Types Of Amino Acids Research Articles

Chirality-Induced Spin Selectivity in Heterochiral Short-Peptide-Carbon-Nanotube Hybrid Networks: Role of Supramolecular Chirality.

Supramolecular short-peptide assemblies have been widely used for the development of biomaterials with potential biomedical applications. These peptides can self-assemble in a multitude of chiral hierarchical structures triggered by the application of different stimuli, such as changes in temperature, pH, solvent, etc. The self-assembly process is sensitive to the chemical composition of the peptides, being affected by specific amino acid sequence, type, and chirality. The resulting supramolecular chirality of these materials has been explored to modulate protein and cell interactions. Recently, significant attention has been focused on the development of chiral materials with potential spintronic applications, as it has been shown that transport of charge carriers through a chiral environment polarizes the carrier spins. This effect, named chirality-induced spin selectivity or CISS, has been studied in different chiral organic molecules and materials, as well as carbon nanotubes functionalized with chiral molecules. Nevertheless, this effect has been primarily explored in homochiral systems in which the chirality of the medium, and hence the resulting spin polarization, is defined by the chirality of the molecule, with limited options for tunability. Herein, we have developed heterochiral carbon-nanotube-short-peptide materials made by the combination of two different chiral sources: that is, homochiral peptides (l/d) + glucono-δ-lactone. We show that the presence of a small amount of glucono-δ-lactone with fixed chirality can alter the supramolecular chirality of the medium, thereby modulating the sign of the spin signal from "up" to "down" and vice versa. In addition, small amounts of glucono-δ-lactone can even induce nonzero spin polarization in an otherwise achiral and spin-inactive peptide-nanotube composite. Such "chiral doping" strategies could allow the development of complementary CISS-based spintronic devices and circuits on a single material platform.

Utilization of amino acid for selective leaching of critical metals from spent hydrodesulfurization catalyst.

While spent catalysts can cause serious environmental pollution, they can be considered an essential secondary metal source due to their high critical metal grades. The formation of the amino acid-metal complex is often seen in nature, and its potential application in hydrometallurgy can be foreseen. Alanine (Ala) was first screened as the most effective type of amino acid to be used for the selective leaching of spent hydrodesulfurization catalyst (consisting of MoS2 and Co3S4 supported on Al2O3, at 10% Mo and 2.4% Co grades). The sequential 3-step leaching (Step-1: Alkaline Ala leaching at 45°C, Step-2: Hot water leaching at 70°C, Step-3: Second alkaline Ala leaching at 45°C) was conducted where the role of Ala was found to be at least three-fold; 1) maintaining alkalinity by amino acid’s buffering capacity to assist Mo leaching, 2) selectively precipitating Co by forming Co-Ala complex with a distinctive pink color, which can readily re-dissolve in hot water to be separated from spent catalyst particles. 3) Effectively suppressing unwanted dissolution of Al throughout the reaction without needing pH control. Consequently, highly metal-selective, two separate Co-rich (<1% Mo and 79% Co dissolved, Al not detected) and Mo-rich (96% Mo, 19% Co, and 2.1% Al dissolved) leachates were obtained. This study highlighted the potential utility of amino acids as non-toxic, alternative metal lixiviant as well as a metal precipitant for selective leaching of critical metals from spent hydrodesulfurization catalyst.

Electron transfer characteristics of amino acid adsorption on epitaxial graphene FETs on SiC substrates

Clarifying the adsorption characteristics of biomolecules on graphene surfaces is critical for the development of field-effect transistor (FET)-based biosensors for detecting pH, DNA, proteins, and other biomarkers. Although there are many reports on biomolecule detection using graphene FETs, the detection mechanism has not yet been clarified. In this study, the adsorption behavior and electron transfer characteristics of 20 proteinogenic amino acids on graphene field-effect transistors are investigated. Large single-crystal graphene films were epitaxially grown on SiC substrates by a resist-free metal stencil mask lithography process then patterned by air plasma etching to form FET devices. Amino acids with different charge conditions (positive or negative charge) were introduced onto the epitaxial graphene surface in solution. The charge neutral points of the drain current vs gate voltage curves shifted in the negative gate voltage direction after the introduction of all amino acids, regardless of the type of amino acid and its charge condition. These amino acid adsorption characteristics agree well with previously reported protein adsorption characteristics on epitaxial graphene surfaces, indicating that the adsorption of proteins in the liquid phase occurs by electron doping to the graphene surface. These results indicate that non-specific protein binding always leads to electron doping of epitaxial graphene FETs.

