Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins

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.

Elastin-Hyaluronan Bioconjugate as Bioactive Component in Electrospun Scaffolds

Hyaluronic acid or hyaluronan (HA) and elastin-inspired peptides (EL) have been widely recognized as bioinspired materials useful in biomedical applications. The aim of the present work is the production of electrospun scaffolds as wound dressing materials which would benefit from synergic action of the bioactivity of elastin peptides and the regenerative properties of hyaluronic acid. Taking advantage of thiol-ene chemistry, a bioactive elastin peptide was successfully conjugated to methacrylated hyaluronic acid (MAHA) and electrospun together with poly-D,L-lactide (PDLLA). To the best of our knowledge, limited reports on peptide-conjugated hyaluronic acid were described in literature, and none of these was employed for the production of electrospun scaffolds. The conformational studies carried out by Circular Dichroism (CD) on the bioconjugated compound confirmed the preservation of secondary structure of the peptide after conjugation while Scanning Electron Microscopy (SEM) revealed the supramolecular structure of the electrospun scaffolds. Overall, the study demonstrates that the bioconjugation of hyaluronic acid with the elastin peptide improved the electrospinning processability with improved characteristics in terms of morphology of the final scaffolds.

Forbidden Secondary Structures Found in Gel-Forming Fibrils of Glycylphenylalanylglycine

The zwitterionic l-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils in an aqueous solution, which causes the formation of an exceptionally strong gel phase (G' ∼ 5 × 10⁶ Pa). The Rietveld refinement analysis of its powder X-ray diffraction (PXRD) pattern reveals a unit cell with four peptides forming a P2₁2₁2₁ space group and adopting an inverse polyproline II conformation, that is, a right-handed helical structure that occupies the "forbidden" region of the Ramachandran plot. This unusual structure is stabilized by a plethora of intermolecular interactions facilitated by the large number of different functional groups of the unblocked tripeptide. Comparisons of simulated and experimental Fourier transform infrared and vibrational circular dichroism (VCD) amide I' profiles corroborate the PXRD structure. Our experimental setup reduces the sample to a quasi-two-dimensional network of fibrils. We exploited the influence of this reduced dimensionality on the amide I VCD to identify the main fibril axis. We demonstrate that PXRD, vibrational spectroscopy, and amide I simulations provide a powerful toolset for secondary structure and fibril axis determination.

Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films

We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm-1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm-1 that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.

Acetic Acid Enables Precise Tailoring of the Mechanical Behavior of Protein-Based Hydrogels

Engineering viscoelastic and biocompatible materials with tailored mechanical and microstructure properties capable of mimicking the biological stiffness (<17 kPa) or serving as bioimplants will bring protein-based hydrogels to the forefront in the biomaterials field. Here, we introduce a method that uses different concentrations of acetic acid (AA) to control the covalent tyrosine-tyrosine cross-linking interactions at the nanoscale level during protein-based hydrogel synthesis and manipulates their mechanical and microstructure properties without affecting protein concentration and (un)folding nanomechanics. We demonstrated this approach by adding AA as a precursor to the preparation buffer of a photoactivated protein-based hydrogel mixture. This strategy allowed us to synthesize hydrogels made from bovine serum albumin (BSA) and eight repeats protein L structure, with a fine-tailored wide range of stiffness (2-35 kPa). Together with protein engineering technologies, this method will open new routes in developing and investigating tunable protein-based hydrogels and extend their application toward new horizons.

Kinetics and Mechanisms of Saccharomyces boulardii Release from Optimized Whey Protein-Agavin-Alginate Beads under Simulated Gastrointestinal Conditions

Encapsulation is a process in which a base material is encapsulated in a wall material that can protect it against external factors and/or improve its bioavailability. Among the different encapsulation techniques, ionic gelation stands out as being useful for thermolabile compounds. The aim of this work was to encapsulate Saccharomyces boulardii by ionic gelation using agavins (A) and whey protein (WP) as wall materials and to evaluate the morphostructural changes that occur during in vitro gastrointestinal digestion. Encapsulations at different levels of A and WP were analyzed using microscopic, spectroscopic and thermal techniques. Encapsulation efficiency and cell viability were evaluated. S. boulardii encapsulated at 5% A: 3.75% WP (AWB6) showed 88.5% cell survival after the simulated gastrointestinal digestion; the bead showed a significantly different microstructure from the controls. The mixture of A and WP increased in the survival of S. boulardii respect to those encapsulated with alginate, A or WP alone. The binary material mixture simultaneously allowed a controlled release of S. boulardii by mostly diffusive Fickian mechanisms and swelling. The cell-release time was found to control the increment of the Damköhler number when A and WP were substrates for S. boulardii, in this way allowing greater protection against gastrointestinal conditions.

