Bioinformatic Study of Possible Acute Regulation of Acid Secretion in the Stomach.

The gastric H+,K+-ATPase is an integral membrane protein which derives energy from the hydrolysis of ATP to transport H+ ions from the parietal cells of the gastric mucosa into the stomach in exchange for K+ ions. It is responsible for the acidic environment of the stomach, which is essential for digestion. Acid secretion is regulated by the recruitment of the H+,K+-ATPase from intracellular stores into the plasma membrane on the ingestion of food. The similar amino acid sequences of the lysine-rich N-termini α-subunits of the H+,K+- and Na+,K+-ATPases, suggests similar acute regulation mechanisms, specifically, an electrostatic switch mechanism involving an interaction of the N-terminal tail with the surface of the surrounding membrane and a modulation of the interaction via regulatory phosphorylation by protein kinases. From a consideration of sequence alignment of the H+,K+-ATPase and an analysis of its coevolution with protein kinase C and kinases of the Src family, the evidence points towards a phosphorylation of tyrosine-7 of the N-terminus by either Lck or Yes in all vertebrates except cartilaginous fish. The results obtained will guide and focus future experimental research.

Isolation and antioxidant activity of peptides from Chinese hairy tofu.

Hairy tofu is a famous Chinese snack that is made from soybeans and rich in various nutrients. In order to further explore the antioxidant peptides of hairy tofu hydrolysates, seven proteases were used to hydrolyze hairy tofu. The results of in vitro radical scavenging activity showed that hairy tofu hydrolysates obtained by pancreatin exhibited the highest antioxidant activity. After Sephadex G-25 gel filtration and reversed-phase high-performance liquid chromatography (RP-HPLC), 97 peptides were identified in the most antioxidant fraction using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Among them, nine peptides were synthesized and their antioxidant activities were assessed using a H2 O2 -induced oxidative 293T cell model. Finally, four peptides (QCESHK, LAWNEGR, NLQGENEWDQK, and FTEMWR) at concentrations of < 50 µg/ml significantly decreased the malondialdehyde content compared with the model group, displaying in vivo antioxidant activity and low cytotoxicity. Overall, this research provided the choice of using hairy tofu peptides as antioxidant products in the pharmaceutical and food industries.

Unique Patterns in Amino Acid Sequences of Aging-Related Proteins.

Aging has strong genetic components and the list of genes that may regulate the aging process is collected in the GenAge database. There may be characteristic patterns in the amino acid sequences of aging-related proteins that distinguish them from other proteins and this information will lead to a better understanding of the aging process. To test this hypothesis, human protein sequences are extracted from the UniProt database and the relative frequency of every amino acid residue in aging-related proteins and the remaining proteins is calculated. The main observation is that the mean relative frequency of aspartic acid (D) is consistently higher, while the mean relative frequencies of tryptophan (W) and leucine (L) are consistently lower in aging-related proteins compared to the non-aging-related proteins for the human and four examined model organisms. It is also observed that the mean relative frequency of aspartic acid is higher, while the mean relative frequency of tryptophan is lower in pro-longevity proteins compared to anti-longevity proteins in model organisms. Finally, it is found that aging-related proteins tend to be longer than non-aging-related proteins. It is hoped that this analysis initiates further computational and experimental research to explore the underlying mechanisms of these findings.

Bioinformatics Analysis of Global Diversity in Meningococcal Vaccine Antigens over the Past 10 Years: Vaccine Efficacy Prognosis.

Neisseria meningitidis (N. meningitidis) serogroup B (MenB) is the leading cause of invasive meningococcal disease worldwide. The pathogen has a wide range of virulence factors, which are potential vaccine components. Studying the genetic variability of antigens within a population, especially their long-term persistence, is necessary to develop new vaccines and predict the effectiveness of existing ones. The multicomponent 4CMenB vaccine (Bexsero), used since 2014, contains three major genome-derived recombinant proteins: factor H-binding protein (fHbp), Neisserial Heparin-Binding Antigen (NHBA) and Neisserial adhesin A (NadA). Here, we assessed the prevalence and sequence variations of these vaccine antigens in a panel of 5667 meningococcal isolates collected worldwide over the past 10 years and deposited in the PubMLST database. Using multiple amino acid sequence alignments and Random Forest Classifier machine learning methods, we estimated the potential strain coverage of fHbp and NHBA vaccine variants (51 and about 25%, respectively); the NadA antigen sequence was found in only 18% of MenB genomes analyzed, but cross-reactive variants were present in less than 1% of isolates. Based on our findings, we proposed various strategies to improve the 4CMenB vaccine and broaden the coverage of N. meningitidis strains.

