Mid-infrared spectroscopy for protein analysis: potential and challenges

RNA targeting by an anthracycline drug: spectroscopic and in silico evaluation of epirubicin interaction with tRNA

Anthracyclines are putative anticancer agents used to treat a wide range of cancers. Among these anthracyclines, epirubicin is derived from the doxorubicin by the subtle difference in the orientation of C4-hydroxyl group at sugar molecule. Epirubicin has great significance as it has propitious anticancer potential with lesser cardiotoxicity and faster elimination from the body. The present study is done to understand the molecular aspect of epirubicin binding to tRNA. We have used various spectroscopic techniques like Fourier transform infrared spectroscopy (FTIR), absorption spectroscopy and circular dichroism to illustrate the binding sites, the extent of binding and conformational changes associated with tRNA after interacting with epirubicin. From infrared studies, we infer that epirubicin interacts with guanine and uracil bases of tRNA. Results obtained from infrared and CD studies suggest that epirubicin complexation with tRNA does not result in any conformational change in tRNA structure. Binding constant (2.1 × 10³ M^-1) calculated from the absorbance data illustrates that epirubicin has a weak interaction with tRNA molecule. These spectroscopic results like the binding site of epirubicin and binding energy of epirubicin-tRNA complex were also verified by the molecular docking. Results of the present study provide information that aids in the development of efficient RNA targeted drugs from the existing drugs by certain chemical modification in their structure resulting in lesser side effects and better efficacy.Communicated by Ramaswamy H. Sarma.

Gold-nanostar-based SERS substrates for studying protein aggregation processes

Aggregation of proteins has been related to some neurodegenerative diseases such as Alzheimer's and Parkinson's among others. Raman spectroscopy is a useful technique for the investigation of protein conformation and of changes in their secondary structure. In this study, a surface enhanced Raman spectroscopy (SERS) substrate based on the immobilization of plasmonic gold nanostars on a glass slide via silanization of the surface has been prepared and characterized. Gold nanostars were synthesized via a seed-growth method using gold nanoparticles as seeds obtained via stainless steel as the reducing agent. The plasmonic substrate provided an enhancement of 5.7 × 102 fold, as shown for the Raman signal of crystal violet. Using this SERS-active substrate, the investigation of aggregation processes of bovine serum albumin (BSA) and myoglobin proteins upon temperature and solvent modification has been enabled with enhanced sensitivity. Both curve fitting and deconvolution of the amide I band, as well as 2D correlation analysis, were employed for the evaluation of the changes in the SERS spectra of the protein samples. The amide I band within the SERS spectra of the BSA protein revealed a decrease in the α-helix structures within the secondary structure of the protein while the presence of β-sheet structures increased with temperature and solvent concentration.

Chem/bio sensing with non-classical light and integrated photonics

Modern quantum technology currently experiences extensive advances in applicability in communications, cryptography, computing, metrology and lithography. Harnessing this technology platform for chem/bio sensing scenarios is an appealing opportunity enabling ultra-sensitive detection schemes. This is further facilliated by the progress in fabrication, miniaturization and integration of visible and infrared quantum photonics. Especially, the combination of efficient single-photon sources together with waveguiding/sensing structures, serving as active optical transducer, as well as advanced detector materials is promising integrated quantum photonic chem/bio sensors. Besides the intrinsic molecular selectivity and non-destructive character of visible and infrared light based sensing schemes, chem/bio sensors taking advantage of non-classical light sources promise sensitivities beyond the standard quantum limit. In the present review, recent achievements towards on-chip chem/bio quantum photonic sensing platforms based on N00N states are discussed along with appropriate recognition chemistries, facilitating the detection of relevant (bio)analytes at ultra-trace concentration levels. After evaluating recent developments in this field, a perspective for a potentially promising sensor testbed is discussed for reaching integrated quantum sensing with two fiber-coupled GaAs chips together with semiconductor quantum dots serving as single-photon sources.

Mid-infrared broadband superluminescent light emitter arrays

Mid-infrared (MIR) room-temperature (RT) and continuous-wave (CW) broadband quantum cascade superluminescent light emitters (QCSLEs) have emerged as ideal broadband light sources for a number of applications of biomedical imaging, security inspection, and gas detection. It is quite challenging to attain a RT-CW output power up to milliwatt level due to the very low efficiency of the spontaneous emission in the intersubband transitions in QCSLEs. In this work, for the first time to the best of our knowledge, a compact light emitter array is realized by integrating several single emitters exhibiting a very high RT-CW power of 2.4 mW, which is attributed to the sufficient low reflectivity provided by the waveguide structure that includes three sections with a short straight part adjacent to a tilted stripe and to a J-shaped waveguide, and the two-phonon resonance QC active structure. This advancement is certainly a big step forward to the applications of broadband light sources towards MIR photonics.

Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions

In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B₂₂, and the diffusion interaction coefficient, k_D. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.

Polycrystalline Diamond Thin-Film Waveguides for Mid-Infrared Evanescent Field Sensors

Photonic design and optimization of thin-film polycrystalline diamond waveguides are shown, serving as advanced evanescent field transducers in the mid-infrared fingerprint regime (2000-909 cm^-1; 5-11 μm). Design constraints inherent to optical/system considerations and the material were implemented in a finite element method (FEM)-based simulation method that allowed three-dimensional modeling of the overall structure. Thus, lateral mode confinement, attenuation in the direction of radiation propagation, and physical resilience were evaluated. In a final step, the designed structures were fabricated, and their utility in combination with a broadly tunable external cavity quantum cascade laser for chemical sensing of a liquid phase analyte was demonstrated.

Room-temperature quantum cascade superluminescent light emitters with wide bandwidth and high temperature stability

The realization of room-temperature (RT) mid-infrared (MIR) broadband light sources is fundamentally interesting and highly desirable for a number of applications. Recently, superluminescent light emitters (SLEs) based on quantum cascade (QC) structures have emerged as excellent candidates among mid-infrared broadband light sources. However, it is challenging to achieve RT-QCSLEs due to the very low efficiency of the spontaneous emission in the intersubband transitions. Here, we demonstrate the realization of a set of ~5 μm RT-SLEs under continuous wave (CW) or quasi-CW (10% duty circle) operation by using a two-phonon resonant QC active region and monolithic integrated waveguide structures. In addition, with the design of an inclined tapered cavity, the SLEs exhibit high milliwatt power, large spectral width of more than 200 cm^-1 and good temperature characteristic. These demonstrated results are believed to be a big step forward to the applications of broadband MIR semiconductor light sources.

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.

Near-infrared and mid-infrared semiconductor broadband light emitters

Semiconductor broadband light emitters have emerged as ideal and vital light sources for a range of biomedical sensing/imaging applications, especially for optical coherence tomography systems. Although near-infrared broadband light emitters have found increasingly wide utilization in these imaging applications, the requirement to simultaneously achieve both a high spectral bandwidth and output power is still challenging for such devices. Owing to the relatively weak amplified spontaneous emission, as a consequence of the very short non-radiative carrier lifetime of the inter-subband transitions in quantum cascade structures, it is even more challenging to obtain desirable mid-infrared broadband light emitters. There have been great efforts in the past 20 years to pursue high-efficiency broadband optical gain and very low reflectivity in waveguide structures, which are two key factors determining the performance of broadband light emitters. Here we describe the realization of a high continuous wave light power of >20 mW and broadband width of >130 nm with near-infrared broadband light emitters and the first mid-infrared broadband light emitters operating under continuous wave mode at room temperature by employing a modulation p-doped InGaAs/GaAs quantum dot active region with a 'J'-shape ridge waveguide structure and a quantum cascade active region with a dual-end analogous monolithic integrated tapered waveguide structure, respectively. This work is of great importance to improve the performance of existing near-infrared optical coherence tomography systems and describes a major advance toward reliable and cost-effective mid-infrared imaging and sensing systems, which do not presently exist due to the lack of appropriate low-coherence mid-infrared semiconductor broadband light sources.

High-resolution spectral analysis of ammonia near 6.2 μm using a cw EC-QCL coupled with cavity ring-down spectroscopy

High-resolution cavity ring-down spectra of ammonia near 6.2 μm for trace gas sensing and biomedical applications.

Analysis of human menisci degeneration via infrared attenuated total reflection spectroscopy

Degeneration of human meniscal tissue induces impairment of normal knee functions, and is a highly relevant etiology of knee joint tears and osteoarthritis.