Identification of hepatocellular carcinoma and paracancerous tissue based on the peak area in FTIR microspectroscopy

Hepatocellular carcinoma (HCC) is one of the most common primary hepatic malignancies across the world. The annual incidence and death rates have increased at the highest rate of all cancers in recent years. Surgical resection is a potentially curative option for solitary HCC or unilobar disease without evidence of metastases or vascular invasion. This study focuses on the molecular differences between the HCC foci and paracancerous tissues and provides some valuable biomarkers based on the vibrational spectrum. Fourier transform infrared (FTIR) spectroscopy is a non-invasive and qualitative and semi-quantitative analysis technique that has been widely applied for the identification of macromolecular changes in biological tissues. In this study, the FTIR spectra of the HCC foci and the paracancerous tissues were recorded separately, and ten areas under the absorption peaks of all the specimens were calculated. The result demonstrates that the areas of protein-related absorption peaks at 1398 cm^-1, 1548 cm^-1, 1654 cm^-1 and 3070 cm^-1 may be the key indicators of the two different regions. After coupling with the classification algorithms of k-nearest neighbor (KNN), random forest (RF) and support vector machine (SVM), it was found that SVM with an RBF kernel performed best with the AUC (area under the ROC curve) reaching 0.997, and the performance was better than the feature based on the full spectrum. This reveals that the peak area-based FTIR spectra combined with the SVM algorithm may be a promising tool in identifying the HCC foci and the paracancerous tissues.

In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale

The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca²⁺ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.

Self-assembly pathways in a triphenylalanine peptide capped with aromatic groups

Peptide derivatives and, most specifically, their self-assembled supramolecular structures are being considered in the design of novel biofunctional materials. Although the self-assembly of triphenylalanine homopeptides has been found to be more versatile than that of homopeptides containing an even number of residues (i.e. diphenylalanine and tetraphenylalanine), only uncapped triphenylalanine (FFF) and a highly aromatic analog blocked at both the N- and C-termini with fluorenyl-containing groups (Fmoc-FFF-OFm), have been deeply studied before. In this work, we have examined the self-assembly of a triphenylalanine derivative bearing 9-fluorenylmethyloxycarbonyl and benzyl ester end-capping groups at the N- and C-termini, respectively (Fmoc-FFF-OBzl). The antiparallel arrangement clearly dominates in β-sheets formed by Fmoc-FFF-OBzl, whereas the parallel and antiparallel dispositions are almost isoenergetic in Fmoc-FFF-OFm β-sheets and the parallel one is slightly favored for FFF. The effects of both the peptide concentration and the medium on the self-assembly process have been examined considering Fmoc-FFF-OBzl solutions in a wide variety of solvent:co-solvent mixtures. In addition, Fmoc-FFF-OBzl supramolecular structures have been compared to those obtained for FFF and Fmoc-FFF-OFm under identical experimental conditions. The strength of π-π stacking interactions involving the end-capping groups plays a crucial role in the nucleation and growth of supramolecular structures, which determines the resulting morphology. Finally, the influence of a non-invasive external stimulus, ultrasounds, on the nucleation and growth of supramolecular structures has been examined. Overall, FFF-based peptides provide a wide range of supramolecular structures that can be of interest in the biotechnological field.

Protein secondary structure in spider silk nanofibrils

Nanofibrils play a pivotal role in spider silk and are responsible for many of the impressive properties of this unique natural material. However, little is known about the internal structure of these protein fibrils. We carry out polarized Raman and polarized Fourier-transform infrared spectroscopies on native spider silk nanofibrils and determine the concentrations of six distinct protein secondary structures, including β-sheets, and two types of helical structures, for which we also determine orientation distributions. Our advancements in peak assignments are in full agreement with the published silk vibrational spectroscopy literature. We further corroborate our findings with X-ray diffraction and magic-angle spinning nuclear magnetic resonance experiments. Based on the latter and on polypeptide Raman spectra, we assess the role of key amino acids in different secondary structures. For the recluse spider we develop a highly detailed structural model, featuring seven levels of structural hierarchy. The approaches we develop are directly applicable to other proteinaceous materials.

Secondary fibril structure is a key component of the mechanical properties of protein materials like silk, yet, limited information is known about the internal structure of these protein fibrils. Here, the authors report on the use of polarised Raman and FTIR spectroscopy to study silk materials and identify six distinct secondary structures.

Monitoring the Progression of Cell-Free Expression of Microbial Rhodopsins by Surface Enhanced IR Spectroscopy: Resolving a Branch Point for Successful/Unsuccessful Folding

The translocon-unassisted folding process of transmembrane domains of the microbial rhodopsins sensory rhodopsin I (HsSRI) and II (HsSRII), channelrhodopsin II (CrChR2), and bacteriorhodopsin (HsBR) during cell-free expression has been investigated by Surface-Enhanced Infrared Absorption Spectroscopy (SEIRAS). Up to now, only a limited number of rhodopsins have been expressed and folded into the functional holoprotein in cell free expression systems, while other microbial rhodopsins fail to properly bind the chromophore all-trans retinal as indicated by the missing visible absorption. SEIRAS experiments suggest that all investigated rhodopsins lead to the production of polypeptides, which are co-translationally inserted into a solid-supported lipid bilayer during the first hour after the in-vitro expression is initiated. Secondary structure analysis of the IR spectra revealed that the polypeptides form a comparable amount of α-helical structure during the initial phase of insertion into the lipid bilayer. As the process progressed (&gt;1 h), only HsBR exhibited a further increase and association of α-helices to form a compact tertiary structure, while the helical contents of the other rhodopsins stagnated. This result suggests that the molecular reason for the unsuccessful cell-free expression of the two sensory rhodopsins and of CrChR2 is not due to the translation process, but rather to the folding process during the post-translational period. Taking our previous observation into account that HsBR fails to form a tertiary structure in the absence of its retinal, we infer that the chromophore retinal is an integral component of the compaction of the polypeptide into its tertiary structure and the formation of a fully functional protein.

