Protein Chain Research Articles

Improving the bioaccessibility of lipophilic ingredient in its oral intestinal delivery by ultrasound and biological cross-linker.

Great efforts have been made to improve the oral bioaccessibility of lipophilic ingredients with multi-functionalities. Achieving intestinal delivery of lipophilic ingredients and their encapsulation in micelles composed of bile salts and lipid hydrolysates (i.e. fatty acids) is critical for improving oral bioaccessibility. Therefore, oil-core microcapsules are considered ideal carriers of lipophilic ingredients. Previous studies have reported oil-core/zein-shell microcapsules constructed by a one-step anti-solvent process. Still, its efficacy as an intestinal delivery system was limited because if the porous shell structure. Zein solution was pretreated with ultrasound and tannic acid (TA) cross-linking. Composite oil-core microcapsule (COM) with a compact shell structure was successfully prepared by using modified zein solution in the anti-solvent process. Fourier-transform infrared spectroscopy and circular dichroism analyses indicated that ultrasound and TA synergistically promote the conformational transition of zein from α-helix to β-sheet and enhance the hydrophobic interactions among protein chains. The above changes contribute to the strengthen of shell zein network. Correspondingly, COM presents superior encapsulation efficiency and environmental stability over the simple oil-core microcapsule (SOM) prepared without the use of ultrasound and TA. Furthermore, antioxidant activity of β-carotene was well retained during the encapsulation process. In vitro studies indicated that COM was more resistant to digestibility and acid-induced swelling. More than 87% of β-carotene could be released in the intestine in a sustainable way. The controllable release behavior thus promoted a significant increase in bioaccessibility of β-carotene encapsulated in COM compared to SOM (85.9% versus 48.5%). The COM generated here shows potential for bioaccessibility improvement of lipophilic ingredients. © 2022 Society of Chemical Industry.

Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium.

A vast number of intracellular membraneless bodies also known as biomolecular condensates form through a liquid-liquid phase separation (LLPS) of biomolecules. To date, phase separation has been identified as the main driving force for a membraneless organelles such as nucleoli, Cajal bodies, stress granules, and chromatin compartments. Recently, the protein-RNA condensation is receiving increased attention, because it is closely related to the biological function of cells such as transcription, translation, and RNA metabolism. Despite the multidisciplinary efforts put forth to study the biophysical properties of protein-RNA condensates, there are many fundamental unanswered questions regarding the mechanism of formation and regulation of protein-RNA condensates in eukaryotic cells. Major challenges in studying protein-RNA condensation stem from (i) the molecular heterogeneity and conformational flexibility of RNA and protein chains and (ii) the nonequilibrium nature of transcription and cellular environment. Computer simulations, bioinformatics, and mathematical models are uniquely positioned for shedding light on the microscopic nature of protein-RNA phase separation. To this end, there is an urgent need for innovative models with the right spatiotemporal resolution for confronting the experimental observables in a comprehensive and physics-based manner. In this chapter, we will summarize the currently emerging research efforts, which employ atomistic and coarse-grained molecular models and field theoretical models to understand equilibrium and nonequilibrium aspects of protein-RNA condensation.

Protein folding problem: enigma, paradox, solution.

The ability of protein chains to spontaneously form their three-dimensional structures is a long-standing mystery in molecular biology. The most conceptual aspect of this mystery is how the protein chain can find its native, "working" spatial structure (which, for not too big protein chains, corresponds to the global free energy minimum) in a biologically reasonable time, without exhaustive enumeration of all possible conformations, which would take billions of years. This is the so-called "Levinthal's paradox." In this review, we discuss the key ideas and discoveries leading to the current understanding of protein folding kinetics, including folding landscapes and funnels, free energy barriers at the folding/unfolding pathways, and the solution of Levinthal's paradox. A special role here is played by the "all-or-none" phase transition occurring at protein folding and unfolding and by the point of thermodynamic (and kinetic) equilibrium between the "native" and the "unfolded" phases of the protein chain (where the theory obtains the simplest form). The modern theory provides an understanding of key features of protein folding and, in good agreement with experiments, it (i) outlines the chain length-dependent range of protein folding times, (ii) predicts the observed maximal size of "foldable" proteins and domains. Besides, it predicts the maximal size of proteins and domains that fold under solely thermodynamic (rather than kinetic) control. Complementarily, a theoretical analysis of the number of possible protein folding patterns, performed at the level of formation and assembly of secondary structures, correctly outlines the upper limit of protein folding times.

