Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins

Combined In Silico and In Vitro Study to Reveal the Structural Insights and Nucleotide-Binding Ability of the Transcriptional Regulator PehR from the Phytopathogen Ralstonia solanacearum

The transcriptional regulator PehR regulates the synthesis of the extracellular plant cell wall-degrading enzyme polygalacturonase, which is essential in the bacterial wilt of plants caused by one of the most devastating plant phytopathogens, Ralstonia solanacearum. The bacterium has a wide global distribution infecting many different plant species, resulting in massive agricultural and economic losses. Because the PehR molecular structure has not yet been determined and the structural consequences of PehR on ligand binding have not been thoroughly investigated, we have used an in silico approach combined with in vitro experiments for the first time to characterize the PehR regulator from a local isolate (Tezpur, Assam, India) of the phytopathogenic bacterium R. solanacearum F1C1. In this study, an in silico approach was employed to model the 3D structure of the PehR regulator, followed by the binding analysis of different ligands against this regulatory protein. Molecular docking studies suggest that ATP has the highest binding affinity for the PehR regulator. By using molecular dynamics (MD) simulation analysis, involving root-mean-square deviation, root-mean-square fluctuations, hydrogen bonding, radius of gyration, solvent-accessible surface area, and principal component analysis, it was possible to confirm the sudden conformational changes of the PehR regulator caused by the presence of ATP. We used an in vitro approach to further validate the formation of the PehR-ATP complex. In this approach, recombinant DNA technology was used to clone, express, and purify the gene encoding the PehR regulator from R. solanacearum F1C1. Purified PehR was used in ATP-binding experiments using fluorescence spectroscopy and Fourier transform infrared spectroscopy, the outcomes of which showed a potent binding to ATP. The putative PehR-ATP-binding analysis revealed the importance of the amino acids Lys190, Glu191, Arg192, Arg375, and Asp378 for the ATP-binding process, but further study is required to confirm this. It will be simpler to comprehend the catalytic mechanisms of a crucial PehR regulator process in R. solanacearum with the aid of the ATP-binding process hints provided by these structural biology applications.

Scanning Tunneling Microscopy Study of Lipoic Acid, Mannose, and cRGD@AuNPs Conjugates

The functionalization of AuNPs with different biological elements was achieved to investigate their possibility in biomedical applications such as drug delivery, vaccine development, sensing, and imaging. Biofunctionalized AuNPs are pursued for applications such as drug delivery, vaccine development, sensing, and imaging. In this study, AuNPs with diameters of 20 nm were functionalized with lipoic acid, mannose, or the cRGD peptide. By using UV-vis spectroscopy, Fourier transform infrared spectroscopy, dynamic light scattering, transmission electron microscopy, and scanning tunneling microscopy techniques, we showed that AuNPs can be functionalized by these biomolecules in a reliable way to obtain conjugates to explore potential biomedical applications. In particular, we demonstrate that the STM technique can be employed to analyze biofunctionalized AuNPs, and the obtained information can be valuable in the design of biomedical applications.

Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy

Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.

Crowding alters F-actin secondary structure and hydration

Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin's secondary structure, leading to a decrease in β-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbed α-helices and nearly "locked" β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG.

Purification and fractionation of phycobiliproteins from Arthrospira platensis and Corallina officinalis with evaluating their biological activities

Phycobiliproteins (PBPs) are a class of water-soluble pigments with a variety of biological functions that are present in red macroalgae and cyanobacterial species. The crude forms of phycocyanin (C-PC) from the blue green alga Arthrospira platensis and allophycocyanin (APC) from the red macroalga Corallina officinalis were extracted and purified by ammonium sulphate precipitation, anion exchange chromatography, and size exclusion chromatography methods, respectively. The obtained C-PC and APC from A. platensis and C. officinalis were 0.31 mg/mL and 0.08 mg/mL, respectively, with molecular masses of "17.0 KDa and 19.0 KDa" and "15.0 KDa and 17.0 KDa" corresponding to α and β subunits, respectively. FT-IR was used to characterize the purified APC and C-PC in order to look into their structures. Highly purified extracts (A620/A280 > 4.0) were obtained from subtractions' PC3 and PC4 that were tested for their biological activities. APC and C-PC crude extracts plus their fractions exhibited potent anti-oxidant in different ratios by using three techniques. PC1 showed high anti-inflammatory (75.99 and 74.55%) and anti-arthritic (78.89 and 76.92%) activities for C. officinalis and A. platensis, respectively compared with standard drugs (72.02 and 71.5%). The methanolic and water extracts of both species showed greater antibacterial efficacy against Gram +ve than Gram -ve marine bacteria. Our study shed light on the potential medical uses of C-PC and APC extracted from the tested species as natural substances in a variety of foods and drugs. Further investigations are required to explore the diverse chemical natures of distinct PBPs from different cyanobacteria and red algae because their amino acid sequences vary among different algal species.