A Novel Artificial Hemoglobin Carrier Based on Heulandite-Calcium Mesoporous Aluminosilicate Particles

Tetraethyl-orthosilicate (TEOS)-based nanoparticles are most extensively used as a silica-based hemoglobin carrier system. However, TEOS-based nanoparticles induce adverse effects on the hemoglobin structure. Therefore, a heulandite-calcium-based carrier was investigated as a novel silica-based hemoglobin carrier system. The heulandite-calcium mesoporous aluminosilicate particles (MSPs) were fabricated by a patented tribo-mechanical activation process, according to the manufacturer, and its structure was assessed by X-ray diffraction analysis. Upon hemoglobin encapsulation, alternation in the secondary and tertiary structure was observed. The hemoglobin-particle interactions do not cause heme degradation or decreased activity. Once encapsulated inside the particle pores, the hemoglobin shows increased thermal stability, and higher loading capacity per gram of particles (by a factor of >1.4) when compared to TEOS-based nanoparticles. Futhermore, we introduced a PEGlyted lipid bilayer which significantly decreases the premature hemoglobin release and increases the colloidal stability. The newly developed hemoglobin carrier shows no cytotoxicity to human umbilical vein endothelial cells (HUVEC).

Interfacial protein-protein displacement at fluid interfaces

Protein blends are used to stabilise many traditional and emerging emulsion products, resulting in complex, non-equilibrated interfacial structures. The interface composition just after emulsification is dependent on the competitive adsorption between proteins. Over time, non-adsorbed proteins are capable of displacing the initially adsorbed ones. Such rearrangements are important to consider, since the integrity of the interfacial film could be compromised after partial displacement, which may result in the physical destabilisation of emulsions. In the present review, we critically describe various experimental techniques to assess the interfacial composition, properties and mechanisms of protein displacement. The type of information that can be obtained from the different techniques is described, from which we comment on their suitability for displacement studies. Comparative studies between model interfaces and emulsions allow for evaluating the impact of minor components and the different fluid dynamics during interface formation. We extensively discuss available mechanistic physical models that describe interfacial properties and the dynamics of complex mixed systems, with a focus on protein in-plane and bulk-interface interactions. The potential of Brownian dynamic simulations to describe the parameters that govern interfacial displacement is also addressed. This review thus provides ample information for characterising the interfacial properties over time in protein blend-stabilised emulsions, based on both experimental and modelling approaches.

Pathway Dependence of the Formation and Development of Prefibrillar Aggregates in Insulin B Chain

Amyloid fibrils have been an important subject as they are involved in the development of many amyloidoses and neurodegenerative diseases. The formation of amyloid fibrils is typically initiated by nucleation, whereas its exact mechanisms are largely unknown. With this situation, we have previously identified prefibrillar aggregates in the formation of insulin B chain amyloid fibrils, which have provided an insight into the mechanisms of protein assembly involved in nucleation. Here, we have investigated the formation of insulin B chain amyloid fibrils under different pH conditions to better understand amyloid nucleation mediated by prefibrillar aggregates. The B chain showed strong propensity to form amyloid fibrils over a wide pH range, and prefibrillar aggregates were formed under all examined conditions. In particular, different structures of amyloid fibrils were found at pH 5.2 and pH 8.7, making it possible to compare different pathways. Detailed investigations at pH 5.2 in comparison with those at pH 8.7 have suggested that the evolution of protofibril-like aggregates is a common mechanism. In addition, different processes of evolution of the prefibrillar aggregates have also been identified, suggesting that the nucleation processes diversify depending on the polymorphism of amyloid fibrils.

Biophysical and Computational Approaches to Unravel pH-Dependent Conformational Change of PspA Assist PspA-PspF Complex Formation in Yersinia enterocolitica

In enteropathogen, Yersinia enterocolitica, the genes encoding phage shock proteins are organized in an operon (pspA-E), which is activated at the various types of cellular stress (i.e., extracytoplasmic or envelop stress) whereas, PspA negatively regulates PspF, a transcriptional activator of pspA-E and pspG, and is also involved in other cellular machinery maintenance processes. The exact mechanism of association and dissociation of PspA and PspF during the stress response is not entirely clear. In this concern, we address conformational change of PspA in different pH conditions using various in-silico and biophysical methods. At the near-neutral pH, CD and FTIR measurements reveal a ß-like conformational change of PspA; however, AFM measurement indicates the lower oligomeric form at the above-mentioned pH. Additionally, the results of the MD simulation also support the conformational changes which indicate salt-bridge strength takes an intermediate position compared to other pHs. Furthermore, the bio-layer interferometry study confirms the stable complex formation that takes place between PspA and PspF at the near-neutral pH. It, thus, appears that PspA conformational change in adverse pH conditions abandons PspF from having a stable complex with it, and thus, the latter can act as a trans-activator. Taken together, it seems that PspA alone can transduce adverse signals by changing its conformation.

