-plane symmetry in parameter space, we achieve high-quality factor (up to 180) modes under normal incidence. The out-of-plane symmetry breaking can be fine-tuned by the nanofins' triangle angle, opening a pathway to precisely control the ratio of radiative to intrinsic losses. This enables access to the under-, critical, and over-coupled regimes, which we exploit for pixelated molecular sensing. We observe a strong dependence of the sensing performance on the coupling regime, demonstrating the importance of judicious tailoring of light-matter interactions. Our demonstration provides a metasurface platform for enhanced light-matter interaction with a wide range of applications.

A Scalable CMOS Molecular Electronics Chip for Single-Molecule Biosensing

This work reports the first CMOS molecular electronics chip. It is configured as a biosensor, where the primary sensing element is a single molecule "molecular wire" consisting of a ∼100 GΩ, 25 nm long alpha-helical peptide integrated into a current monitoring circuit. The engineered peptide contains a central conjugation site for attachment of various probe molecules, such as DNA, proteins, enzymes, or antibodies, which program the biosensor to detect interactions with a specific target molecule. The current through the molecular wire under a dc applied voltage is monitored with millisecond temporal resolution. The detected signals are millisecond-scale, picoampere current pulses generated by each transient probe-target molecular interaction. Implemented in a 0.18 μm CMOS technology, 16k sensors are arrayed with a 20 μm pitch and read out at a 1 kHz frame rate. The resulting biosensor chip provides direct, real-time observation of the single-molecule interaction kinetics, unlike classical biosensors that measure ensemble averages of such events. This molecular electronics chip provides a platform for putting molecular biosensing "on-chip" to bring the power of semiconductor chips to diverse applications in biological research, diagnostics, sequencing, proteomics, drug discovery, and environmental monitoring.

Study on the in vitro digestion process of green wheat protein: Structure characterization and product analysis

In this study, the in vitro digestion process of green wheat protein (GWP) was explored by simulating the gastrointestinal digestion. The digestibility of GWP was 65.23%, and was mainly digested by trypsin. During the digestion process of GWP, large-size particles are digested by pepsin, and medium-sized particles are digested by trypsin into smaller particles; irregular large block structure with smooth surface was gradually turned into smaller blocks with porous surface; and the spatial conformation was loosened mainly by the unfolding of β-sheet structure. Gel electrophoresis demonstrated that HMW glutenin and ω-gliadins in GWP were completely digested, while LMW glutenin and α/β/γ-gliadins were partially digested. Additionally, the peptide lengths were relatively dispersed after pepsin digestion. Most of the peptides (76.5%) fell into the range 3-15 amino acid after pepsin and trypsin digestion. The molecular weight (MW) of most pepsin digestion products was above 2000 Da, whereas the MW of trypsin digestion products was mainly concentrated in 500-2000 Da. Besides, the sensitizing peptide sequence of wheat protein was detected in the final digestion products of GWP. This research provided a theoretical guidance for the development and application of GWP.

Generation of 8–20 μm Mid-Infrared Ultrashort Femtosecond Laser Pulses via Difference Frequency Generation

Mid-infrared (MIR) ultrashort laser pulses have a wide range of applications in the fields of environmental monitoring, laser medicine, food quality control, strong-field physics, attosecond science, and some other aspects. Recent years have seen great developments in MIR laser technologies. Traditional solid-state and fiber lasers focus on the research of the short-wavelength MIR region. However, due to the limitation of the gain medium, they still cannot cover the long-wavelength region from 8 to 20 µm. This paper summarizes the developments of 8–20 μm MIR ultrafast laser generation via difference frequency generation (DFG) and reviews related theoretical models. Finally, the feasibility of MIR power scaling by nonlinear-amplification DFG and methods for measuring the power of DFG-based MIR are analyzed from the author’s perspective.

Investigation of protective effect of ethanol on the natural structure of protein with infrared spectroscopy

The stability of biological drugs with protein as an active substance depends heavily on the retention of natural protein structure during freeze-drying. Stabilizers have become important substances in the process of protein freeze-drying. In order to further understand the mechanism of the interaction between protein and stabilizers, human serum albumin (HSA) and simple hydroxyl compound ethanol were used as models. Infrared (IR) spectroscopy combined with chemometrics was implemented to investigate the changes of secondary structure and hydration of HSA when different concentrations of ethanol were considered as interference. Through the analysis of the protein secondary structure and hydrated layer, we found that the addition of ethanol-d6 increased the α-helix of HSA and reduced the disordered structure. The hydrogen bond structure around HSA was enhanced and intermolecular aggregation was reduced through the action of the water molecules. The hypothesis was verified by circular dichroism (CD) and transmission electron microscopy (TEM) observation by adding different concentrations of ethanol-d6. It was found that a small amount of ethanol could protect the native conformation of HSA. In conclusion, this study revealed the mechanism of ethanol as a protein protector, provided a new idea for protein purification process and a theoretical basis for biomolecular interaction.