Kinetic control in amyloid polymorphism: Different agitation and solution conditions promote distinct amyloid polymorphs of alpha-synuclein

Aggregation of neuronal protein α-synuclein is implicated in synucleinopathies, including Parkinson's disease. Despite abundant in vitro studies, the mechanism of α-synuclein assembly process remains ambiguous. In this work, α-synuclein aggregation was induced by its constant mixing in two separate modes, either by agitation in a 96-well microplate reader (MP) or in microcentrifuge tubes using a shaker incubator (SI). Aggregation in both modes occurred through a sigmoidal growth pattern with a well-defined lag, growth, and saturation phase. The end-stage MP- and SI-derived aggregates displayed distinct differences in morphological, biochemical, and spectral signatures as discerned through AFM, proteinase-K digestion, FTIR, Raman, and CD spectroscopy. The MP-derived aggregates showed irregular morphology with a significant random coil conformation, contrary to SI-derived aggregates, which showed typical β-sheet fibrillar structures. The end-stage MP aggregates convert to β-rich SI-like aggregates upon 1) seeding with SI-derived aggregates and 2) agitating in SI. We conclude that end-stage MP aggregates were in a kinetically trapped conformation, whose kinetic barrier was bypassed upon either seeding by SI-derived fibrils or shaking in SI. We further show that MP-derived aggregates that form in the presence of sorbitol, an osmolyte, displayed a β-rich signature, indicating that the preferential exclusion effect of osmolytes helped overcome the kinetic barrier. Our findings help in unravelling the kinetic origin of different α-synuclein aggregated polymorphs (strains) that encode diverse variants of synucleinopathies. We demonstrate that kinetic control shapes the polymorphic landscape of α-synuclein aggregates, both through de novo generation of polymorphs, and by their interconversion.

Underwater Bonding with a Biobased Adhesive from Tannic Acid and Zein Protein

Herein are presented several adhesive formulations made from zein protein and tannic acid that can bind to a wide range of surfaces underwater. Higher performance comes from more tannic acid than zein, whereas dry bonding required the opposite case of more zein than tannic acid. Each adhesive works best in the environment that it was designed and optimized for. We show underwater adhesion experiments done on different substrates and in different waters (sea water, saline solution, tap water, deionized water). Surprisingly, the water type does not influence the performance to a great deal but the substrate type does. An additional unexpected result was bond strength increasing over time when exposed to water, contradicting general experiments of working with glues. Initial adhesion underwater was stronger compared to benchtop adhesion, suggesting that water helps to make the glue stick. Temperature effects were determined, indicating maximum bonding at about 30 °C and then another increase at higher temperatures. Once the adhesive was placed underwater, a protective skin formed on the surface, keeping water from entering the rest of the material immediately. The shape of the adhesive could be manipulated easily and, once in place, the skin could be broken to induce faster bond formation. Data indicated that underwater adhesion was predominantly induced by tannic acid, cross-linking within the bulk for adhesion and to the substrate surfaces. The zein protein provided a less polar matrix that helped to keep the tannic acid molecules in place. These studies provide new plant-based adhesives for working underwater and for creating a more sustainable environment.

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.

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.

Recent development of surface-enhanced Raman scattering for biosensing

Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented.

The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins

Over the last thirty years the unfolded state of proteins has attracted considerable interest owing to the discovery of intrinsically disordered proteins which perform a plethora of functions despite resembling unfolded proteins to a significant extent. Research on both, unfolded and disordered proteins has revealed that their conformational properties can deviate locally from random coil behavior. In this context results from work on short oligopeptides suggest that individual amino acid residues sample the sterically allowed fraction of the Ramachandran plot to a different extent. Alanine has been found to exhibit a peculiarity in that it has a very high propensity for adopting polyproline II like conformations. This Perspectives article reviews work on short peptides aimed at exploring the Ramachandran distributions of amino acid residues in different contexts with experimental and computational means. Based on the thus provided overview the article discussed to what extent short peptides can serve as tools for exploring unfolded and disordered proteins and as benchmarks for the development of a molecular dynamics force field.

Prediction of detailed blood metabolic profile using milk infrared spectra and machine learning methods in dairy cattle