Evaluation of formation and proportion of secondary structure in γ-polyglutamic acid by terahertz time-domain spectroscopy

The study of secondary structure is essential for understanding peptides and proteins. Here, we measured the terahertz (THz) spectra of γ-polyglutamic acid (γ-PGA) dominated by α-helix and random coil (RC) respectively. The α-helix has two absorption peaks in the THz region, but no absorption peak is observed in the RC conformation. We believe this is because the hydrogen bonding effect leads to a higher orientation in the helix-dominated γ-PGA. At lower pH, the absorption intensity of γ-PGA increases with the induction time. Similar changes were obtained in the Fourier infrared spectroscopy (FTIR). Through the correlation analysis of THz and IR spectroscopy, it is found that the characteristic peak at 1.2 THz can be used as a sensitive indicator of the intermediate conformation of the α-helical structure. In addition, the transformation of α-helix-RC conformation is related to the peak intensity at 1.99 THz (R² = 0.991), which preliminarily indicates that terahertz time-domain spectroscopy (THz-TDS) has the potential to become a new effective method for characterizing and evaluating secondary structure.

Microstructural and Physicochemical Analysis of Collagens from the Skin of Lizardfish (Saurida tumbil Bloch, 1795) Extracted with Different Organic Acids

Marine fish collagen has attracted considerable attention due to its characteristics, including its biodegradability, biocompatibility, and weak antigenicity, and is considered a safer material compared to collagen from terrestrial animals. The aim of this study was to extract and characterize collagen from the skin of lizardfish (Saurida tumbil Bloch, 1795) with three different acids. The yields of acetic acid-extracted collagen (AESkC), lactic acid-extracted collagen (LESkC), and citric acid-extracted collagen (CESkC) were 11.73 ± 1.14%, 11.63 ± 1.10%, and 11.39 ± 1.05% (based on wet weight), respectively. All extracted collagens were categorized as type I collagen with mainly alpha chains (α₁ and α₂) detected and γ and β chains to some extent. Fourier transform infrared (FTIR) spectra showed an intact triple-helical structure in the AESkC, LESkC, and CESkC. UV-vis spectra and X-ray diffraction further demonstrated the similarity of the extracted collagens to previously reported fish skin collagens. AESkC (T_max = 40.24 °C) had higher thermostability compared to LESkC (T_max = 38.72 °C) and CESkC (T_max = 36.74 °C). All samples were highly soluble in acidic pH and low concentrations of NaCl (0-20 g/L). Under field emission scanning electron microscopy (FESEM) observation, we noted the loose, fibrous, and porous structures of the collagens. The results suggest that the lizardfish skin collagens could be a potential alternative source of collagen, especially the AESkC due to its greater thermostability characteristic.

Spectroscopic Studies for Rhodium (III) Binding to Apo-Transferrin

Transferrin belongs to a class of monomeric glycoproteins, which sequestrate and transport iron inside the body. Apart from iron, transferrin binds with various other metal ions and is assumed to deliver medicinally important metal ions to cells. Hence, the investigation of binding characteristics may provide crucial information for new drug developments. To study the biological impacts of medicinally important metal ions, in this work, we explored the binding behavior of Rh(III) ion with serum apo-transferrin (ApoHST) using FT-IR and UV-Vis spectroscopy. In FT-IR, interaction of Rh(III) with ApoHST was studied at three concentrations (0.25, 0.5, and 1 mM) of metal ion at different time intervals (15, 30, and 60 min). The IR spectra of Rh(III)-ApoHST coordinates revealed a marked reduction in amide I and II band intensities with alterations in band positions. The α-helical part of protein secondary structure reduced considerably (from 53% to 49%, 42%, and 39%), followed by an increment in β-sheet and β-turn components with the increasing concentrations of metal ion. Saturation level reached at 1 mM concentration of Rh(III) ion. In the UV-Vis spectroscopic study, absorption of metal ion-protein coordinates successively raised as concentration of Rh(III) ion increased. The binding constant (K) was calculated as $1.16\times {10}^4{\text{M}}^{-1}$ , which showed a strong binding of the test metal ion with the protein. Upon coordination with a metal ion, the microenvironment of aromatic protein residues changed, which was detected by these spectroscopic techniques. The results revealed the existence of a significant interaction between Rh (III) ion and ApoHST. These research outcome may present new insight into the possible utilization of Rh(III) ion-based compounds in biomedicine. However, more investigations are needed to interpret the exact cellular mechanism.

Preservation of Terrestrial Microorganisms and Organics Within Alteration Products of Chondritic Meteorites from the Nullarbor Plain, Australia

Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well-understood chemistry of meteorites and their recent discovery on Mars by rovers, a similarly weathered meteorite on Mars could preserve organic and fossil evidence of a putative past biosphere at the martian surface. Here, we used several techniques to assess the potential of alteration minerals to preserve microfossils and biogenic organics in terrestrially weathered ordinary chondrites from the Nullarbor Plain, Australia. We used acid etching of ordinary chondrites to reveal entombed fungal hyphae, modern biofilms, and diatoms within alteration minerals. We employed synchrotron X-ray fluorescence microscopy of alteration mineral veins to map the distribution of redox-sensitive elements of relevance to chemolithotrophic organisms, such as Mn-cycling bacteria. We assessed the biogenicity of fungal hyphae within alteration veins using a combination of Fourier-transform infrared spectroscopy and pyrolysis gas chromatography-mass spectrometry, which showed that alteration minerals sequester and preserve organic molecules at various levels of decomposition. Our combined analyses results show that fossil microorganisms and the organic molecules they produce are preserved within calcite-gypsum admixtures in meteorites. Furthermore, the distributions of redox-sensitive elements (e.g., Mn) within alteration minerals are localized, which qualitatively suggests that climatically or microbially facilitated element mobilization occurred during the meteorite's residency on Earth. If returned as part of a sample suite from the martian surface, ordinary chondrites could preserve similar, recognizable evidence of putative past life and/or environmental change.