The Biological Action and Structural Characterization of Eryngitin 3 and 4, Ribotoxin-like Proteins from Pleurotus eryngii Fruiting Bodies.

Ribotoxin-like proteins (RL-Ps) are specific ribonucleases found in mushrooms that are able to cleave a single phosphodiester bond located in the sarcin-ricin loop (SRL) of the large rRNA. The cleaved SRL interacts differently with some ribosomal proteins (P-stalk). This action blocks protein synthesis because the damaged ribosomes are unable to interact with elongation factors. Here, the amino acid sequences of eryngitin 3 and 4, RL-Ps isolated from Pleurotus eryngii fruiting bodies, were determined to (i) obtain structural information on this specific ribonuclease family from edible mushrooms and (ii) explore the structural determinants which justify their different biological and antipathogenic activities. Indeed, eryngitin 3 exhibited higher toxicity with respect to eryngitin 4 against tumoral cell lines and model fungi. Structurally, eryngitin 3 and 4 consist of 132 amino acids, most of them identical and exhibiting a single free cysteinyl residue. The amino acidic differences between the two toxins are (i) an additional phenylalanyl residue at the N-terminus of eryngitin 3, not retrieved in eryngitin 4, and (ii) an additional arginyl residue at the C-terminus of eryngitin 4, not retrieved in eryngitin 3. The 3D models of eryngitins show slight differences at the N- and C-terminal regions. In particular, the positive electrostatic surface at the C-terminal of eryngitin 4 is due to the additional arginyl residue not retrieved in eryngitin 3. This additional positive charge could interfere with the binding to the SRL (substrate) or with some ribosomal proteins (P-stalk structure) during substrate recognition.

Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations.

This study aims to the investigation of the advantages of designing new proteins presume upon a 'bias' sequence of amino acids, based on the reversed sequence of parent proteins, such as the retro ones. The structural simplicity of wtRop offers a very attractive model system to study these aspects. The current work is based on all-atom Molecular Dynamics (MD) simulations and corresponding experimental evidence on two different types of reversed wtRop protein, one with a fully reversed sequence of amino acids (rRop) and another with a partially reversed sequence (prRop), where only the five residues of the loop region (30ASP-34GLN) were not reversed. The exploration of the structure of the two retro proteins is performed highlighting the similarities and the differences with their parent protein, by employing various measures. Two models have been studied for both reversed proteins, a dimeric and a monomeric with the former one found to be more stable than the latter. Preferable equilibrium structures that the protein molecule can attain are explored, indicating the equilibration pathway. Simulation findings indicate a disruption of the α-helical structure and the appearance of additional secondary structures for both retro proteins. Reduced structural stability compared to their parent protein (wtRop) is also found. A corruption of the hydrophobic core is observed in the dimeric models. Furthermore, the simulations findings are consistent with the experimental characterization of prRop by circular dichroism spectroscopy (CD) which highlights an unstable, highly α-helical protein.Communicated by Ramaswamy H. Sarma.

Ameliorative effect of mussel-derived ACE inhibitory peptides on spontaneous hypertension rats.

PURPOSE: The purpose of this study was to prepare the novel mussel-derived ACE inhibitory peptides (MEPs) by enzymatic hydrolysis of Mytilus edulis and investigate their antihypertensive effects in vivo. METHODS: After assessing the stability of MEPs in vitro, we investigated the effect of MEPs on hypertension using spontaneously hypertensive rats (SHRs). Subsequently, MEPs were purified and identified by ultrafiltration, gel filtration chromatography and liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS: Our study demonstrated that MEPs could keep stable ACE inhibitory activity after treatment with heat, acid, alkali, metal ions and simulated gastrointestinal digestive fluid. Additionally, the animal experiments showed that both short-term and long-term treatment with MEPs resulted in a significant reduction in systolic and diastolic blood pressure in SHRs. Mechanistically, the results suggested that MEPs could reduce vascular remodeling, regulate renin-angiotensin system (RAS), and inhibit kidney and myocardial fibrosis. Finally, we isolated and identified five peptides from MEPs, with the peptide Ile-Leu-Thr-Glu-Arg showed the highest ACE inhibition rate. CONCLUSION: Our findings demonstrate the potential use of MEPs as active components in functional foods designed to lower blood pressure.