Observation of tunable surface plasmon resonances and surface enhanced infrared absorption (SEIRA) based on indium tin oxide (ITO) nanoparticle substrates

The application of surface enhanced infrared absorption (SEIRA) is severely restricted in many fields due to the SEIRA substrates are constructed mainly from expensive noble metals. Therefore, the development of new SEIRA substrates other than the noble metallic ones is very valuable. Here we introduced a new semiconductor SEIRA substrate, the indium tin oxide (ITO) nanoparticles (NPs), to study the SEIRA property. The results demonstrate that the ITO NPs show the SEIRA property and the enhancement is dependent to the doping ratio of the heteroatoms of tin. The ITO NPs with the 5% atomic doping ratio show the highest SEIRA enhancement factor (EF), which is about 24. The limit of detection (LOD) of the 1,1'-dicarboxyferrocene (dcFc) molecule was as low as 10^-5 mol/L. The present study proves that the tin-doped indium oxide can be used as a new and inexpensive semiconductor SEIRA substrate. It also proves that the doped semiconductor NPs have strong potentials for being used as emerging SEIRA substrates.

Development and preliminary validation of infrared spectroscopic device for transdermal assessment of elevated cardiac troponin

Background

The levels of circulating troponin are principally required in addition to electrocardiograms for the effective diagnosis of acute coronary syndrome. Current standard-of-care troponin assays provide a snapshot or momentary view of the levels due to the requirement of a blood draw. This modality further restricts the number of measurements given the clinical context of the patient. In this communication, we present the development and early validation of non-invasive transdermal monitoring of cardiac troponin-I to detect its elevated state.

Methods

Our device relies on infrared spectroscopic detection of troponin-I through the dermis and is tested in stepwise laboratory, benchtop, and clinical studies. Patients were recruited with suspected acute coronary syndrome.

Results

We demonstrate a significant correlation (r = 0.7774, P < 0.001, n = 52 biologically independent samples) between optically-derived data and blood-based immunoassay measurements with and an area under receiver operator characteristics of 0.895, sensitivity of 96.3%, and specificity of 60% for predicting a clinically meaningful threshold for defining elevated Troponin I.

Conclusion

This preliminary work introduces the potential of a bloodless transdermal measurement of troponin-I based on molecular spectroscopy. Further, potential pitfalls associated with infrared spectroscopic mode of inquiry are outlined including requisite steps needed for improving the precision and overall diagnostic value of the device in future studies.

The number one cause of death in the US is heart disease. With 10 million patients visiting the emergency departments in a year with chest pain, 8 million are unrelated to cardiac issues. This places a burden on hospitals leading to suboptimal patient outcomes. In patients with cardiac issues, the time clinicians take to intervene dictates reversible or irreversible heart damage. However, current markers used to test for cardiac issues require blood sampling, limiting access to and frequency of testing. This study introduces a non-invasive cardiac marker measurement device without any form of blood draw, based on measurements taken by a wearable device through the skin. Preliminary studies show high conformance to the standard of care technologies, indicating that the technology has potential to enable more rapid, frequent, accessible and non-invasive detection of cardiac issues such as heart attacks.

Titus et al. develop a technological platform for the non-invasive transdermal measurement of cardiac troponin-I, a marker of myocardial injury. Preliminary testing of their device, which works via infrared spectroscopy, indicates that troponin can be detected with reasonable performance, in the absence of a blood draw.

Absolute frequency referencing in the long wave infrared using a quantum cascade laser frequency comb

Optical frequency combs (OFCs) based on quantum cascade lasers (QCLs) have transformed mid-infrared spectroscopy. However, QCL-OFCs have not yet been exploited to provide a broadband absolute frequency reference. We demonstrate this possibility by performing comb-calibrated spectroscopy at 7.7 µm (1305 cm^-1) using a QCL-OFC referenced to a molecular transition. We obtain 1.5·10^-10 relative frequency stability (100-s integration time) and 3·10^-9 relative frequency accuracy, comparable with state-of-the-art solutions relying on nonlinear frequency conversion. We show that QCL-OFCs can be locked with sub-Hz-level stability to a reference for hours, thus promising their use as metrological tools for the mid-infrared.

Structural Characterization and In Vitro Antioxidant Activity of Metallothionein from Oratosquilla oratoria

We report here the purification of a novel metal-binding protein from Oratosquilla oratoria (O. oratoria MT-1) by gel and ion-exchange chromatography. SDS-PAGE and MALDI-TOF analyses demonstrated that isolated O. oratoria MT-1 was of high purity with a molecular weight of 12.4 kDa. The fluorescence response to SBD-F derivatives revealed that O. oratoria MT-1 contained a large number of sulfhydryl groups, which is a general property of metallothioneins. Zn and Cu metal stoichiometries for O. oratoria MT-1 were 3.97:1 and 0.55:1, respectively. The proportion of cysteine (Cys) residues in the amino acid composition was 32.69%, and aromatic amino acids were absent. The peptide sequence coverage with Macrobrachium rosenbergii calmodulin (accession AOA3S8FSK5) was 60%. Infrared spectroscopy of O. oratoria MT-1 revealed two obvious peaks at absorption frequencies for the amide I band and the amide II band. CD spectra revealed that the secondary structure was mainly composed of random coil (57.6%) and β-sheet (39.9%). An evaluation of in vitro antioxidant activity revealed that isolated O. oratoria MT-1 has strong reducing activities, exhibiting scavenging rates for DPPH and OH of 77.8% and 75.8%, respectively (IC₅₀ values 0.57 mg/mL and 1.1 mg/mL). O. oratoria MT-1 may be used as a functional additive in cosmetics, health foods, and medical products, as well as a reference material for quantitative analysis of metallothionein in such products.