Evolutionary Transformations of Albumin Using the Example of Model Species of Jawless Agnatha and Bony Jawed Fish (Review)

Issues of the organization of albumin (a protein belonging to the superfamily of albuminoids) are considered using the example of model representatives of lower aquatic vertebrates: jawless Agnatha (Cyclostomata) and jawed bony lobe-finned (Sarcopterygii) and ray-finned (Actinopterygii: Chondrostei, Holostei, Teleostei) fish. A comparative analysis is carried out of the total length and the length of coding and noncoding sequences of the albumin gene; the number of exons, the length of introns, and the presence of repeated DNA elements in them; and the presence/absence of paralogous genes, their chromosomal affiliation, and the composition of syntenic groups. A comparative analysis of the length of the amino acid sequence, the number of domains, and S–S bonds in the albumin structure is also carried out. The issues of the emergence of the ancestral gene for albuminoids, the “expansion” and “narrowing” of the albuminoid repertoire in different groups of vertebrates, the appearance of a cluster of paralogous genes within a single chromosome in the Sarcopterygii branch and paralogous genes on different chromosomes in the Actinopterygii branch in the representatives of cartilaginous ganoids and teleost fish, the elongation of the gene and protein chain of albumin in the lamprey line, and losses of the albumin gene in the largest groups of teleost fish (Ostariophysi and Acanthopterygii) are discussed. The listed scenarios are considered in light of their consistency with the events of whole genome, local, and segment duplications. The problem of compensating for the functions of the “lost” albumin gene due to multiple osmotically active plasma proteins is discussed using the example of the group of teleost fish.

RARE UNSTABLE ALPHA GLOBIN VARIANT HB TAYBE (HBA1:C.118_120DELACC) WITH HBA2 POLY A MUTATIONS, CAUSES TO HEMOLYTIC ANEMIA IN TWO CASES FROM AZERBAIJAN

Sequence variants are usually silent and rarer in α-globin, some may lead to an unstable protein with hemolytic or thalassemic phenotype. The most common HBA variant is ConstantSpring which is leading to an unstable elongated protein chain. Others may be due to ins/del in the α-globin, one of them Hb-Taybe caused deletion of Thr residue at codon 40 of the HBA1. We report, for the first time, 2 cases with hemolytic anemia due to the presence of Hb-Taybe in trans with HBA2 poly-A mutations. Patients were managed in the Thalassemia Unit of the National Hematology Center. Detailed pedigrees are drawn, medical recordings are reviewed and peripheral blood samples are collected. Sanger sequencing was perfomed with in house designed primers ( HBA1, NM_000558.5 and HBA2 , NM_000517.6) on genome analyser (ABI3500). Deletion and duplication analysis is performed by MLPA. P-1: A 4-yr-old male who was diagnosed at the age of 1 yr with congenital hemolytic anemia. He presented with jaundice, the blood film showed moderate hypochromia and anisopoikilocytosis. He was transfusion dependent. P-2: A 45-yr-old female who was diagnosed at the age of 5 yr with congenital hemolytic anemia. She underwent splenectomy at the age of 32 yr due to moderate anemia. After splenectomy she was not transfusion dependent. Relevant clinical and laboratory data is presented at table. The clinical presentation is variable from mild hemolytic anemia to regular transfusion requirement. One patient had to have splenectomy in order to ameliorate the transfusion requirement. This study supports the requirement of α-globin gene analyses, and a careful evaluation of cases with hemolytic anemia, particularly in populations where thalassemias are endemic, in order to avoid missing any of the rare globin variants and to offer accurate genetic counseling.