The adoption of preventive management decisions is crucial to dealing with metabolic impairments in dairy cattle. Various serum metabolites are known to be useful indicators of the health status of cows. In this study, we used milk Fourier-transform mid-infrared (FTIR) spectra and various machine learning (ML) algorithms to develop prediction equations for a panel of 29 blood metabolites, including those related to energy metabolism, liver function/hepatic damage, oxidative stress, inflammation/innate immunity, and minerals. For most traits, the data set comprised observations from 1,204 Holstein-Friesian dairy cows belonging to 5 herds. An exception was represented by β-hydroxybutyrate prediction, which contained observations from 2,701 multibreed cows pertaining to 33 herds. The best predictive model was developed using an automatic ML algorithm that tested various methods, including elastic net, distributed random forest, gradient boosting machine, artificial neural network, and stacking ensemble. These ML predictions were compared with partial least squares regression, the most commonly used method for FTIR prediction of blood traits. Performance of each model was evaluated using 2 cross-validation (CV) scenarios: 5-fold random (CV_r) and herd-out (CV_h). We also tested the best model's ability to classify values precisely in the 2 extreme tails, namely, the 25th (Q25) and 75th (Q75) percentiles (true-positive prediction scenario). Compared with partial least squares regression, ML algorithms achieved more accurate performance. Specifically, elastic net increased the R² value from 5% to 75% for CV_r and 2% to 139% for CV_h, whereas the stacking ensemble increased the R² value from 4% to 70% for CV_r and 4% to 150% for CV_h. Considering the best model, with the CV_r scenario, good prediction accuracies were obtained for glucose (R² = 0.81), urea (R² = 0.73), albumin (R² = 0.75), total reactive oxygen metabolites (R² = 0.79), total thiol groups (R² = 0.76), ceruloplasmin (R² = 0.74), total proteins (R² = 0.81), globulins (R² = 0.87), and Na (R² = 0.72). Good prediction accuracy in classifying extreme values was achieved for glucose (Q25 = 70.8%, Q75 = 69.9%), albumin (Q25 = 72.3%), total reactive oxygen metabolites (Q25 = 75.1%, Q75 = 74%), thiol groups (Q75 = 70.4%), total proteins (Q25 = 72.4%, Q75 = 77.2.%), globulins (Q25 = 74.8%, Q75 = 81.5%), and haptoglobin (Q75 = 74.4%). In conclusion, our study shows that FTIR spectra can be used to predict blood metabolites with relatively good accuracy, depending on trait, and are a promising tool for large-scale monitoring.

Despite their structural similarities, the cytosolic isoforms of human Hsp90 show different behaviour in thermal unfolding due to their conformation: An FTIR study

Heat shock proteins 90 (Hsp90) are chaperones that promote the proper folding of other proteins under high temperature stress situations. Hsp90s are highly conserved and ubiquitous proteins, and in mammalian cells, they are localized in the cytoplasm, endoplasmic reticulum, and mitochondria. Cytoplasmic Hsp90 are named Hsp90α and Hsp90β and differ mainly in their expression pattern: Hsp90α is expressed under stress conditions, while Hsp90β is a constitutive protein. Structurally, both share the same characteristics by presenting three well-conserved domains, one of which, the N-terminal domain, has a binding site for ATP to which various drugs targeting this protein, including radicicol, can bind. The protein is mainly found in dimeric form and adopts different conformations depending on the presence of ligands, co-chaperones and client proteins. In this study, some aspects of structure and thermal unfolding of cytoplasmic human Hsp90 were analysed by infrared spectroscopy. The effect on Hsp90β of binding with a non-hydrolysable ATP analogue and radicicol was also examined. The results obtained showed that despite the high similarity in secondary structure the two isoforms exhibit substantial differences in their behaviour during thermal unfolding, as Hsp90α exhibits higher thermal stability, slower denaturation process and different event sequence during unfolding. Ligand binding strongly stabilizes Hsp90β and slightly modifies the secondary structure of the protein as well. Most likely, these structural and thermostability characteristics are closely related to the conformational cycling of the chaperone and its propensity to exist in monomer or dimer form.

Structural polymorphism of the low-complexity C-terminal domain of TDP-43 amyloid aggregates revealed by solid-state NMR

Aberrant aggregation of the transactive response DNA-binding protein (TDP-43) is associated with several lethal neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Cytoplasmic neuronal inclusions of TDP-43 are enriched in various fragments of the low-complexity C-terminal domain and are associated with different neurotoxicity. Here we dissect the structural basis of TDP-43 polymorphism using magic-angle spinning solid-state NMR spectroscopy in combination with electron microscopy and Fourier-transform infrared spectroscopy. We demonstrate that various low-complexity C-terminal fragments, namely TDP-13 (TDP-43300–414), TDP-11 (TDP-43300–399), and TDP-10 (TDP-43314–414), adopt distinct polymorphic structures in their amyloid fibrillar state. Our work demonstrates that the removal of less than 10% of the low-complexity sequence at N- and C-termini generates amyloid fibrils with comparable macroscopic features but different local structural arrangement. It highlights that the assembly mechanism of TDP-43, in addition to the aggregation of the hydrophobic region, is also driven by complex interactions involving low-complexity aggregation-prone segments that are a potential source of structural polymorphism.

Integrating biopolymer design with physical unclonable functions for anticounterfeiting and product traceability in agriculture

Smallholder farmers and manufacturers in the Agri-Food sector face substantial challenges because of increasing circulation of counterfeit products (e.g., seeds), for which current countermeasures are implemented mainly at the secondary packaging level, and are generally vulnerable because of limited security guarantees. Here, by integrating biopolymer design with physical unclonable functions (PUFs), we propose a cryptographic protocol for seed authentication using biodegradable and miniaturized PUF tags made of silk microparticles. By simply drop casting a mixture of variant silk microparticles on a seed surface, tamper-evident PUF tags can be seamlessly fabricated on a variety of seeds, where the unclonability comes from the stochastic assembly of spectrally and visually distinct silk microparticles in the tag. Unique, reproducible, and unpredictable PUF codes are generated from both Raman mapping and microscopy imaging of the silk tags. Together, the proposed technology offers a highly secure solution for anticounterfeiting and product traceability in agriculture.