Effectiveness of visible - Near infrared spectroscopy coupled with simulated annealing partial least squares analysis to predict immunoglobulins G, A, and M concentration in bovine colostrum

Visible - near infrared spectroscopy coupled with variable selection using simulated annealing PLS regression was tested to predict immunoglobulin fractions (g/L) of bovine colostrum, namely IgG, IgA and IgM. Immunoglobulins were quantified in 678 samples using the gold standard radial immunodiffusion. Samples were divided in calibration (50%) and validation (50%) datasets. Maximum number of selected variables were limited to 200 and root mean squared error in cross validation (RMSE_CV) was used as loss function. Performance of the final model developed using the calibration dataset was assessed on the validation dataset. Overall, simulated annealing PLS improved validation RMSE_CV compared to ordinary PLS regression by 3% to 17%. The present study demonstrated the effectiveness of the calibration model for accurate quantification of IgG, the most abundant immunoglobulin of bovine colostrum (RMSE_CV = 13.28 g/L; R² = 0.83). These outcomes could be useful to assess colostrum quality intended for animal and human usage.

Analysis and comparison of protein secondary structures in the rachis of avian flight feathers

Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.

Infrared Spectroscopy in Aqueous Solutions: Capabilities and Challenges

Fourier-transform infrared (FTIR) spectroscopy provides rapid, reliable, quantitative, and qualitative analysis of samples in different aggregation states, i.e., gases, thin films, solids, liquids, etc. However, when analyzing aqueous solutions, particular issues associated with the rather pronounced IR absorption characteristics of water appear to interfere with the solute determination. In this review, Fourier-transform infrared spectroscopic techniques and their analytical capabilities for analyzing aqueous solutions are reviewed, and highlight examples are discussed.

Analyzing the Interaction between Anthocyanins and Native or Heat-Treated Whey Proteins Using Infrared Spectroscopy

The color stability of anthocyanins (ACN) has been shown to be improved by interaction with whey proteins (WP). In this study, we explore the ACN–WP interaction using Fourier transform infrared spectroscopy (IR). ACN from purple corn, grape, and black carrot (50 μM) were evaluated. IR spectra (4000–700 cm⁻¹) were collected for native and preheated (40–80 °C) WP (5 mg/mL) and ACN–WP mixtures at pH 7.4. Soft independent modeling of class analogy was used to analyze the IR data. The WP secondary structure changed after heat treatments and after interaction with ACN. As expected, the WP α-helices decreased, and β-sheet increased after heat treatment. The intensities of the WP amide I and II bands decreased after ACN addition, revealing a decrease in the WP α-helix content. Higher preheating temperatures (70–80 °C) resulted in a more disordered WP structure that favored stronger WP–ACN interactions related to amide III changes. Addition of ACN stabilized WP structure due to heat denaturation, but different ACN structures had different binding affinities with WP. WP structure had less change after interaction with ACN with simpler structures. These results increase our understanding of ACN–WP interactions, providing a potential strategy to extend anthocyanin color stability by WP addition.

Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures

Proteins in biological fluids (blood, urine, cerebrospinal fluid) are important biomarkers of various pathological conditions. Protein biomarkers detection and quantification have been proven to be an indispensable diagnostic tool in clinical practice. There is a growing tendency towards using portable diagnostic biosensor devices for point-of-care (POC) analysis based on microfluidic technology as an alternative to conventional laboratory protein assays. In contrast to universally accepted analytical methods involving protein labeling, label-free approaches often allow the development of biosensors with minimal requirements for sample preparation by omitting expensive labelling reagents. The aim of the present work is to review the variety of physical label-free techniques of protein detection and characterization which are suitable for application in micro-fluidic structures and analyze the technological and material aspects of label-free biosensors that implement these methods. The most widely used optical and impedance spectroscopy techniques: absorption, fluorescence, surface plasmon resonance, Raman scattering, and interferometry, as well as new trends in photonics are reviewed. The challenges of materials selection, surfaces tailoring in microfluidic structures, and enhancement of the sensitivity and miniaturization of biosensor systems are discussed. The review provides an overview for current advances and future trends in microfluidics integrated technologies for label-free protein biomarkers detection and discusses existing challenges and a way towards novel solutions.

Rearrangement of protein structures on a gold nanoparticle surface is regulated by ligand adsorption modes

With development of the nanomedicine field and increasing hazards of exposure to nanobiological materials, research on the protein corona is urgently required. In particular, the understanding of the mechanism of structural changes of protein on a nanosurface should be improved. Herein, we focus on exploring the role of ligand adsorption modes (physiosorbed citrates or chemisorbed GSH) in the regulation of conformational rearrangement of three blood proteins (serum albumin, globulin, and fibrinogen) on the surface of gold nanoparticles. Through experimental measurements, protein adsorption features (thermodynamics, kinetics, adsorption orientation, and structural changes) were estimated. Molecular dynamics simulations further indicated that physiosorbed citrates could be gradually peeled off by approaching proteins and that the bare Au surface provided a stronger interface interaction than the chemisorbed GSH layer. Protein structure rearrangements were due to the reduction in protein internal energy, with an increase in H-bond formation involving a decrease in the α-helical content and an increase in the β-sheet content, to offset the high interfacial energy. Rearrangement of protein structures could occur either intramolecularly or intermolecularly. These findings enhanced our understanding of nano-protein interaction in the biological milieu and facilitate biomedical exploration of engineered nanomaterials.