Neural Network Models for Sequence-Based TCR and HLA Association Prediction.

T cells rely on their T cell receptors (TCRs) to recognize foreign antigens presented by human leukocyte antigen (HLA) proteins. TCRs contain a record of an individual's past immune activities, and some TCRs are observed only in individuals with certain HLA alleles. As a result, characterising TCRs requires a thorough understanding of TCR-HLA associations. To this end, we propose a neural network method named Deep learning Prediction of TCR-HLA association (DePTH) to predict TCR-HLA associations based on their amino acid sequences. We show that the DePTH can be used to quantify the functional similarities of HLA alleles, and that these HLA similarities are associated with the survival outcomes of cancer patients who received immune checkpoint blockade treatment.

Bioindustrial applications of thermostable Endoglucanase purified from Trichoderma viride towards the conversion of agrowastes to value-added products.

Importance of biocatalytic reactions and biotransformations mediated by fungal enzymes has increased tremendously in various industries. Endoglucanase obtained from Trichoderma viride has been utilized for bioconversion of agrowastes; wheat straw (WS) and corn stover (CS) as biomass into citric acid and single cell protein (SCP) as value-added products. The enzyme was purified to apparent homogeneity with Mr:44.67 kDa; purification-fold, yield, specific activity to be 19.5-, 29.2%, and 150.4 Units.mg-1, respectively, with thermostability up to 70 °C. The enzyme showed a novel N-terminal peptide and its computational analysis revealed a conserved 'SG' amino acid sequence alike microbial cellulases. The experimental results have shown the potential of endoglucanase for the conversion of agrowastes; wheat straw (WS) and corn stover (CS) into citric acid, maximum yield (KgM-3) found in submerged (WS:50;CS:45) fermentation process. Single-cell protein (SCP) production in WS (68 KgM-3) hydrolysate was superior to both CS hydrolysate (60 KgM-3) and YEPD (standard medium) (58 KgM-3).

Deciphering anti-biofilm property of Arthrospira platensis-origin peptides against Staphylococcusaureus.

Arthrospira platensis is a valuable natural health supplement consisting of various types of vitamins, dietary minerals, and antioxidants. Although different studies have been conducted to explore the hidden benefits of this bacterium, its antimicrobial property has been poorly understood. To decipher this important feature, here, we extended our recently introduced optimization algorithm (Trader) for aligning amino acid sequences associated with the antimicrobial peptides (AMPs) of Staphylococcus aureus and A.platensis. As a result, similar amino acid sequences were identified, and several candidate peptides were generated accordingly. The obtained peptides were then filtered based on their potential biochemical and biophysical properties, and their 3D structures were simulated based on homology modeling techniques. Next, to investigate how the generated peptides can interact with S. aureus proteins (i.e., heptameric state of the hly and homodimeric form of the arsB), molecular docking approaches were used. The results indicated that four peptides included better molecular interactions relative to the other generated ones in terms of the number/average length of hydrogen bonds and hydrophobic interactions. Based on the outcomes, it can be concluded that the antimicrobial property of A.platensis might be associated with its capability in disturbing the membrane of pathogens and their functions.

Low Complexity Regions in Proteins and DNA are Poorly Correlated.

Low complexity sequences (LCRs) are well known within coding as well as non-coding sequences. A low complexity region within a protein must be encoded by the underlying DNA sequence. Here, we examine the relationship between the entropy of the protein sequence and that of the DNA sequence which encodes it. We show that they are poorly correlated whether starting with a low complexity region within the protein and comparing it to the corresponding sequence in the DNA or by finding a low complexity region within coding DNA and comparing it to the corresponding sequence in the protein. We show this is the case within the proteomes of five model organisms: Homo sapiens, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana. We also report a significant bias against mononucleic codons in LCR encoding sequences. By comparison with simulated proteomes, we show that highly repetitive LCRs may be explained by neutral, slippage-based evolution, but compositionally biased LCRs with cryptic repeats are not. We demonstrate that other biological biases and forces must be acting to create and maintain these LCRs. Uncovering these forces will improve our understanding of protein LCR evolution.

Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics.

Metaproteomics is a relatively young field that has only been studied for approximately 15 years. Nevertheless, it has the potential to play a key role in disease research by elucidating the mechanisms of communication between the human host and the microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match.