BON domain-containing protein-mediated co-selection of antibiotic and heavy metal resistance in bacteria

The widespread antibiotic resistance of bacteria has become one of the most severe threats to public health. However, the mechanisms that allow microbial acquisition of resistance are still poorly understood. In the present study, a novel BON domain-containing protein was heterologously expressed in Escherichia coli. It functions as an efflux pump-like to confer resistance to various antibiotics, especially for ceftazidime, with a >32-fold increase in minimum inhibitory concentration (MIC). The fluorescence spectroscopy experiment indicated that BON protein could interact with several metal ions, such as copper and silver, which has been associated with the induced co-regulation of antibiotic and heavy metal resistance in bacteria. Furthermore, the BON protein was demonstrated to spontaneously self-assemble into a trimer and generate a central pore-like architecture for antibiotic transporting. A WXG motif as a molecular switch is essential for forming the transmembrane oligomeric pores and controls the interaction between BON protein and cell membrane. Based on these findings, a mechanism termed "one-in, one-out", was proposed for the first time. The present study provides new insights into the structure and function of BON protein and a previously unidentified antibiotic resistance mechanism, filling the knowledge gap in understanding BON protein-mediated intrinsic antibiotic resistance.

Spectroscopic and Theoretical Analysis of the Interaction between Plasma Proteins and Phthalimide Analogs with Potential Medical Application

One of the groups of organic compounds with potential use in medicine and pharmacy is phthalimide derivatives. They are characterized by a wide range of properties such as antibacterial, antifungal, and anti-inflammatory. In this study, we focused on research on four phthalimide derivatives with proven non-toxicity, which are cyclooxygenase inhibitors. With the use of molecular docking study and spectroscopic methods, such as fluorescence, circular dichroism, and FT-IR spectroscopies, we analyzed the way the tested compounds interact with plasma proteins. Among the many proteins present in the plasma, we selected three: albumin, α1-acid glycoprotein, and gamma globulin, which play significant roles in the human body. The obtained results showed that all tested compounds bind to the analyzed proteins. They interact most strongly with albumin, which is a transport protein. However, interactions with serum albumin and orosomucoid do not cause significant changes in their structures. Only in the case of gamma globulins significant changes were observed in protein secondary structure.

Removal and concurrent reduction of Cr(VI) by thermoacidophilic Cyanidiales: a novel extreme biomaterial enlightened for acidic and neutral conditions

Thermoacidophilic Cyanidiales maintain a competitive edge in inhabiting extreme environments enriched with metals. Here, species of Cyanidioschyzon merolae (Cm), Cyanidium caldarium (Cc), and Galdieria partita (Gp) were exploited to remove hexavalent chromium [Cr(VI)]. Cm and Gp could remove 168.1 and 93.7 mg g^-1 of Cr(VI) at pH 2.0 and 7.0, respectively, wherein 89% and 62% of sorbed Cr on Cm and Gp occurred as trivalent chromium [Cr(III)]. Apart from surface-sorbed Cr(VI), the in vitro Cr(III) bound with polysaccharide and in vivo chromium(III) hydroxide [Cr(OH)₃] attested to the reduction capability of Cyanidiales. The distribution of Cr species varied as a function of sorbed Cr amount, yet a relatively consistent proportion of Cr(OH)₃, irrespective of Cr sorption capacity, was found only on Cm and Cc at pH 2.0. In conjunction with TXM (transmission X-ray microscopy) images that showed less impaired cell integrity and possible intracellular Cr distribution on Cm and Cc at pH 2.0, the in vivo Cr(OH)₃ might be the key to promoting the Cr sorption capacity (≥ 152 mg g^-1). Cyanidiales are promising candidates for the green and sustainable remediation of Cr(VI) due to their great removal capacity, the spontaneous reduction under oxic conditions, and in vivo accumulation.

Development of a novel silk sericin-based hydrogel film by mixture design

Sericin has been used in functional and potentially biodegradable materials for cosmetics, biomedical, agricultural, and food applications. It is a natural polymer with applications in absorbent materials, such as hydrogels, because of its hydrophilic character. However, sericin by itself is brittle, and in contact with water has low structural stability, being necessary its blending with other polymers or the application of crosslinking processes. In this work, hydrogel films were prepared from different mixtures containing sericin (SS), carboxymethylcellulose (CMC), and polyvinyl alcohol (PVA), using a simple and environmentally friendly method consisting of a gelling process followed by solvent casting. A mixture design was applied to assess the incidence of each component and its interaction with the output variables of interest. Two response variables were evaluated in each formulation: water absorption capacity (WA) and gel fraction (GF). It was also possible to model the output variables based on the proportions of the sample components. In addition, a set of formulations were used to produce hydrogels with high water absorption rates while maintaining their structural stability. The optimal hydrogel formulation (HF) was structurally and thermally characterized by FTIR and TGA, respectively. Hydrogel morphology was also studied by scanning electron microscopy (SEM). The results of this study constitute an important contribution to the design of novel processing routes to extend the use of silk sericin in the development of new materials.