Experimental Treatment of Hazardous Ash Waste by Microbial Consortium Aspergillus niger and Chlorella sp.: Decrease of the Ni Content and Identification of Adsorption Sites by Fourier-Transform Infrared Spectroscopy

Despite the negative impact on the environment, incineration is one of the most commonly used methods for dealing with waste. Besides emissions, the production of ash, which usually shows several negative properties, such as a higher content of hazardous elements or strongly alkaline pH, is problematic from an environmental viewpoint as well. The subject of our paper was the assessment of biosorption of Ni from ash material by a microbial consortium of Chlorella sp. and Aspergillus niger. The solid substrate represented a fraction of particles of size <0.63 mm with a Ni content of 417 mg kg-1. We used a biomass consisting of two different organisms as the sorbent: a non-living algae culture of Chlorella sp. (an autotrophic organism) and the microscopic filamentous fungus A. niger (a heterotrophic organism) in the form of pellets. The experiments were conducted under static conditions as well as with the use of shaker (170 rpm) with different modifications: solid substrate, Chlorella sp. and pellets of A. niger; solid substrate and pellets of A. niger. The humidity-temperature conditions were also changed. Sorption took place under dry and also wet conditions (with distilled water in a volume of 30-50 ml), partially under laboratory conditions at a temperature of 25°C as well as in the exterior. The determination of the Ni content was done using inductively coupled plasma optical emission spectrometry (ICP-OES). The removal of Ni ranged from 13.61% efficiency (Chlorella sp., A. niger with the addition of 30 ml of distilled water, outdoors under static conditions after 48 h of the experiment) to 46.28% (Chlorella sp., A. niger with the addition of 30 ml of distilled water, on a shaker under laboratory conditions after 48 h of the experiment). For the purpose of analyzing the representation of functional groups in the microbial biomass and studying their interaction with the ash material, we used Fourier-transform infrared (FTIR) spectroscopy. We observed that the amount of Ni adsorbed positively correlates with absorbance in the spectral bands where we detect the vibrations of several organic functional groups. These groups include hydroxyl, aliphatic, carbonyl, carboxyl and amide structural units. The observed correlations indicate that, aside from polar and negatively charged groups, aliphatic or aromatic structures may also be involved in sorption processes due to electrostatic attraction. The correlation between absorbance and the Ni content reached a maximum in amide II band (r = 0.9; P < 0.001), where vibrations of the C=O, C-N, and N-H groups are detected. The presented results suggest that the simultaneous use of both microorganisms in biosorption represents an effective method for reducing Ni content in a solid substrate, which may be useful as a partial process for waste disposal.

Comparison between Mid-Infrared (ATR-FTIR) Spectroscopy and Official Analysis Methods for Determination of the Concentrations of Alcohol, SO2, and Total Acids in Wine

The determination of alcohol, SO2, and total acids in wine through conventional laboratory techniques have some limitations related to the amount of the samples, analytical preparation of laboratory staff, and time to carry out the analysis. In recent years, spectroscopic and chromatographic methods have been proposed to determinate simultaneously multiple analytical parameters. The new methods claim the speed of analysis and easy execution. However, they need a validation process that guarantees the reliability of the results to be used in official determinations. This study aimed to evaluate the usefulness of FT-infrared reflectance (FT-IR) to quantify total acid, alcohol, and SO2 concentration in the wines. For this purpose, 156 DOC Italian wines were tested with IR technology, and results were compared to those obtained by official analysis methods. The comparison was performed using two non-parametric statistical methods: the Bland & Altman test and Passing & Bablok regression. Our results showed that the spectrophotometric methods make errors due to interfering contaminants in the sample that can be corrected by blank determination. Therefore, the spectrophotometric methods that use the infrared region of the electromagnetic spectrum can be used by the wine industry and regulators for the wine routine as an alternative to official methodologies.

Ultraviolet/Visible and Near-Infrared Dual Spectroscopic Method for Detection and Quantification of Low-Level Malaria Parasitemia in Whole Blood

The scourge of malaria infection continues to strike hardest against pregnant women and children in Africa and South East Asia. For global elimination, testing methods that are ultrasensitive to low-level ring-staged parasitemia are urgently required. In this study, we used a novel approach for diagnosis of malaria infection by combining both electronic ultraviolet-visible (UV/vis) spectroscopy and near infrared (NIR) spectroscopy to detect and quantify low-level (1-0.000001%) ring-staged malaria-infected whole blood under physiological conditions uisng Multiclass classification using logistic regression, which showed that the best results were achieved using the extended wavelength range, providing an accuracy of 100% for most parasitemia classes. Likewise, partial least-squares regression (PLS-R) analysis showed a higher quantification sensitivity (R² = 0.898) for the extended spectral region compared to UV/vis and NIR (R² = 0.806 and 0.556, respectively). For quantifying different-stage blood parasites, the extended wavelength range was able to detect and quantify all thePlasmodium falciparum accurately compared to testing each spectral component separately. These results demonstrate the potential of a combined UV/vis-NIR spectroscopy to accurately diagnose malaria-infected patients without the need for elaborate sample preparation associated with the existing mid-IR approaches.