Modeling amide-I vibrations of alanine dipeptide in solution by using neural network protocol

Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.

Isolation, biochemical characterization, and development of a biodegradable antimicrobial film from Cirrhinus mrigala scale collagen

Collagen is a promising candidate for food and pharmaceutical applications due to its excellent biocompatibility, low antigenicity, and controlled biodegradability; however, its heavy price restricts its utilization. Fish scales generated during the processing are generally regarded as waste material and an environmental pollutant, though they are a promising source of collagen. In the present study, Cirrhinus mrigala scales were demineralized and extracted for acid-soluble collagen (ASC) using acetic acid, with a collagen yield of 2.7%. UV-Vis spectra, SDS-PAGE, FTIR analyses, and amino acid composition confirmed the type I nature of the collagen extracted. The denaturation temperature of the collagen was found to be 30.09 °C using differential scanning calorimetry (DSC). The collagen was highly soluble at acidic pH and lower NaCl concentrations while its solubility was lowered in alkaline conditions and NaCl concentrations above 0.5 M. The collagen exhibited good emulsifying potential with an emulsion activity index (EAI) and emulsion stability index (ESI) of 21.49 ± 0.22 m² g^-1 and 15.67 ± 0.13 min, respectively. Owing to the good physicochemical characteristics of the extracted collagen, collagen-chitosan-neem extract (CCN) films were prepared subsequently which showed good antimicrobial activity against Bacillus subtilis NCIM 2635, Staphylococcus aureus NCIM 2654, Escherichia coli NCIM 2832, and Pseudomonas aeruginosa NCIM 5032, suggesting the potential of collagen in the development of antimicrobial films. These results demonstrate that the collagen from fish waste could be valorized and used effectively along with chitosan and neem extract for the synthesis of novel biodegradable films with antimicrobial efficacy.

Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure

Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H₂O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H₂O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.

c-Axis-Oriented Platelets of Crystalline Hydroxyapatite in Biomimetic Intrafibrillar Mineralization of Polydopamine-Functionalized Collagen Type I

Mineralized collagen fibrils are important basic building blocks of calcified tissues, such as bone and dentin. Polydopamine (PDA) can introduce functional groups, i.e., hydroxyl and amine groups, on the surfaces of type I collagen (Col-I) as possible nucleation sites of calcium phosphate (CaP) crystallization. Molecular bindings in between PDA and Col-I fibrils (Col-PDA) have been found to significantly reduce the interfacial energy. The wetting effect, mainly hydrophilicity due to the functional groups, escalates the degree of mineralization. The assembly of Col-I molecules into fibrils was initiated at the designated number of collagenous molecules and PDA. In contrast to the infiltration of amorphous calcium phosphate (ACP) precursors into the Col-I matrix by polyaspartic acid (pAsp), this collagen assembly process allows nucleation and ACP to exist in advance by PDA in the intrafibrillar matrix. PDA bound to specific sites, i.e., gap and overlap zones, by the regular arrangement of Col-I fibrils enhanced ACP nucleation and thus mineralization. As a result, the c-axis-oriented platelets of crystalline hydroxyapatite in the Col-I fibril matrix were observed in the enhanced mineralization through PDA functionalization.

Graphene Oxide/Silver Nanoparticles Platforms for the Detection and Discrimination of Native and Fibrillar Lysozyme: A Combined QCM and SERS Approach

We propose a sensing platform based on graphene oxide/silver nanoparticles arrays (GO/AgNPs) for the detection and discrimination of the native and toxic fibrillar forms of an amyloid-prone protein, lysozyme, by means of a combination of Quartz Crystal Microbalance (QCM) and Surface Enhanced Raman Scattering (SERS) measurements. The GO/AgNPs layer system was obtained by Langmuir-Blodgett assembly of the silver nanoparticles followed by controlled adsorption of GO sheets on the AgNPs array. The adsorption of native and fibrillar lysozyme was followed by means of QCM, the measurements provided the kinetics and the mechanism of adsorption as a function of protein concentration as well as the mass and thickness of the adsorbed protein on both nanoplatforms. The morphology of the protein layer was characterized by Confocal Laser Scanning Microscopy experiments on Thioflavine T-stained samples. SERS experiments performed on arrays of bare AgNPs and of GO coated AgNP after native, or fibrillar, lysozyme adsorption allowed for the discrimination of the native form and toxic fibrillar structure of lysozyme. Results from combined QCM/SERS studies indicate a general construction paradigm for an efficient sensing platform with high selectivity and low detection limit for native and amyloid lysozyme.