Chitosan as a Promising Support of a CDH Activity Preservation System for Biomedical and Industrial Applications

Cellobiose dehydrogenase (CDH) is an extracellular hemoflavoprotein catalyzing the oxidation reaction of β-1,4-glycosidic-bonded sugars (lactose or cellobiose), which results in the formation of aldobionic acids and hydrogen peroxide as a byproduct. The biotechnological application of CDH requires the immobilization of the enzyme on a suitable support. As a carrier of natural origin used for CDH immobilization, chitosan seems to increase the catalytic potential of the enzyme, especially for applications as packaging in the food industry and as a dressing material in medical applications. The present study aimed to immobilize the enzyme on chitosan beads and determine the physicochemical and biological properties of immobilized CDHs obtained from different fungal sources. The chitosan beads with immobilized CDHs were characterized in terms of their FTIR spectra or SEM microstructure. The most effective method of immobilization in the proposed modification was the covalent bonding of enzyme molecules using glutaraldehyde, resulting in efficiencies ranging from 28 to 99%. Very promising results, compared to free CDH, were obtained in the case of antioxidant, antimicrobial, and cytotoxic properties. Summarizing the obtained data, chitosan seems to be a valuable material for the development of innovative and effective immobilization systems for biomedical applications or food packaging, preserving the unique properties of CDH.

Interactions of SARS-CoV-2 and MERS-CoV fusion peptides measured using single-molecule force methods

We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide (FP) sequences within coronavirus (CoV) spike proteins. Within the FPs of severe acute respiratory syndrome CoV 2 and Middle East respiratory syndrome CoV (MERS-CoV), a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. Although a non-polar triad (Leu-Leu-Phe (LLF)) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS-2 and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9, respectively). Here we explore whether single-molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask whether sequence variations between FP1 from SARS-2 and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single-molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 ± 0.03 nN versus 0.68 ± 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single-residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single-residue diversity in viral FPs, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts.

Interaction of Lysozyme with Poly(L-lysine)/Hyaluronic Acid Multilayers: An ATR-FTIR Study

Polyelectrolyte multilayers (PEM) loaded with bioactive molecules such as proteins serve as excellent mimics of an extracellular matrix and may find applications in fields such as biomedicine and cell biology. A question which is crucial to the successful employment of PEMs is whether conformation and bioactivity of the loaded proteins is preserved. In this work, the polarized attenuated total reflection Fourier transform infrared (ATR-FTIR) technique is applied to investigate the conformation of the protein lysozyme (Lys) loaded into the poly(L-lysine)/hyaluronic acid (PLL/HA) multilayers. Spectra are taken from the protein in the PEMs coated onto an ATR crystal during protein adsorption and desorption. For comparison, a similar investigation is performed for the case of Lys in contact with the uncoated crystal. The study highlights the presence of both "tightly" and "poorly bound" Lys fractions in the PEM. These fractions differ in their conformation and release behavior from the PEM upon washing. Comparison of spectra recorded with different polarizations suggests preferential orientation of alpha helical structures, beta sheets and turns in the "tightly bound" Lys. In contrast, the "poorly bound" fraction shows isotropic orientation and its conformation is well preserved.

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length. This article is protected by copyright. All rights reserved.

Structural characteristics of a low molecular weight velvet antler protein and the anti-tumor activity on S180 tumor-bearing mice

Velvet antler is a traditional Chinese medicine with various pharmacological values, which is an important raw material for traditional Chinese medicinal wine. Nevertheless, the chemical compositions and bioactivities of velvet antler residue used for making medicinal wine are rarely reported, leading to a waste of resources. In this study, a velvet antler protein (VA-pro) was extracted from velvet antler residue by simulating the gastrointestinal digestion, and its composition, structural characteristics and in vivo anti-tumor activities were determined and investigated. VA-pro possessed high purity with a relatively low molecular weight as 22.589 kDa under HPLC, one- and two-dimensional electrophoresis, and it contained high contents of Pro, Gly, Glu and Ala. Besides, the secondary structure of VA-pro was dominated by β-turn and β-sheet, and VA-pro possessed similar protein sequence, isoelectric point and amino acid compositions to hypothetical protein G4228_020061. The in vivo results substantiated that VA-pro could improve the body weights and immune organ indices, increase the expressions of sera cytokines and regulate the distributions of T and B lymphocytes subsets in peripheral blood of S180 tumor-bearing mice. Furthermore, VA-pro could effectively inhibit solid S180 tumors growth by inducing S phase cell cycle arrest mediated through mitochondria. To summarize, our study provided theoretical support that VA-pro had the potential to be used as an immunopotentiator in immunocompromised or cancer-bearing hosts.