Cuticular Lipid Topology on Insect Body Surfaces Studied by Synchrotron Radiation FTIR ATR Microspectroscopy

The cuticular lipid covering the integument of insects is exposed to the environment and involved in a variety of functions offered by insect body surfaces, ranging from protection against the environment, such as the control of water transpiration, the reduction of abrasive damage, and the prevention of pathogen intrusion, to the communication between insects from intraspecific to interspecific interactions. In comparison with the importance of their physiological functions, there is remarkably little information on the structure and physical property of cuticular lipids on insect body surfaces. The lipid layer on the outer exoskeleton is very thin, estimated on the order of 0.01-1 μm or less, and this has led to a lack of practical methodologies for detailed structural analyses. To fill this devoid, we have exploited the characteristics of Fourier transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy, which allows us to conduct a chemical analysis on insect body surfaces and also to investigate depth-dependent structural changes. We have applied a combination of FTIR ATR microspectroscopy with IR radiation provided by a synchrotron facility to obtain in situ two-dimensional (2D) information of the cuticular lipid layer on the surface of the integument. The 2D FTIR spectra measured on the two-spotted cricket and the American cockroach show that the IR bands due to the cuticular lipid, such as CH₂ symmetric and antisymmetric stretch, ν_a(CH₂) and ν_s(CH₂), change in intensity significantly, depending on the location of measurements. As if to keep pace with this, the bands of the amide group for the underlying cuticular layer also change in intensity significantly, although the changes are in the opposite direction; as the lipid bands increase in intensity, the amide band decreases, and vice versa. The ATR spectral analysis, which takes into account the characteristics of the evanescent wave, points out that the lipid layer would vary tens of times in the range of 0.01-1 μm significantly. The ν_a(CH₂) and ν_s(CH₂) bands show frequency shifts, which correlate to some extent with their intensity changes, suggesting that the drastic uneven distribution of the cuticular lipid would be related to the solid-liquid phase separation and also the coarsening of the solid phase domains. The formation of such topological features, significant heterogeneity in the lipid layer thickness, and solid-liquid phase ratios would be accompanied by the partitioning of lipid components according to molecular structures and physicochemical properties. Considering that each lipid component in insect body surface lipids is involved in various physiological roles, the segregation of lipid components during the formation of such heterogeneous structures is thought to have a significant impact on the functionality of the insect body surface.

The Progress of Label-Free Optical Imaging in Alzheimer's Disease Screening and Diagnosis

As the major neurodegenerative disease of dementia, Alzheimer's disease (AD) has caused an enormous social and economic burden on society. Currently, AD has neither clear pathogenesis nor effective treatments. Positron emission tomography (PET) and magnetic resonance imaging (MRI) have been verified as potential tools for diagnosing and monitoring Alzheimer's disease. However, the high costs, low spatial resolution, and long acquisition time limit their broad clinical utilization. The gold standard of AD diagnosis routinely used in research is imaging AD biomarkers with dyes or other reagents, which are unsuitable for in vivo studies owing to their potential toxicity and prolonged and costly process of the U.S. Food and Drug Administration (FDA) approval for human use. Furthermore, these exogenous reagents might bring unwarranted interference to mechanistic studies, causing unreliable results. Several label-free optical imaging techniques, such as infrared spectroscopic imaging (IRSI), Raman spectroscopic imaging (RSI), optical coherence tomography (OCT), autofluorescence imaging (AFI), optical harmonic generation imaging (OHGI), etc., have been developed to circumvent this issue and made it possible to offer an accurate and detailed analysis of AD biomarkers. In this review, we present the emerging label-free optical imaging techniques and their applications in AD, along with their potential and challenges in AD diagnosis.

FTIR based approach to study EnaC mechanosensory functions

The pulmonary epithelial sodium ion channel (ENaC) is gaining importance for its sodium gating and mechanosensitive roles. The mechano functional studies on ENaC suggest direct molecular interactions between the ENaC protein with cytoskeleton microtubules and other extracellular matrix components. Also, in few mechanotransduction studies, ENaC was shown to respond both to membrane stretch as well as cell volume changes. However, the conformational characteristic of ENaC during sodium and mechano gating are yet to be fully elucidated. Thus obtaining ENaC protein conformational spectrum based on Fourier Transform Infrared Radiation (FTIR) spectroscopy in solution will be useful in predicting the nature of conformational changes occurring during any cell volume changes in an epithelial cell. The conformational spectrum looks promising in studying the disease biology of cystic fibrosis (CF) and CF like conditions that arise due to abnormal ion conductance membrane proteins and subsequent frequent fluid retentions. This review article presents the basics of epithelial ENaC protein as a gated mechanosensor and FTIR for developing fluid dynamics of ENaC protein. This can be applied to develop an ENaC based quantum mechanosensor for the prognosis as well as diagnosis of cystic fibrosis (CF) and allied lung diseases.