Infrared and Raman spectroscopy for purity assessment of extracellular vesicles

Extracellular vesicles (EVs) are a complex and heterogeneous population of nanoparticles involved in cell-to-cell communication. Recently, numerous studies have indicated the potential of EVs as therapeutic agents, drug carriers and diagnostic tools. However, the results of these studies are often difficult to evaluate, since different characterization methods are used to assess the purity, physical and biochemical characteristics of the EV samples. In this study, we compared four methods for the EV sample characterization and purity assessment: i) the particle-to-protein ratio based on particle analyses with nanoparticle tracking and protein concentration by bicinchoninic acid assay, ii) Western Blot analysis for specific EV biomarkers, iii) two spectroscopic lipid-to-protein ratios by either the attenuated total reflection Fourier transform infrared (ATR-FTIR) or Raman spectroscopy. The results confirm the value of Raman and ATR-FTIR spectroscopy as robust, fast and operator independent tools that require only a few microliters of EV sample. We propose that the spectroscopic lipid-to-protein (Li/Pr) ratios are reliable parameters for the purity assessment of EV preparations. Moreover, apart from determining protein concentrations, we show that ATR-FTIR spectroscopy can also be used for indirect measurements of EV concentrations. Nevertheless, the Li/Pr ratios do not represent full characterization of the EV preparations. For a complete characterization of selected EV preparations, we recommend also additional use of particle size distribution and EV biomarker analysis.

Comparison of the interactions of flupyrimin and nitenpyram with serum albumins via multiple analysis methods

Flupyrimin and nitenpyram are emerging neonicotinoid insecticides that may cause potential harm to the human body. In the present work, the interactions of flupyrimin/nitenpyram with serum albumins under normal physiological conditions were thoroughly studied by using multiple spectroscopic techniques, DFT calculations and molecular docking. Flupyrimin/nitenpyram can quench the endogenous fluorescence of HSA/BSA and form a complex with HSA/BSA through a static process, causing conformational and secondary structure changes of HSA/BSA. Thermodynamic analysis shows that the combination of flupyrimin/nitenpyram with HSA/BSA is a spontaneous process, mainly driven by hydrogen bonds and hydrophobic forces. Site marking and molecular docking experiments indicated that flupyrimin/nitenpyram binds with HSA/BSA at site II (subdomain IIIA). The binding constant K_a in HSA-flupyrimin, HSA-nitenpyram, BSA-flupyrimin and BSA-nitenpyram systems at 298 K was 2.11 × 10⁵ M^-1, 2.35 × 10⁵ M^-1, 1.91 × 10⁵ M^-1 and 2.11 × 10⁵ M^-1, respectively. The binding constant K_a of nitenpyram with HSA/BSA was greater than flupyrimin, indicating that nitenpyram binds HSA/BSA was more stable than that of flupyrimin, which was consistent with the DFT calculation. In addition, the acute toxicity bioassay showed that flupyrimin and nitenpyram exhibited low toxicity to zebrafish, with 96 h LC₅₀ values of 181.662 and 250.658 mg a. i. L^-1, respectively. These results can help understand the interactions of flupyrimin/nitenpyram with HSA/BSA.

SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data

A protein's structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600-1700 cm-1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.

Anisotropic Composition and Mechanical Behavior of a Natural Thin-Walled Composite: Eagle Feather Shaft

Flight feather shafts are outstanding bioinspiration templates due to their unique light weight and their stiff and strong characteristics. As a thin wall of a natural composite beam, the keratinous cortex has evolved anisotropic features to support flight. Here, the anisotropic keratin composition, tensile response, dynamic properties of the cortex, and fracture behaviors of the shafts are clarified. The analysis of Fourier transform infrared (FTIR) spectra indicates that the protein composition of calamus cortex is almost homogeneous. In the middle and distal shafts (rachis), the content of the hydrogen bonds (HBs) and side-chain is the highest within the dorsal cortex and is consistently lower within the lateral wall. The tensile responses, including the properties and dominant damage pattern, are correlated with keratin composition and fiber orientation in the cortex. As for dynamic properties, the storage modulus and damping of the cortex are also anisotropic, corresponding to variation in protein composition and fibrous structure. The fracture behaviors of bent shafts include matrix breakage, fiber dissociation and fiber rupture on compressive dorsal cortex. To clarify, ‘real-time’ damage behaviors, and an integrated analysis between AE signals and fracture morphologies, are performed, indicating that calamus failure results from a straight buckling crack and final fiber rupture. Moreover, in the dorsal and lateral walls of rachis, the matrix breakage initially occurs, and then the propagation of the crack is restrained by ‘ligament-like’ fiber bundles and cross fiber, respectively. Subsequently, the further matrix breakage, interface dissociation and induced fiber rupture in the dorsal cortex result in the final failure.