Structural insight on the liquid silk from the middle silk gland of non-mulberry silkworm Antheraea assamensis

This study highlights the preliminary characterization of liquid silk from the middle silk gland (MSG) along with the in-silico analysis of the sericin protein of a less explored non mulberry silkworm Antheraea assamensis which is endemic to the North Eastern region of India. Various biophysical methods have been applied to elucidate the conformational patterns of the liquid silk present inside the MSG without removing the sericin layer. This will help us to know the actual features of the in vivo transitional status of the silk in the MSG which travel towards the anterior silk gland (ASG) prior to spinning. The SDS PAGE analysis represented the existence of the both fibroin and sericin bands in the sample. The structural pattern of the MSG liquid silk as revealed by various methods denoted the occurrence of β-sheet component along with some random coil and β-turn components which in turn suggests the transitional state of the liquid silk attributed to the existence of both the crystalline and amorphous contents. The thermo gravimetric study and the aggregation behavior analysis results proposed the occurrence of intermolecular hydrogen bonding between the sericin and fibroin in the MSG. This study will sensitize the better understanding of the behavior of the liquid silk in the MSG of non-mulberry silkworm A. assamensis and will open avenues for various application-based studies of this silk.Communicated by Ramaswamy H. Sarma.

Orientation of the Dysferlin C2A Domain is Responsive to the Composition of Lipid Membranes

Dysferlin is a 230 kD protein that plays a critical function in the active resealing of micron-sized injuries to the muscle sarcolemma by recruiting vesicles to patch the injured site via vesicle fusion. Muscular dystrophy is observed in humans when mutations disrupt this repair process or dysferlin is absent. While lipid binding by dysferlin's C2A domain (dysC2A) is considered fundamental to the membrane resealing process, the molecular mechanism of this interaction is not fully understood. By applying nonlinear surface-specific vibrational spectroscopy, we have successfully demonstrated that dysferlin's N-terminal C2A domain (dysC2A) alters its binding orientation in response to a membrane's lipid composition. These experiments reveal that dysC2A utilizes a generic electrostatic binding interaction to bind to most anionic lipid surfaces, inserting its calcium binding loops into the lipid surface while orienting its β-sheets 30-40° from surface normal. However, at lipid surfaces, where PI(4,5)P2 is present, dysC2A tilts its β-sheets more than 60° from surface normal to expose a polybasic face, while it binds to the PI(4,5)P2 surface. Both lipid binding mechanisms are shown to occur alongside dysC2A-induced lipid clustering. These different binding mechanisms suggest that dysC2A could provide a molecular cue to the larger dysferlin protein as to signal whether it is bound to the sarcolemma or another lipid surface.

Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces

Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.

A study on the material properties of novel PEGDA/gelatin hybrid hydrogels polymerized by electron beam irradiation

Gelatin-based hydrogels are highly desirable biomaterials for use in wound dressing, drug delivery, and extracellular matrix components due to their biocompatibility and biodegradability. However, insufficient and uncontrollable mechanical properties and degradation are the major obstacles to their application in medical materials. Herein, we present a simple but efficient strategy for a novel hydrogel by incorporating the synthetic hydrogel monomer polyethylene glycol diacrylate (PEGDA, offering high mechanical stability) into a biological hydrogel compound (gelatin) to provide stable mechanical properties and biocompatibility at the resulting hybrid hydrogel. In the present work, PEGDA/gelatin hybrid hydrogels were prepared by electron irradiation as a reagent-free crosslinking technology and without using chemical crosslinkers, which carry the risk of releasing toxic byproducts into the material. The viscoelasticity, swelling behavior, thermal stability, and molecular structure of synthesized hybrid hydrogels of different compound ratios and irradiation doses were investigated. Compared with the pure gelatin hydrogel, 21/9 wt./wt. % PEGDA/gelatin hydrogels at 6 kGy exhibited approximately up to 1078% higher storage modulus than a pure gelatin hydrogel, and furthermore, it turned out that the mechanical stability increased with increasing irradiation dose. The chemical structure of the hybrid hydrogels was analyzed by Fourier-transform infrared (FTIR) spectroscopy, and it was confirmed that both compounds, PEGDA and gelatin, were equally present. Scanning electron microscopy images of the samples showed fracture patterns that confirmed the findings of viscoelasticity increasing with gelatin concentration. Infrared microspectroscopy images showed that gelatin and PEGDA polymer fractions were homogeneously mixed and a uniform hybrid material was obtained after electron beam synthesis. In short, this study demonstrates that both the presence of PEGDA improved the material properties of PEGDA/gelatin hybrid hydrogels and the resulting properties are fine-tuned by varying the irradiation dose and PEGDA/gelatin concentration.