Sequence and structure alignments in post-AlphaFold era.

Sequence alignment is fundamental for analyzing protein structure and function. For all but closely-related proteins, alignments based on structures are more accurate than alignments based purely on amino-acid sequences. However, the disparity between the large amount of sequence data and the relative paucity of experimentally-determined structures has precluded the general applicability of structure alignment. Based on the success of AlphaFold (and its likes) in producing high-quality structure predictions, we suggest that when aligning homologous proteins, lacking experimental structures, better results can be obtained by a structural alignment of predicted structures than by an alignment based only on amino-acid sequences. We present a quantitative evaluation, based on pairwise alignments of sequences and structures (both predicted and experimental) to support this hypothesis.

Effects of Sequence Composition, Patterning and Hydrodynamics on the Conformation and Dynamics of Intrinsically Disordered Proteins.

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and IDRs dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures and dynamics, with different experimental techniques often offering seemingly contradictory results. Although experimental and theoretical evidence indicates that some IDP properties can be understood based on their average biophysical properties and amino acid composition, other aspects of IDP function are dictated by the specifics of the amino acid sequence. We investigate the effects of several key variables on the dimensions and the dynamics of IDPs using coarse-grained polymer models. We focus on the sequence "patchiness" informed by the sequence and biophysical properties of different classes of IDPs-and in particular FG nucleoporins of the nuclear pore complex (NPC). We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence-specific. We find that in good solvent conditions highly heterogeneous sequences of IDPs can be well mapped onto averaged minimal polymer models for the purpose of prediction of the IDPs dimensions and dynamic relaxation times. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for the further applications of mesoscopic models of FG nucleoporins and IDPs more broadly.

ProFeatX: A parallelized protein feature extraction suite for machine learning.

Machine learning algorithms have been successfully applied in proteomics, genomics and transcriptomics. and have helped the biological community to answer complex questions. However, most machine learning methods require lots of data, with every data point having the same vector size. The biological sequence data, such as proteins, are amino acid sequences of variable length, which makes it essential to extract a definite number of features from all the proteins for them to be used as input into machine learning models. There are numerous methods to achieve this, but only several tools let researchers encode their proteins using multiple schemes without having to use different programs or, in many cases, code these algorithms themselves, or even come up with new algorithms. In this work, we created ProFeatX, a tool that contains 50 encodings to extract protein features in an efficient and fast way supporting desktop as well as high-performance computing environment. It can also encode concatenated features for protein-protein interactions. The tool has an easy-to-use web interface, allowing non-experts to use feature extraction techniques, as well as a stand-alone version for advanced users. ProFeatX is implemented in C++ and available on GitHub at https://github.com/usubioinfo/profeatx. The web server is available at http://bioinfo.usu.edu/profeatx/.

Antioxidant peptides: Overview of production, properties, and applications in food systems.

In recent years, several studies have reported the beneficial effects of antioxidant peptides in delaying oxidation reactions. Thus, a growing number of food proteins have been investigated as suitable sources for obtaining these antioxidant peptides. In this study, some of the most critical developments in the discovery of peptidic antioxidants are discussed. Initially, the primary methods to release, purify, and identify these antioxidant peptides from various food-derived sources are reviewed. Then, computer-based screening methods of the available peptides are summarized, and methods to interpret their structure-activity relationship are illustrated. Finally, approaches to the large-scale production of these bioactive peptides are described. In addition, the applications of these antioxidants in food systems are discussed, and gaps, future challenges, and opportunities in this field are highlighted. In conclusion, various food items can be considered promising sources to obtain these novel antioxidant peptides, which present various opportunities for food applications in addition to health promotion. The lack of in-depth data on the link between the structure and activity of these antioxidants, which is critical for the prediction of possible bioactive amino acid sequences and their potency in food systems and in vivo conditions (rather than in vitro systems), requires further attention. Consequently, future collaborative research activities between the industry and academia are required to realize the commercialization objectives of these novel antioxidant peptides.

Darwinian Evolution of Intelligence.