Edible Bird’s Nest, a Valuable Glycoprotein Source: Current Research Prospects and Challenges in Malaysia

Edible bird's nest (EBN) is a salivary secretion of swiftlets which consist of protein and carbohydrate rich glycoproteins. This natural ingredient is very valuable, nutritional and medically valuable. The EBN industry have grown rapidly and benefited the Malaysian economy, hence, it is viewed seriously and it is actively supported by the government. This review discusses the progress and development of EBN industry as well as the R&D activities and endeavours especially that which involves deriving peptides with biological activities from EBN and its by-product sources. Many studies have documented the therapeutic properties of EBN such as antiaging, antiviral, antioxidant, and antihypertensive. Studies have also been conducted to produce glycoprotein hydrolysates from EBN through enzymatic hydrolysis, and findings showed that these bioactive peptides increase solubility as well as antioxidant and antihypertensive activities. Enzymatic hydrolysis breaks long protein chains at specific sites and releases amino acids and small peptides with lower molecular weights. The EBN hydrolysates produced can improve bioactivity and overcome insolubility and low absorption of EBN prepared and consumed through traditional means. Further studies need to be carried out to optimise EBN glycoprotein hydrolysates production as well as maximising their bioavailability and efficacy in the human gastrointestinal system. In addition, EBN by-products produced during EBN cleaning process should be fully utilised to recover the high-value glycoproteins, while reducing pollution and wastage. By enhancing R&D activities of EBN, bioactive glycopeptides produced from EBN may become an important functional food ingredient for various uses and innovative value-added products in the future.

Recording of cellular physiological histories along optically readable self-assembling protein chains

Recording of cellular physiological histories along optically readable self-assembling protein chains

Serum glial fibrillary acidic protein and neurofilament light chain in patients with early treated phenylketonuria.

To pave the way for healthy aging in early treated phenylketonuria (ETPKU) patients, a better understanding of the neurological course in this population is needed, requiring easy accessible biomarkers to monitor neurological disease progression in large cohorts. The objective of this pilot study was to investigate the potential of glial fibrillary acidic protein (GFAP) and neurofilament light chain (NfL) as blood biomarkers to indicate changes of the central nervous system in ETPKU. In this single-center cross-sectional study, GFAP and NfL concentrations in serum were quantified using the Simoa® multiplex technology in 56 ETPKU patients aged 6–36 years and 16 age matched healthy controls. Correlation analysis and hierarchical linear regression analysis were performed to investigate an association with disease-related biochemical parameters and retinal layers assessed by optical coherence tomography. ETPKU patients did not show significantly higher GFAP concentrations (mean 73 pg/ml) compared to healthy controls (mean 60 pg/ml, p = 0.140). However, individual pediatric and adult ETPKU patients had GFAP concentrations above the healthy control range. In addition, there was a significant association of GFAP concentrations with current plasma tyrosine concentrations (r = −0.482, p = 0.036), a biochemical marker in phenylketonuria, and the retinal inner nuclear layer volume (r = 0.451, p = 0.04). There was no evidence of NfL alterations in our ETPKU cohort. These pilot results encourage multicenter longitudinal studies to further investigate serum GFAP as a complementary tool to better understand and monitor neurological disease progression in ETPKU. Follow-up investigations on aging ETPKU patients are required to elucidate the potential of serum NfL as biomarker.

Extensive Molecular Dynamics Simulations Disclosed the Stability of mPGES-1 Enzyme and the Structural Role of Glutathione (GSH) Cofactor.

A deep in silico investigation of various microsomal prostaglandin E2 synthase-1 (mPGES-1) protein systems is here reported using molecular dynamics (MD) simulations. Firstly, eight different proteins models (Models A-H) were built, starting from the active enzyme trimer system (Model A), namely that bound to three glutathione (GSH) cofactor molecules, and then gradually removing the GSHs (Models B-H), simulating each of them for 100 ns in explicit solvent. The analysis of the obtained data disclosed the structural role of GSH in the chemical architecture of mPGES-1 enzyme, thus suggesting the unlikely displacement of this cofactor, in accordance with experimentally determined protein structures co-complexed with small molecule inhibitors. Afterwards, Model A was submitted to microsecond-scale molecular dynamics simulation (total simulation time=10 μs), in order to shed light about the dynamical behaviour of this enzyme at atomic level and to obtain further structural features and protein function information. We confirmed the structural stability of the enzyme machinery, observing a conformational rigidity of the protein, with a backbone RMSD of ∼3 Å along the simulation time, and highlighting the strong active contribution of GSH molecules due to their active role in packing the protein chains through a tight binding at monomer interfaces. Furthermore, the focused analysis on R73 residue disclosed its role in solvent exchange events, probably excluding its function as route for GSH to enter towards the endoplasmic reticulum membrane, in line with the recently reported function of cap domain residues F44-D66 as gatekeeper for GSH entrance into catalytic site.