Inconsistent hydrogen bond-mediated vibrational coupling of amide I

Using infrared spectroscopy and density functional theory (DFT) calculations, we scrutinized an amide (dimethylformamide) as a "model" compound to interpret the interactions of amide 1 with different phenol derivatives (para-chlorophenol (PCP) and para-cresol (CP)) as "model guest molecules". We established the involvement of amide I in vibrational coupling with symmetric and asymmetric C[double bond, length as m-dash]C modes of different phenolic derivatives and how their coupling was dependent upon different guest aromatic phenolic compounds. Interestingly, substitution of phenol perturbed the pattern of vibrational coupling with amide I. The symmetric and asymmetric C[double bond, length as m-dash]C modes of PC were coupled significantly with amide 1. For PCP, the symmetric C[double bond, length as m-dash]C mode coupled significantly, but the asymmetric mode coupled negligibly, with amide I. Here, we reveal the nature of vibrational coupling based on the structure of a guest molecule hydrogen-bonded with amide I. Our conclusions could be valuable for depiction of the unusual dynamics of coupled amide-I modes as well as the dependency of vibrational coupling on altered factors.

Hydrogen peroxide induces heme degradation and protein aggregation in human neuroglobin: roles of the disulfide bridge and hydrogen-bonding in the distal heme cavity

In the present study, human neuroglobin (hNgb) was found to undergo H₂ O₂ -induced breakdown of the heme center at a much slower rate than other globins, namely in the timescale of hours against minutes. We investigated how the rate of the process is affected by the Cys46/Cys55 disulfide bond and the network of non-covalent interactions in the distal heme side involving Tyr44, Lys67, the His64 heme iron axial ligand and the heme propionate-7. The rate is increased by the Tyr44 to Ala and Phe mutations; however the rate is lowered by Lys67 to Ala swapping. The absence of the disulfide bridge slows down the reaction further. Therefore, the disulfide bond-controlled accessibility of the heme site and the residues at position 44 and 67 affect the activation barrier of the reaction. Wild-type and mutated species form β-amyloid aggregates in the presence of H₂ O₂ producing globular structures. Furthermore, the C46A/C55A, Y44A, Y44F and Y44F/C46A/C55A variants yield potentially harmful fibrils. Finally, the nucleation and growth kinetics for the aggregation of the amyloid structures can be successfully described by the Finke-Watzky model.

ELISA Based Immunoreactivity Reduction of Soy Allergens through Thermal Processing

Allergens are proteins and are, therefore, likely to be denatured when subjected to thermal treatment. Traditional cooking has so far been able to reduce allergen sensitivity by around 70–90%. This study was aimed at evaluating the effect of a broad range of thermal treatments on the reduction of soy immunoreactivity (IR) in a 5% slurry using a sandwich ELISA technique. Cooking at 100 °C (10–60 min) and different thermal processing conditions, such as in commercial sterilization (with a process lethality (Fo) between 3 and 5 min) and selected severe thermal processing conditions (Fo > 5 and up to 23 min) were used in the study to evaluate their influence on allergen IR. Based on an IR comparison with an internal soy allergen standard, the allergen concentration in the untreated soy sample was calculated to be equivalent to 333 mg/kg (ppm). Cooking conditions only reduced the IR sensitivity to about 10 mg/kg (~1.5 log reductions), while the thermal processing treatments lowered the allergen IR up to 23 × 10−3 mg/kg (or 23 ppb) (>4 log reductions). FTIR analysis indicated significant changes in protein structure resulting from the thermal processing treatments, with a higher degree of allergen reduction corresponding with a higher value of random coil percentages. The influence of process severity on color and rheological properties was, however, minimal.

In Situ Identification of Secondary Structures in Unpurified Bombyx mori Silk Fibrils Using Polarized Two-Dimensional Infrared Spectroscopy

The mechanical properties of biomaterials are dictated by the interactions and conformations of their building blocks, typically proteins. Although the macroscopic behavior of biomaterials is widely studied, our understanding of the underlying molecular properties is generally limited. Among the noninvasive and label-free methods to investigate molecular structures, infrared spectroscopy is one of the most commonly used tools because the absorption bands of amide groups strongly depend on protein secondary structure. However, spectral congestion usually complicates the analysis of the amide spectrum. Here, we apply polarized two-dimensional (2D) infrared spectroscopy (IR) to directly identify the protein secondary structures in native silk films cast from Bombyx mori silk feedstock. Without any additional peak fitting, we find that the initial effect of hydration is an increase of the random coil content at the expense of the helical content, while the β-sheet content is unchanged and only increases at a later stage. This paper demonstrates that 2D-IR can be a valuable tool for characterizing biomaterials.

Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin

Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E-F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a ¹³C, ¹⁵N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the ¹³C, ¹⁵N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm^-1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E-F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins.