Highly sensitive crumpled 2D material-based plasmonic biosensors

We propose surface plasmon resonance biosensors based on crumpled graphene and molybdenum disulphide (MoS₂) flakes supported on stretchable polydimethylsiloxane (PDMS) or silicon substrates. Accumulation of specific biomarkers resulting in measurable shifts in the resonance wavelength of the plasmon modes of two-dimensional (2D) material structures, with crumpled structures demonstrating large refractive index shifts. Using theoretical calculations based on the semiclassical Drude model, combined with the finite element method, we demonstrate that the interaction between the surface plasmons of crumpled graphene/MoS₂ layers and the surrounding analyte results in high sensitivity to biomarker driven refractive index shifts, up to 7499 nm/RIU for structures supported on silicon substrates. We can achieve a high figure of merit (FOM), defined as the ratio of the refractive index sensitivity to the full width at half maximum of the resonant peak, of approximately 62.5 RIU^-1. Furthermore, the sensing properties of the device can be tuned by varying crumple period and aspect ratio through simple stretching and integrating material interlayers. By stacking multiple 2D materials in heterostructures supported on the PDMS layer, we produced hybrid plasmon resonances detuned from the PDMS absorbance region allowing higher sensitivity and FOM compared to pure crumpled graphene structures on the PDMS substrates. The high sensitivity and broad mechanical tunability of these crumpled 2D material biosensors considerable advantages over traditional refractive index sensors, providing a new platform for ultrasensitive biosensing.

Enhanced synthesis of succinylated whey protein isolate by pulsed electric field pretreatment

The objective of this study was to investigate the feasibility of pulse electric field (PEF) as a pretreatment for whey protein isolate (WPI) before its succinylation. The degree of succinylation (DS) of WPI increased from 88.31% for native WPI to 93.45% for PEF-pretreated WPI (PWPI, initial pH 10.0) for the same succinic anhydride (SA) to WPI ratio (1:1). Fourier transform infrared spectroscopy and scanning electron microscopy analysis proved the successful succinylation of WPI. For PWPIs, the surface hydrophobicity, exposed sulphydryl, and total sulphydryl decreased, which indicates the occurrence of changes in protein structures with more hydrophilic groups and better protein dispersion. Moreover, PEF may expose more amino acid residues binding sites that are present inside the protein, which is more suitable for succinylation. Therefore, the PEF pretreatment of proteins can improve their efficient use that is expected to play a critical role in succinylation industry.

PARAFAC study of L-cys@CdTe QDs interaction to BSA, cytochrome c and trypsin: An approach through electrostatic and covalent bonds

Utilizing fluorescence spectroscopy, non-covalent and covalent interactions of L-cys@CdTe quantum dots to bovine serum albumin (BSA), cytochrome c and trypsin were investigated. L-cys@CdTe QDs with the emission maximum at 530 nm and an average diameter of 2.6 nm were synthesized in the aqueous medium. Formaldehyde, N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride (EDC) with N-hydroxysuccinimide (NHS), and glutaraldehyde was applied as cross-linkers. In the case of both electrostatic and covalent strategies PARAFAC, as a powerful multi-way chemometrics technique, was utilized to analyze fluorescence excitation-emission (EEM) spectra. For non-covalent and covalent bonding, two and three significant components composed the PARAFAC models. Resolved EEM shows that in the presence of formaldehyde, a new component with an emission peak similar to BSA was obtained. Using EDC-NHS cross-linker, the fluorescence peak of the newly formed component was in a distinct wavelength with similar emission intensity, compared to L-cys@CdTe QDs and BSA. Employing glutaraldehyde, a distinguished component was easily detected at emission wavelengths higher than that of L-cys@CdTe QDs and proteins. It was concluded that the choice of cross-linker is a critical step to create different emission spectra when dealing with nano-bio-conjugations. This study shows that glutaraldehyde cross-linker leads to increase sensitivity, selectivity, and accuracy of protein analysis.

pH-controlled stacking direction of the β-strands in peptide fibrils

Peptides provide a framework for generating functional biopolymers. In this study, the pH-dependent structural changes in the 21-29 fragment peptide of β2-microglobulin (β2m21-29) during self-aggregation, i.e., the formation of an amyloid fibril, were discussed. The β-sheet structures formed during parallel stacking under basic conditions (pH ≥ 7.7) adopted an anti-parallel stacking configuration under acidic conditions (pH ≤ 7.6). The parallel and anti-parallel β-sheets existed separately at the intermediate pH (pH = 7.6-7.7). These results were attributed to the rigidity of the β-sheets in the fibrils, which prevented the stable hydrogen bonding interactions between the parallel and anti-parallel β-sheet moieties. This observed pH dependence was ascribed to two phenomena: (i) the pH-dependent collapse of the β2m21-29 fibrils, which consisted of 16 ± 3 anti-parallel β-sheets containing a total of 2000 β-strands during the deprotonation of the NH3+ group (pKa = 8.0) of the β-strands that occurred within 0.7 ± 0.2 strands of each other and (ii) the subsequent formation of the parallel β-sheets. We propose a framework for a functional biopolymer that could alternate between the two β-sheet structures in response to pH changes.