Cardiovascular Factors Associated with COVID-19 from an International Registry of Primarily Japanese Patients.

Aims: We developed an international registry to examine cardiovascular complications of COVID-19. Methods: A REDCap form was created in March 2020 at Mayo Clinic in collaboration with the International Society of Cardiomyopathy, Myocarditis and Heart Failure (ISCMF) and data were entered from April 2020 through April 2021. Results: Of the 696 patients in the COVID-19 Registry, 411 (59.2%) were male and 283 (40.8%) were female, with a sex ratio of 1.5:1 male to female. In total, 95.5% of the patients were from Japan. The average age was 52 years with 31.5% being >65 years of age. COVID-19 patients with a history of cardiovascular disease (CVD) had more pre-existing conditions including type II diabetes (p < 0.0001), cancer (p = 0.0003), obesity (p = 0.001), and kidney disease (p = 0.001). They also had a greater mortality of 10.1% compared to 1.7% in those without a history of CVD (p < 0.0001). The most common cardiovascular conditions in patients with a history of CVD were hypertension (33.7%), stroke (5.7%) and arrhythmias (5.1%). We found that troponin T, troponin I, brain natriuretic peptide (BNP), N-terminal pro-BNP (NT-proBNP), C-reactive protein (CRP), IL-6 and lambda immunoglobulin free light chains (Ig FLC) were elevated above reference levels in patients with COVID-19. Myocarditis is known to occur mainly in adults under the age of 50, and when we examined biomarkers in patients that were ≤50 years of age and had no history of CVD we found that a majority of patients had elevated levels of troponin T (71.4%), IL-6 (59.5%), creatine kinase/CK-MB (57.1%), D-dimer (57.8%), kappa Ig FLC (75.0%), and lambda Ig FLC (71.4%) suggesting myocardial injury and possible myocarditis. Conclusions: We report the first findings to our knowledge of cardiovascular complications from COVID-19 in the first year of the pandemic in a predominantly Japanese population. Mortality was increased by a history of CVD and pre-existing conditions including type II diabetes, cancer, obesity, and kidney disease. Our findings indicate that even in cases where no abnormalities are found in ECG or ultrasound cardiography that myocardial damage may occur, and cardiovascular and inflammatory biomarkers may be useful for the diagnosis.

Nuclear Molecular Imaging of Disease Burden and Response to Treatment for Cardiac Amyloidosis

Simple SummaryCardiac amyloidosis (CA) is characterized by extracellular infiltration and deposition of amyloid fibrils primarily derived from the circulating transthyretin protein (TTR) or immunoglobulin light chain (AL). With the development of non-invasive diagnostic approaches and the emergence of new pharmacotherapeutic treatments for CA, the transformative effects of bone scintigraphy have been important in diagnosing TTR-CA. Positron emission tomography (PET) imaging is another promising, non-invasive option for the diagnosis of CA and may help differentiate between ATTR and AL amyloidosis. Bone-seeking single-photon emission tomography/computed tomography (SPECT/CT) quantification and amyloid-targeting PET imaging could be useful as a new strategy for disease burden and therapy monitoring to provide more insights into therapy response assessed by quantifying the amyloid burden in CA.Cardiac amyloidosis (CA) is a heterogeneous group of diseases in which extracellular insoluble amyloid proteins are deposited in specific organs and tissues locally or systemically, thereby interfering with physiological function. Transthyretin protein (TTR) and light chain (AL) amyloidosis are the most common types of cardiac amyloidosis. Radionuclide bone scintigraphy has recently become the most common non-invasive test for the diagnosis of TTR-CA but is of limited value for the diagnosis of AL-CA. PET has proved promising for the diagnosis of CA and its applications are expected to expand in the future. This review summarizes the current bone scintigraphy and amyloid-targeting Positron emission tomography (PET) imaging, the binding imaging properties of radiotracers, and the values of diagnosis, prognosis, and monitoring therapy response in CA.