Application of SPRA Technology for Delivery of Erythropoietin: Stability Evaluation of Conjugated Erythropoietin with Adamantane and in SPRA Inclusion Complex

Background

As a widely used therapeutic protein, recombinant human erythropoietin (rhEPO) is currently one of the most effective biopharmaceuticals on the market for the treatment of anemia in patients with chronic renal disease. Increasing in vivo rhEPO half-life and its bioactivity is a significant challenge. It was hypothesized that the application of self-assembly PEGylation retaining activity, named supramolecular (SPRA) technology, could prolong the protein half-life without a significant loss of bioactivity.

Objectives

This study aimed to assess the stability of rhEPO during synthetic reactions, including the conjugation with adamantane and the formation of the SPRA complex. To do this, the secondary structure of the protein was also evaluated.

Methods

FTIR, ATR-FTIR, Far-UV-CD, and SDS-PAGE methods were employed. Thermal stability studies of SPRA-rhEPO complex and rhEPO were investigated at 37°C for ten days using a nanodrop spectrophotometer.

Results

The secondary structure of lyophilized rhEPO, AD-rhEPO, and rhEPO (pH 8) was compared to rhEPO. Results showed that the secondary structure of the protein was unaffected by lyophilization, pH change, and the formation of covalent bonds in conjugation reaction. SPRA-rhEPO complex was also stable for seven days in phosphate buffer (pH 7.4) at 37°C.

Conclusions

It was concluded that the stability of rhEPO could increase by complexation using SPRA technology.

Emulation of the structure of the Saposin protein fold by a lung surfactant peptide construct of surfactant Protein B

The three-dimensional structure of the synthetic lung Surfactant Protein B Peptide Super Mini-B was determined using an integrative experimental approach, including mass spectrometry and isotope enhanced Fourier-transform infrared (FTIR) spectroscopy. Mass spectral analysis of the peptide, oxidized by solvent assisted region-specific disulfide formation, confirmed that the correct folding and disulfide pairing could be facilitated using two different oxidative structure-promoting solvent systems. Residue specific analysis by isotope enhanced FTIR indicated that the N-terminal and C-terminal domains have well defined α-helical amino acid sequences. Using these experimentally derived measures of distance constraints and disulfide connectivity, the ensemble was further refined with molecular dynamics to provide a medium resolution, residue-specific structure for the peptide construct in a simulated synthetic lung surfactant lipid multilayer environment. The disulfide connectivity combined with the α-helical elements stabilize the peptide conformationally to form a helical hairpin structure that resembles critical elements of the Saposin protein fold of the predicted full-length Surfactant Protein B structure.

Study of fluorescence spectroscopy and molecular mechanisms for the interaction of Hg2+ ions and R-phycoerythrin from marine algae (Porphyra yezoensis)

Heavy metal is a worldwide hazardous material, and many efforts were made to detect them sensitively and selectively. R-phycoerythrin (R-PE), a marine fluorescent protein, is abundant in red algae and participates in photosynthesis. In this work, the fluorescence spectroscopy and molecular mechanism of Hg2+ ions and R-PE were further explored through fluorescence spectrum measurements, time-resolved fluorescence lifetimes, peak fitting of Fourier transform infrared spectroscopy, and molecular docking simulation in this study. It was proved by fluorescent spectrum measurements that Hg2+ ions could lead to static fluorescence quenching. Besides, the interaction was a spontaneous and exothermic process driven by hydrogen bond and Van der Waals (VDW) force. Importantly, Hg2+ ions bound to 78LYS and 82CYS on the α chain and 73CYS and 82CYS on the β chain, which resulted in the structural changes of the peptide chain and affected the secondary structure contents of R-PE. This study further explained the effect of Hg2+ ions on marine fluorescent protein R-PE.

Effect of the N-Alkyl Side Chain on the Amide-Water Interactions

Amide-water interactions influence the structure and functions of amide-based systems, such as proteins and homopolymers. In particular, the N-alkylation of the amide unit appears to play a critical role in defining the interactions of the amide group. Previous studies have linked the thermal behavior of amide-based polymers to the nature of their N-alkyl side chain. However, the connection between the chemical structure of the N-alkyl and the hydration of the amide remains elusive. In this study, the solvation structure and dynamics of amides, having differing N-alkyl groups, are investigated using a combination of linear and nonlinear infrared spectroscopies and computational methods. Interestingly, the dynamics of the amide local environment do not slow down as the N-alkyl side chain becomes bulkier, but rather speeds up. Computational calculations confirm the hydration dynamics and assign the effect to smaller amplitude and faster rotations of the bulkier group. It is also observed experimentally that the hydrogen-bond making and breaking between water and the amide carbonyl do not directly relate to the size of the N-alkyl side chain. The bulkier N-isopropyl substituent presents significantly slower chemical exchange dynamics than smaller chains (ethyl and methyl), but the two small groups do not present a major difference. The hydrogen-bond making and breaking disparities and similarities among groups are well modeled by the theory demonstrating that the N-alkyl group affects the amide hydration structure and dynamics via a steric effect. In summary, the results presented here show that the size of the N-substituted alkyl group significantly influences the hydration dynamics of amides and stress the importance of considering this effect on much larger systems, such as polymers.