Ceruloplasmin in flatland: the relationship between enzyme catalytic activity and surface hydrophilicity

The effective immobilization of the enzyme on the substrate surface plays a key role especially in biocatalysis, medicine or industry. Herein, we showed the influence of substrate hydrophilicity on the activity of the physically immobilized ceruloplasmin. To control the hydrophilicity of the substrate, thiols with various terminal groups were used. We have found that the effectiveness of the catalytic process of multimeric protein is the highest in the situation of application of the highly hydrophilic substrate. In the case of physical adsorption, the orientation of the enzyme is random, however the application of the appropriate modifying layer enforces the desired enzyme orientation. The quartz crystal microbalance with dissipation (QCM-D) results showed that the crucial parameter for the highest and most durable catalytic activity of the enzyme is the orientation, not the amount of the physically adsorbed enzyme.

Surface hydrophilicity – the way to control the activity of the immobilized enzyme.

Structural stability of biofilms produced from silkworm cocoon fibers

Biofilms were obtained from cocoons of the silkworm, Bombyx mori, involving the removal of sericin, extraction and solubilization of fibroin fibers, dialysis of fibroin dispersions and preparation of biofilms by the casting process. Biofilm transparency was verified by UV?Vis spectroscopy and thermal stability by thermogravimetric/differential scanning calorimetry (TG/DSC). Soon after preparation, the solidification of the fibroin solution prepared from the cocoons and extracted by the Ajisawa method was monitored until the biofilm stabilized, using attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) as a function of time. The results showed that there was a change in the conformation from the silk I structure (?-helix) to silk II (?-sheet). In order to improve the characterization of the biofilms obtained by the Ajisawa method and LiBr solubilization of fibroin fibers, Raman spectroscopy was used to verify the stabilization of the different possible molecular conformations for the fibers in these materials, by comparison with the cocoon spectra and those of the solid (freeze-dried precipitated by dialysis for 72 h. By comparing the Raman spectra of the biofilms in terms of the intensities of the broadened band characteristic of amide I, it was possible to assess the conformational changes in both materials based on the possible transitions between ?-sheet conformations and flexible ?-helix and ?-turn structures. The results showed a dispersion of these conformations in the biofilms generated and in the solid freeze-dried hydrogel spectrum, and the ?-sheet conformation was found to be predominant. The TG and DSC curves showed that the materials with higher ?-sheet content exhibited higher thermal stability. Thus, the data obtained further elucidated the properties of these materials that are widely used in various processes.

Synthesis and characterization of new 5,5′-dimethyl- and 5,5′-diphenylhydantoin-conjugated hemorphin derivatives designed as potential anticonvulsant agents

Herein, the synthesis and characterization of some novel N-modified hybrid analogues of hemorphins containing a C-5 substituted hydantoin residue as potential anticonvulsants and for the blockade of sodium channels are presented.

Fast-Folding Kinetics Using Nanosecond Laser-Induced Temperature-Jump Methods

The development of ultrafast kinetic methods is one of the factors that allowed the research on protein folding to flourish over the last 20 years. The introduction of new optical triggering techniques enabled to experimentally investigate the protein dynamics at the nanosecond to millisecond timescale, allowing researchers to test theoretical predictions and providing experimental benchmarks for computer simulations. In this work, the details of how to perform kinetic experiments by the laser-induced temperature-jump technique, using the two most commonly used probing techniques (namely infrared absorption and fluorescence spectroscopy) are given, with a strong emphasis on the practical details.

Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations

In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na⁺, Ca²⁺, Mg²⁺, and Zn²⁺) with backbone (amide C═O) and C-terminal carboxylate (COO^-) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PP_II) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone-cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH₃⁺ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn²⁺) can specifically coordinate to the COO^- group in bidentate and pseudo-bridging forms simultaneously. For Zn²⁺, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides.

Integrative measurement analysis via machine learning descriptor selection for investigating physical properties of biopolymers in hairs

Integrative measurement analysis of complex subjects, such as polymers is a major challenge to obtain comprehensive understanding of the properties. In this study, we describe analytical strategies to extract and selectively associate compositional information measured by multiple analytical techniques, aiming to reveal their relationships with physical properties of biopolymers derived from hair. Hair samples were analyzed by multiple techniques, including solid-state nuclear magnetic resonance (NMR), time-domain NMR, Fourier transform infrared spectroscopy, and thermogravimetric and differential thermal analysis. The measured data were processed by different processing techniques, such as spectral differentiation and deconvolution, and then converted into a variety of “measurement descriptors” with different compositional information. The descriptors were associated with the mechanical properties of hair by constructing prediction models using machine learning algorithms. Herein, the stepwise model refinement via selection of adopted descriptors based on importance evaluation identified the most contributive descriptors, which provided an integrative interpretation about the compositional factors, such as α-helix keratins in cortex; and bounded water and thermal resistant components in cuticle. These results demonstrated the efficacy of the present strategy to generate and select descriptors from manifold measured data for investigating the nature of sophisticated subjects, such as hair.