A novel universal strategy for fabricating soybean protein adhesive with excellent adhesion and anti-mildew performances

Soybean meal (SM) adhesive is a promising alternative to petroleum-based ones. However, the poor water resistance, low bonding strength, and susceptibility to mildew limit its industrial application. Inspired by the micro-nano micelle structure's strengthening mechanism, a facile and green method of synthesizing a high-performance soy protein adhesive by a dual cross-linking strategy was reported. The in-situ self-assembled micelles of benzyldodecyldimethylammonium bromide (BDAB) interacted with protein chains via dynamical bonds, while 1,6-hexanediol diglycidyl ether (HDE) acted as the flexible cross-linker. The BDAB micelles interact with protein chains via non-covalent electrostatic interactions, improving the cross-linking density of the network system and the micelles with numerous amino cations exhibit efficient anti-bacterial properties. The as-obtained adhesive exhibits excellent mechanical properties and stable network structure, showing strong bonding strength and water resistance (2.22 and 1.25 MPa). Especially, the incorporation of HDE and BDAB imparts the modified SM adhesive with excellent antifungal and antibacterial (E. coli and S. aureus) performances, significantly extending the adhesive storage life. Additionally, this work provides a new facile and universal strategy for fabricating formaldehyde-free, environment-friendly, and renewable protein-based adhesives, which is a promising alternative to traditional adhesives in the wood industry.

Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function.

The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and processes such as tumor dissemination and metastatic growth remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines, we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells down-regulate glycolytic mechanisms. These studies demonstrate that discrete perturbations of mitochondrial respiratory chain function impact in vivo tumor growth in a context-specific manner with differential impacts on primary and metastatic tumors.

Green and efficient production of functionalized graphene to achieve soybean meal-based adhesive enhancement

Designing organic-inorganic nanohybrid systems have exhibited considerable potential in fabricating high-performance protein-based adhesives. However, the simplicity of the strategy, renewability, cost and effective dispersion of inorganic nanofillers in a hybrid framework remains challenging. This study proposed a simple, cost-effective, and sustainable design strategy to fabricate soybean meal (SM)-based hybrid adhesives using sodium lignosulfonate-functionalized graphene (SLS@G). SLS@G was simultaneously produced and functionalized via a dry ball milling method from graphite without using toxic reagents and tedious fabrication procedures. SLS@G had stable water dispersion and good compatibility with the SM adhesive matrix. The synergistic hydrogen bonding and hydrophobic interaction between SLS@G and the protein chains remarkedly improved the strength and water resistance of the SM-based adhesive. With minimal addition of the SLS@G (0.10 wt% of SM), the modified adhesive dry and wet shear strengths increased to 2.19 MPa and 1.15 MPa, which were 32.7% and 248.5% higher than the pristine adhesive, respectively. Moreover, the construction of the organic-inorganic nanohybrid structure also contributed to the thermal stability of the SM-based adhesives, leading to the increase in carbon residue rate from 26.6% to 28%. Overall, this facile and green strategy offers a new design pathway for developing advanced and multifunctional bio-adhesives for engineered wood-based composites.

Immunomodulatory activity of glycoproteins isolated from chickpea (Cicer arietinum L.).

Chickpea (Cicer arietinum L.) is a well-known legume widely used as traditional medicine. This study aimed to characterize the structure and evaluate the immunomodulatory activity of one glycoprotein [crude chickpea glycoprotein-1 (CAG-1)] isolated from chickpea. CAG-1 was extracted with hot alkaline water and purified with DEAE-Sepharose Fast Flow and Superdex-200 column chromatography. CAG-1, with a molecular weight of 8,106 Da, contained 57.12% polysaccharide and 35.41% protein. The polysaccharide part was mainly composed of glucose (Glc). The protein part was connected mainly by aspartic (Asp) and glutamic (Glu). The results of nuclear magnetic resonance (NMR) analysis indicated the presence of α-d-Glcp-(1 → 4)-α-d-Glcp-(1 → 4)-α-d-Glcp-(1 → . In addition, the sugar chains of the glycoprotein were not hydrolyzed under alkaline conditions, suggesting that the glycoprotein was N-glycosidic; thus, the sugar chain was linked to the protein chain by Asp. An immunological study showed that CAG-1 stimulated the production of nitric oxide (NO), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and monocyte chemotactic protein 1 (MCP-1) in RAW 264.7 macrophages in a dose-dependent manner.