Mass spectrometric characterization of protein structures and protein complexes in condensed and gas phase

Proteins are essential for almost all physiological processes of life. They serve a myriad of functions which are as varied as their unique amino acid sequences and their corresponding three-dimensional structures. To fulfill their tasks, most proteins depend on stable physical associations, in the form of protein complexes that evolved between themselves and other proteins. In solution (condensed phase), proteins and/or protein complexes are in constant energy exchange with the surrounding solvent. Albeit methods to describe in-solution thermodynamic properties of proteins and of protein complexes are well established and broadly applied, they do not provide a broad enough access to life-science experimentalists to study all their proteins' properties at leisure. This leaves great desire to add novel methods to the analytical biochemist's toolbox. The development of electrospray ionization created the opportunity to characterize protein higher order structures and protein complexes rather elegantly by simultaneously lessening the need of sophisticated sample preparation steps. Electrospray mass spectrometry enabled us to translate proteins and protein complexes very efficiently into the gas phase under mild conditions, retaining both, intact protein complexes, and gross protein structures upon phase transition. Moreover, in the environment of the mass spectrometer (gas phase, in vacuo), analyte molecules are free of interactions with surrounding solvent molecules and, therefore, the energy of inter- and intramolecular forces can be studied independently from interference of the solvating environment. Provided that gas phase methods can give information which is relevant for understanding in-solution processes, gas phase protein structure studies and/or investigations on the characterization of protein complexes has rapidly gained more and more attention from the bioanalytical scientific community. Recent reports have shown that electrospray mass spectrometry provides direct access to six prime protein complex properties: stabilities, compositions, binding surfaces (epitopes), disassembly processes, stoichiometries, and thermodynamic parameters.

Nanoplasmonic mid-infrared biosensor for in vitro protein secondary structure detection

Plasmonic nanoantennas offer new applications in mid-infrared (mid-IR) absorption spectroscopy with ultrasensitive detection of structural signatures of biomolecules, such as proteins, due to their strong resonant near-fields. The amide I fingerprint of a protein contains conformational information that is greatly important for understanding its function in health and disease. Here, we introduce a non-invasive, label-free mid-IR nanoantenna-array sensor for secondary structure identification of nanometer-thin protein layers in aqueous solution by resolving the content of plasmonically enhanced amide I signatures. We successfully detect random coil to cross β-sheet conformational changes associated with α-synuclein protein aggregation, a detrimental process in many neurodegenerative disorders. Notably, our experimental results demonstrate high conformational sensitivity by differentiating subtle secondary-structural variations in a native β-sheet protein monolayer from those of cross β-sheets, which are characteristic of pathological aggregates. Our nanoplasmonic biosensor is a highly promising and versatile tool for in vitro structural analysis of thin protein layers.

Surface enhanced infrared absorption spectroscopy based on gold nanostars and spherical nanoparticles

Plasmonic anisotropic nanoparticles possess a number of hot spots on their surface due to the presence of sharp edges, tips or vertices, leading to a high electric field strength surrounding the nanostructures. In this paper, we explore different plasmonic nanostructures, including anisotropic gold nanostars (AuNSts) and spherical gold nanoparticles, in surface-enhanced infrared absorption spectroscopy (SEIRAS) in an attenuated total reflection (ATR) configuration. In our experiments, we observed up to 10-times enhancement of the infrared (IR) absorption of thioglycolic acid (TGA) and up to 2-times enhancement of signals for bovine serum albumin (BSA) protein on plasmonic nanostructure-based films deposited on a silicon (Si) internal reflection element (IRE) compared to bare Si IRE. The dependence of the observed enhancement on the amount of AuNSts present at the surface of the IRE has been demonstrated. Quantitative studies with both, TGA and BSA were performed, observing that the SEIRA signal can be correlated to the concentration of analyte molecules present within the evanescent field. The calibration curves in the presence of the AuNSts showed enhanced sensitivity as compared with the bare Si IRE. We finally compare efficiencies of anisotropic AuNSts and spherical citrate-capped and "bare" laser-synthesized gold nanoparticles as SEIRAS substrates for the detection of TGA and BSA. The signal obtained from AuNSts was at least 2 times higher for TGA molecules in comparison with spherical gold nanoparticles, which was explained by a more efficient generation of hot spots on anisotropic surface due to the presence of sharp edges, tips or vertices, leading to a high electric field strength surrounding the AuNSts.

Recent advances in hybrid measurement methods based on atomic force microscopy and surface sensitive measurement techniques

This review summaries the recent progress of the combination of optical and non-optical surface sensitive techniques with the atomic force microscopy.