The role of water in the reversibility of thermal denaturation of lysozyme in solid and liquid states

Although unfolding of protein in the liquid state is relatively well studied, its mechanisms in the solid state, are much less understood. We evaluated the reversibility of thermal unfolding of lysozyme with respect to the water content using a combination of thermodynamic and structural techniques such as differential scanning calorimetry, synchrotron small and wide-angle X-ray scattering (SWAXS) and Raman spectroscopy. Analysis of the endothermic thermal transition obtained by DSC scans showed three distinct unfolding behaviors at different water contents. Using SWAXS and Raman spectroscopy, we investigated reversibility of the unfolding for each hydration regime for various structural levels including overall molecular shape, secondary structure, hydrophobic and hydrogen bonding interactions. In the substantially dehydrated state below 37 wt% of water the unfolding is an irreversible process and can be described by a kinetic approach; above 60 wt% the process is reversible, and the thermodynamic equilibrium approach is applied. In the intermediate range of water contents between 37 wt% and 60 wt%, the system is phase separated and the thermal denaturation involves two processes: melting of protein crystals and unfolding of protein molecules. A phase diagram of thermal unfolding/denaturation in lysozyme - water system was constructed based on the experimental data.

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Denaturation of lysozyme in solid and liquid is studied using SAXS, Raman and DSC.

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Denaturation of lysozyme in liquid is reversible, in solid state it is irreversible.

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A phase diagram of lysozyme-water system is constructed.

Sum frequency generation spectroscopy of the attachment disc of a spider

The pyriform silk of the attachment disc of a spider was studied using infrared-visible vibrational sum frequency generation (SFG) spectroscopy. The spider can attach dragline and radial lines to many kinds of substrates in nature (concrete, alloy, metal, glass, plant branches, leaves, etc.) with the attachment disc. The adhesion can bear the spider's own weight, and resist the wind on its orb web. From our SFG spectroscopy study, the NH group of arginine side chain and/or NH₂ group of arginine and glutamine side chain in the amino acid sequence of the attachment silk proteins are suggested to be oriented in the disc. It was inferred from the observed doublet SFG peaks at around 3300 cm^-1 that the oriented peptide contains two kinds of structures.

Evaluation of the safety and healing potential of a fibroin-aloe gel film for the treatment of diabetic foot ulcers

OBJECTIVE

This study aimed to develop a wound dressing prepared from the blending of silkworm fibroin and aloe gel extract for use in the treatment of diabetic foot ulcers (DFUs).

METHODS

Fibroin extracted from silkworm cocoons and aloe gel extract were dissolved in deionised water. pH levels were then adjusted with lactic acid solution. A simple casting technique was used to obtain the fibroin-aloe gel film. The surface morphology, hardness, flexibility and infrared spectrum of the sterilised film were tested. Swelling ratio was measured from changes in weight. The cytocompatibility of the film to human dermal fibroblast was determined using XTT assay. Hard-to-heal DFUs (grade I Wagner score) were treated with the film for four weeks. The application site was assessed for allergic reactions and/or sensitisation. Wound size was measured using standardised digital photography.

RESULTS

A total of five hard-to-heal DFUs were treated. The obtained film sterilised with ozonation showed a non-porous structure. The elongation at break and tensile strength of the wet film were 9.00±0.95% and 6.89±1.21N, respectively. Fourier-transform infrared spectroscopy data indicated the presence of amides I, II and III, of peptide linkage, which are the chemical characteristics of the fibroin. Functional groups relating to healing activity of the aloe gel extract were also found. The swelling ratio of the film immersed in water for 24 hours was 0.8±0.01. In three DFUs (40-50mm² in size), a wound area reduction of 0.4-0.8mm²/day was observed and were healed in 2-3 weeks. The remaining two SFUs (500mm² in size) showed a wound area reduction of 4mm²/day and were almost closed at four weeks. No allergic reaction or infection was observed in any of the wounds.

CONCLUSION

The obtained film showed a non-porous structure, and its strength and flexibility were adequate for storage and handling. The film tended to increase the proliferation of fibroblasts. The wound dressing showed potential for accelerating the healing rate of DFUs.

Human ACE2-Functionalized Gold "Virus-Trap" Nanostructures for Accurate Capture of SARS-CoV-2 and Single-Virus SERS Detection

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold "virus traps" nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 10⁶-fold virus enrichment originating from high-affinity of ACE2 with S protein as well as "virus-traps" composed of oblique gold nanoneedles, and 10⁹-fold enhancement of Raman signals originating from multi-component SERS effects. Furthermore, the identification standard of virus signals is established by machine-learning and identification techniques, resulting in an especially low detection limit of 80 copies mL^-1 for the simulated contaminated water by SARS-CoV-2 virus with complex circumstance as short as 5 min, which is of great significance for achieving real-time monitoring and early warning of coronavirus. Moreover, here-developed method can be used to establish the identification standard for future unknown coronavirus, and immediately enable extremely sensitive and rapid detection of novel virus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40820-021-00620-8.

Factors Affecting Secondary and Supramolecular Structures of Self-Assembling Peptide Nanocarriers

Self-assembling peptides are a popular vector for therapeutic cargo delivery due to their versatility, tunability, and biocompatibility. Accurately predicting secondary and supramolecular structures of self-assembling peptides is essential for de novo peptide design. However, computational modeling of such assemblies is not yet able to accurately predict structure formation for many peptide sequences. This review identifies patterns in literature between secondary and supramolecular structures, primary sequences, and applications to provide a guide for informed peptide design. An overview of peptide structures, their applications as nanocarriers, and analytical methods for characterizing secondary and supramolecular structure is examined. A top-down approach is then used to identify trends between peptide sequence and assembly structure from the current literature, including an analysis of the drivers at work, such as local and nonlocal sequence effects and solution conditions.