Mid-IR refractive index sensor for detecting proteins employing an external cavity quantum cascade laser-based Mach-Zehnder interferometer

Novel laser light sources in the mid-infrared region enable new spectroscopy schemes beyond classical absorption spectroscopy. Herein, we introduce a refractive index sensor based on a Mach-Zehnder interferometer and an external-cavity quantum cascade laser that allows rapid acquisition of high-resolution spectra of liquid-phase samples, sensitive to relative refractive index changes down to 10^-7. Dispersion spectra of three model proteins in deuterated solution were recorded at concentrations as low as 0.25 mg mL^-1. Comparison with Kramers-Kronig-transformed Fourier transform infrared absorbance spectra revealed high conformance, and obtained figures of merit compare well with conventional high-end FTIR spectroscopy. Finally, we performed partial least squares-based multivariate analysis of a complex ternary protein mixture to showcase the potential of dispersion spectroscopy utilizing the developed sensor to tackle complex analytical problems. The results indicate that laser-based dispersion sensing can be successfully used for qualitative and quantitative analysis of proteins.

Review: Detection and quantification of proteins in human urine

Extensive medical research showed that patients, with high protein concentration in urine, have various kinds of kidney diseases, referred to as proteinuria. Urinary protein biomarkers are useful for diagnosis of many health conditions – kidney and cardio vascular diseases, cancers, diabetes, infections. This review focuses on the instrumental quantification (electrophoresis, chromatography, immunoassays, mass spectrometry, fluorescence spectroscopy, the infrared spectroscopy, and Raman spectroscopy) of proteins (the most of all albumin) in human urine matrix. Different techniques provide unique information on what constituents of the urine are. Due to complex nature of urine, a separation step by electrophoresis or chromatography are often used for proteomics study of urine. Mass spectrometry is a powerful tool for the discovery and the analysis of biomarkers in urine, however, costs of the analysis are high, especially for quantitative analysis. Immunoassays, which often come with fluorescence detection, are major qualitative and quantitative tools in clinical analysis. While Infrared and Raman spectroscopies do not give extensive information about urine, they could become important tools for the routine clinical diagnostics of kidney problems, due to rapidness and low-cost. Thus, it is important to review all the applicable techniques and methods related to urine analysis. In this review, a brief overview of each technique's principle is introduced. Where applicable, research papers about protein determination in urine are summarized with the main figures of merits, such as the limit of detection, the detectable range, recovery and accuracy, when available.

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Urinary protein biomarkers are useful for diagnosis of many conditions: kidney and cardio vascular diseases, cancers.

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Liquid chromatography – mass spectroscopy is a powerful tool for urine proteomics, but used mostly in science.

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Immunoassays are widely used in both clinical and bio-analytical laboratories.

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IR and Raman spectroscopies are promising tools for diagnostics of urine due to low-cost and rapidness.

An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

Computational chemistry has become a central tool in spectroscopic studies in most of chemical science. The quality of a calculated vibrational spectrum is commonly expressed as the deviation of the peak position from the experimental reference. With the increasing application of vibrational spectroscopy to complex (biological) systems, this is likely not sustainable. Here we present a quality measure for theoretical vibrational spectra based on matching the spectra to a reference database with the help of correlation coefficients. This approach can easily be applied to large sets of data and complex spectra without easily identifiable peak positions. We demonstrate this on a database of infrared spectra of 670 compounds using six different theoretical (DFT and force field) methods. Most importantly, it is intuitively understandable by both theoreticians and experimentalists.

Reagent-free total protein quantification of intact extracellular vesicles by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy

Extracellular vesicles (EVs) are lipid bilayer–bounded particles that are actively synthesized and released by cells. The main components of EVs are lipids, proteins, and nucleic acids and their composition is characteristic to their type and origin, and it reveals the physiological and pathological conditions of the parent cells. The concentration and protein composition of EVs closely relate to their functions; therefore, total protein determination can assist in EV-based diagnostics and disease prognosis. Here, we present a simple, reagent-free method based on attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy to quantify the protein content of EV samples without any further sample preparation. After calibration with bovine serum albumin, the protein concentration of red blood cell–derived EVs (REVs) were investigated by ATR-FTIR spectroscopy. The integrated area of the amide I band was calculated from the IR spectra of REVs, which was proportional to the protein quantity in the sample‚ regardless of its secondary structure. A spike test and a dilution test were performed to determine the ability to use ATR-FTIR spectroscopy for protein quantification in EV samples, which resulted in linearity with R² values as high as 0.992 over the concentration range of 0.08 to 1 mg/mL. Additionally, multivariate calibration with the partial least squares (PLS) regression method was carried out on the bovine serum albumin and EV spectra. R² values were 0.94 for the calibration and 0.91 for the validation set. The results indicate that ATR-FTIR measurements provide a reliable method for reagent-free protein quantification of EVs.

Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

Infrared spectroscopy can provide significant insight into the structures and dynamics of molecules of all sizes. The information that is contained in the spectrum is, however, often not easily extracted without the aid of theoretical calculations or simulations. We present here the calculation of the infrared spectra of a database of 703 gas phase compounds with four different force fields (CGenFF, GAFF-BCC, GAFF-ESP, and OPLS) using normal-mode analysis. Modern force fields increasingly use virtual sites to describe, e.g., lone-pair electrons or the σ-holes on halogen atoms. This requires some adaptation of code to perform normal-mode analysis of such compounds, the implementation of which into the GROMACS software is briefly described as well. For the quantitative comparison of the obtained spectra with experimental reference data, we discuss the application of two different statistical correlation coefficients, Pearson and Spearman. The advantages and drawbacks of the different methods of comparison are discussed, and we find that both methods of comparison give the same overall picture, showing that present force field methods cannot match the performance of quantum chemical methods for the calculation of infrared spectra.

Infrared biomarkers of impaired cystic fibrosis transmembrane regulator protein biogenesis

The mid-infrared (IR) spectra of human cystic fibrosis (CF) cells acquired by Fourier transform infrared microspectroscopy were compared with those of non-CF cells. Within the 1700 to 1480 cm^-1 spectral domain of amides, unsupervised explorative principal component analysis identified a few variables reflecting quantitative and qualitative vibrations arising from protein secondary structures and amino acid side chains. Their pattern reflected α-helix to β-sheet transitions in bronchial epithelial cells and in immortalized peripheral blood mononuclear cells from patients with R1162X missense or in-frame F508del mutations in the cystic fibrosis transmembrane regulator gene (Cftr). Similar transitions have been described in IR spectra of cells, tissues and body fluids of patients affected with some neurodegenerative diseases characterized by the accumulation of misfolded protein aggregates. The variables pattern was able to distinguish CF cells from non-CF cells and was modified by molecular compounds used to rescue the unbalanced folding process of mutated cystic fibrosis transmembrane regulator (CFTR) anion channel. To our knowledge, this is the first experimental evidence of spectroscopic biomarkers of the impaired biogenesis of CFTR by IR microanalysis in the spectra of human CF bronchial epithelial and lymphoblastoid cells.

Infrared attenuated total reflection and 2D fluorescence spectroscopy for the discrimination of differently aggregated monoclonal antibodies

Antibody aggregates may occur as undesirable by-products during the manufacturing process of biopharmaceutical proteins since parameters such as pH, temperature, ionic strength, protein concentration, oxygen, and shear forces can lead to aggregate formation. These aggregates have to be detected, quantified and removed cost extensively, since they may reduce the safety and efficacy of the product. Protein aggregates can range from small soluble dimers up to large visible agglomerates. Differently aggregated antibody samples were characterized for their soluble and insoluble aggregate concentration by size exclusion chromatography and fluorescence microscopy, respectively. The samples exhibited a high diversity of protein aggregates, which varied in amount, size and shape. For secondary structure characterization, infrared attenuated total reflection (IR-ATR) and two-dimensional fluorescence (2D-FL) spectroscopy were applied. Using direct spectroscopy, only marginal differences of various antibody aggregates were evident. However, using appropriate chemometric strategies, the evaluation of IR-ATR and 2D-FL spectra yielded the discrimination of differently aggregated antibody samples with yet unprecedented precision.

Waveguide Absorption Spectroscopy of Bovine Serum Albumin in the Mid-Infrared Fingerprint Region

Protein sensing in biological fluids provides important information to diagnose many clinically relevant diseases. Mid-infrared (MIR) absorption spectroscopy of bovine serum albumin (BSA) is experimentally demonstrated on a germanium on silicon (GOS) waveguide in the 1900-1000 cm^-1 (5.3-10.0 μm) region of the MIR. GOS waveguides were shown to guide light up to a wavelength of 12.9 μm. The waveguide absorption spectrum of water, showing molecular bending vibrations, was obtained experimentally and compared with a theoretical model showing good agreement. Measurement of a concentration series of BSA protein in phosphate buffered saline (PBS) from 0.1 mg/mL to 100 mg/mL was performed on the waveguide using filter paper as a flow strip, and the amide I, II, and III peaks were observed and quantified.

A MEMS-Based Quad-Wavelength Hybrid Plasmonic-Pyroelectric Infrared Detector

Spectrally selective detection is of crucial importance for diverse modern spectroscopic applications such as multi-wavelength pyrometry, non-dispersive infrared gas sensing, biomedical analysis, flame detection, and thermal imaging. This paper reports a quad-wavelength hybrid plasmonic-pyroelectric detector that exhibited spectrally selective infrared detection at four wavelengths-3.3, 3.7, 4.1, and 4.5 μm. The narrowband detection was achieved by coupling the incident infrared light to the resonant modes of the four different plasmonic perfect absorbers based on Al-disk-array placed on a Al₂O₃-Al bilayer. These absorbers were directly integrated on top of a zinc oxide thin film functioning as a pyroelectric transducer. The device was fabricated using micro-electromechanical system (MEMS) technology to optimize the spectral responsivity. The proposed detector operated at room temperature and exhibited a responsivity of approximately 100-140 mV/W with a full width at half maximum of about 0.9-1.2 μm. The wavelength tunability, high spectral resolution, compactness and robust MEMS-based platform of the hybrid device demonstrated a great advantage over conventional photodetectors with bandpass filters, and exhibited impressive possibilities for miniature multi-wavelength spectroscopic devices.