COMPUTATIONAL ANALYSIS OF FUNCTIONAL EFFECTS OF SINGLE NUCLEOTIDE POLYMORPHISM ON OVINE INTERFERON TAU

The objective of this study was to evaluate the functional effects of Single Nucleotide Polymorphism(SNP) in ovine interferon tau using computational methods. Data on ovine interferon was retrieved from data base of National Center for Biotechnology Information ((GenBank). Functional effects of substitution of Leucin by Proline at position 26 of interferon protein chain was predicted using Protein Variation Effect Analyser, Panther server and Poly phen 2 (Polymorphism phenotyping). Provean score of - 5.828 was obtained, indicating a deleterious effect of the amino acid substitution. Panther server indicated damaging effect of the SNP with Pdel ( probability of deleterious effect) of 0.5. Similarly, Poly phen 2 showed damaging effect of the amino acid substitution. It can be concluded that substitution of Leucin by proline at position 26 of the protein sequence of interferon tau resulted in deleterious effect on the functionality of ovine interferon tau. Studies in Single Nucleotide Polymorphism on ovine interferon tau can provide better understanding of biomarkers associated with efficiency of maternal pregnancy recognition in the ovine species.

Thermodynamics and Conformations of Single Polyalanine, Polyserine, and Polyglutamine Chains within the PRIME20 Model.

Understanding the conformational behavior of proteins has been a long-standing challenge to which computer simulations could contribute significantly. This concerns the folding behavior of proteins as well as the conformational statistics of intrinsically disordered proteins. A well-converged sampling of the conformational statistics over a broad range of control parameters is computationally extremely challenging and best addressed by coarse-grained modeling, for example, with an intermediate resolution model like the PRIME20 model. A comprehensive understanding of the thermodynamics and conformational statistics of individual protein chains is, however, not only a goal in itself but also a prerequisite for a better understanding of their aggregation tendency into oligomers and further into amyloid fibrils. We present here an extensive comparison of the ability of the PRIME20 model (in its documented variants in the literature) to faithfully reproduce the thermodynamics and statistics of three homopeptides having very different folding temperatures and different typical secondary structures.

SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK.

The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.

High-Moisture Shear Processes: Molecular Changes of Wheat Gluten and Potential Plant-Based Proteins for Its Replacement.

Nowadays, a growing offering of plant-based meat alternatives is available in the food market. Technologically, these products are produced through high-moisture shear technology. Process settings and material composition have a significant impact on the physicochemical characteristics of the final products. Throughout the process, the unfolded protein chains may be reduced, or associate in larger structures, creating rearrangement and cross-linking during the cooling stage. Generally, soy and pea proteins are the most used ingredients in plant-based meat analogues. Nevertheless, these proteins have shown poorer results with respect to the typical fibrousness and juiciness found in real meat. To address this limitation, wheat gluten is often incorporated into the formulations. This literature review highlights the key role of wheat gluten in creating products with higher anisotropy. The generation of new disulfide bonds after the addition of wheat gluten is critical to achieve the sought-after fibrous texture, whereas its incompatibility with the other protein phase present in the system is critical for the structuring process. However, allergenicity problems related to wheat gluten require alternatives, hence an evaluation of underutilized plant-based proteins has been carried out to identify those that potentially can imitate wheat gluten behavior during high-moisture shear processing.

Microscopic insight into the interactions between pea protein and fatty acids during high-moisture extrusion processing

To provide a theoretical basis for the quality improvement of plant protein-based meat substitutes with lipids, the interactions between pea protein and fatty acids (stearic, oleic and linoleic acids) and the effect on protein conformational changes during high-moisture extrusion (HME) processing were investigated using a dead-stop operation. The surface hydrophobicity analysis and Fourier transform infrared spectroscopy results revealed that the fatty acids induced the exposure of hydrophobic groups in the pea proteins, weakened hydrogen bonds, affected the aggregation of legumin subunits and promoted the conversion of α-helix and β-sheet structures to β-turn and random coil during HME processing. In the die, unsaturated fatty acids limited the refolding of protein chains and covalent interactions between proteins. Micromorphology analysis indicated that the coalescence of oleic and linoleic acids in the cooling zone hindered the formation of anisotropic structures while stearic acid promoted the formation of fibrous structures by enhanced disulfide bonds.