Intelligence is often discussed in terms of neural networks in the cerebral cortex, whose evolution has presumably been influenced by Darwinian selection. Here we present molecular evidence that one of the many kinesin motors, KIF14, has evolved to exhibit a special feature in its amino acid sequence that could improve neural networks. The improvement is quantified by comparison of NIF14 sequences for 12 species. The special feature is level sets of synchronized hydrophobic extrema in water wave profiles based on several hydropathic scales. The most effective scale is a new one based on fractals indicative of approach of globular curvatures to self-organized criticality, which summarizes evolutionary trends based on intelligent design.

Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics.

Prediction of subcellular localization of proteins from their amino acid sequences has a long history in bioinformatics and is still actively developing, incorporating the latest advances in machine learning and proteomics. Notably, deep learning-based methods for natural language processing have made great contributions. Here, we review recent advances in the field as well as its related fields, such as subcellular proteomics and the prediction/recognition of subcellular localization from image data.

In vitro immunomodulatory and antioxidant effects of oligopeptides and four characteristic peptides in black-bone silky fowl (Gallus gallus domesticus Brisson).

Black-bone silky fowl (Gallus gallus domesticus Brisson) is considered to have strengthening effect on the body and immunomodulatory effects. The black-bone silky fowl peptide (BSFP) was produced by enzymatic digestion of the whole black-bone silky fowl (including the head and claws) after removal of the viscera. Afterwards, the four of the characteristic peptides Glu-Phe (EF), Glu-Glu-Leu (EEL), Glu-His-Pro-Thr (EHPT), Ala-Gly-Gly-His (AGGF) of the BSFP were identified by HPLC-MS/MS. The preventive effects of BSFP and the four characteristic peptides on antioxidant and immunomodulation were investigated. The antioxidant capacity was assessed by in vitro HepG2 intracellular reactive oxygen species (ROS). The immunomodulatory experiments were conducted by measuring the effects of the BSFP and four peptides on the proliferation of splenocytes, T and B lymphocytes cells, the CD4+ /CD8+ T lymphocytes ratio, and the phagocytic capacity of macrophages and the nitric oxide (NO) content of macrophages. The four peptides of BSFP showed strong antioxidant capacity, with the most potent peptide for intracellular ROS being AGGF, with 56% inhibition. AGGF, EF, and BSFP showed highly positive effects on splenocyte proliferation and when Concanavalin A (ConA) was used as a stimulus for T lymphocytes and lipopolysaccharide (LPS) as a stimulus for B lymphocytes, the peptides stimulated cell proliferation in a dose-dependent manner. Of these, EF, AGGF, and BSFP promoted the proliferation of T lymphocytes; EF, EHPT, and BSFP significantly promoted the proliferation of B lymphocytes. EHPT and BSFP increased the CD4+ /CD8+ ratio of T cells. Needle aspiration of neutral red was significantly promoted by macrophages treated with peptides other than EF. In addition, EEL, EHPT, AGGF, and BSFP had a promotive effect on NO production in phagocytes. The results indicate that BSFP is a peptide product with good immunomodulatory functions, four peptides identified from BSFP show outstanding effects in terms of antioxidant properties and immunomodulation. PRACTICAL APPLICATIONS: In this study, the amino acid composition and relative molecular masses of the black-bone silky fowl peptide were analyzed, while the four peptides with significant effects on antioxidant and immunomodulatory properties in black-bone silky fowl peptide were identified by HPLC-MS/MS technique. Positive effects of black-bone silky fowl peptide and its four peptides on antioxidant capacity and immunomodulatory ability as revealed by cell experiments. The results of this experiment provide a preliminary theoretical basis for the development of new functional foods using black-bone silky fowl peptide and their characteristic peptides.

CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences.

Protein phylogenetic analysis focuses on the evolutionary relationships among related protein sequences and can help researchers infer protein functions and developmental trajectories. With the advent of the big data era, the existing protein phylogenetic methods, including distance matrix and character-based methods, are facing challenges in both running time and application scope. Here, we developed an R package that we call CProtMEDIAS that is useful for protein phylogenetic analysis. In contrast to existing phylogenetic analysis methods, CProtMEDIAS utilizes dimensionality reduction algorithms to digitize multiple sequence alignments and quickly conduct phylogenetic analysis with a large number of amino acid sequences from similarly distant protein families and species. We used CProtMEDIAS to perform a dimensionality reduction, clustering, pseudotime, specific residue and evolutionary trajectory analysis of the plant homeobox superfamily. We found that CProtMEDIAS delivers consistent clustering, fast running and elegant presentation and thus provides powerful new tools and methods for protein clustering and evolutionary analysis.