Chao Teri: The Traditional Fish Fermentation from South Sulawesi, Indonesia

Chao fish is a traditional product of the Bugis-Makassar ethnic, which is processed from anchovy fermentation. Chao teri production center is in Pangkep regency of South Sulawesi Province, especially in Liukang Topabiring and Labbakkang subdistricts. In this area, Chao fish is a complement to side dishes flavored with chilies and onions, and consumed with pickled mangoes and cucumbers. The fermentation process for approximately two weeks. Characteristics of fish Chao products are light brown or pink, slightly sour and salty taste, distinctive flavor, and has a paste-shaped texture. The descriptive qualitative and quantitative research method was used to explore processing techniques and volatile compounds in Chao teri. Observation and documentation were conducted to collect primary data. Instrumental analysis using Gas Chromatography-Mass Spectrometry with Solid Phase Micro-Extraction (GC-MS SPME) method is used to determine the volatile compounds. Chao teri can be made from anchovy and shrimp. Chemical characteristics of Chao teri after 2 weeks fermentation obtained pH 6.35, lactic acid 1.20%, and protein 21.15%. The results of the GC-MS SPME analysis produced 73 volatile compounds. The compounds are 31 hydrocarbons,12 alcohols, 9 aldehydes, 8 ketones, 4 esters, 2 organic acids, 1 furan, and 6 other compounds. The dominant types of amino acids found in Chao teri products are glutamic acid, leucine, aspartic acid, and lysine. In this article, the origin of Chao teri, its method of processing, and the scientific perspectives are discussed.

CHARACTERIZATION OF FLAKES MADE IN CORN FLOUR (ZEA MAYS) AND PUMPKIN (CUCURBITA MOSHCATA) WITH ADDITION OF SOYBEAN FLOUR (GLICINE MAX)

ABSTRACT&#x0D; This study aims to determine the effect of adding soybean flour (Glicine max) to the chemical, physical, and organoleptic characteristics of flakes from a combination of corn (Zea mays) and pumpkin (Cucurbita moshcata) and to determine the best treatment for flakes produced based on chemical, physical characteristics, and it's organoleptic. The research method used is an experimental method with descriptive data analysis. This study used 5 treatments and 3 replications: A = (addition of 0 grams of soybean flour), B = (addition of 15 grams of soybean flour), C = (addition of 30 grams of soybean flour), D = (addition of 45 grams of soybean flour), and E = (addition of 60 grams of soybean flour). Observations made were chemical analysis in the form of water content, ash content, protein content, fat content, carbohydrate content, crude fiber content, and total amino acids in treatment C, as well as physical tests in the form of water absorption tests, color tests, and organoleptic tests in the form of color, aroma, taste, and texture. The results showed that the addition of soybean flour in the study of corn and pumpkin flour flakes affected water content, ash content, protein content, fat content, carbohydrate content, crude fiber content, water absorption, brightness (color), and preference level based on the color, flavor, taste, and texture of the resulting flakes. The best treatment of flakes produced was treatment C (addition of 30 grams of soybean flour) based on the panelists' preference level with quality characteristics, is: water content (6.43% ± 0.41), ash content (1.76% ± 0.19), protein content (9.78% ± 0.29), fat content (11.25% ± 0.69), carbohydrate content (70.89% ± 0.57), crude fiber content (2.81% ± 0.29), water absorption 368.31% ± 2.49), °Hue (78.57 ± 0.01) and organoleptic values ??(color 4.35; aroma 3.65; taste 4.10; texture 3, 70) with a total value of 9.72% amino acids and the types of amino acids identified are glutamic acids, leucine, aspartic acid, arginine, alanine, phenylalanine, valine, serine, isoleucine, tyrosine, threonine, lysine, histidine, glycine, and methionine. . threonine, lysine, histidine, glycine, and methionine. . threonine, lysine, histidine, glycine, and methionine.&#x0D; &#x0D; Keywords : Flakes, soybean flour, corn flour, pumpkin, characteristics, protein, amino acids.

Annular elastolytic giant cell granuloma in a patient with Ehlers–Danlos syndrome

The article presents a clinical case of annular elastolytic giant cell granuloma (AEGCG) in a young patient with a vascular type of EhlersDanlos syndrome. The first clinical manifestations of AEGCG appeared on the skin in the right subclavian area about two years ago. Subsequently, new rashes appeared on the skin of the upper and lower extremities up to four new foci per year. The patient underwent ambulatory therapy as a solution of calcium gluconate 10% 5.0 ml No 10 i/v in every other day; a solution of chloropyramine hydrochloride 1.0 ml No 10 i/m every other day; betamethasone + salicylic acid ointment applied to the affected areas of the skin 2 times a day for 2 weeks. The treatment was ineffective, the rashes did not regress. External therapy with tacrolimus was carried out next, 0.1% ointment 2 times a day in the form of applications for 24 weeks but also without effect. The patient by herself started to take a dietary supplement containing 400 mg of collagen in 1 tablet; 3 types of amino acids 20 mg; vitamins B2 1.1 mg; B6 1.5 mg; calcium pantothenate 5 mg 2 tablets a day during meals. A month after the start of the application, she noticed a slight paling of the rashes. At the moment, the patient is under follow up.

Utilization of Biang Fish Flour (Ilisha elongata) as an Enrichment Material for Sago Noodles Nutrient Value.

This study aims to determine the appropriate concentration of lead fish meal for enriching the nutritional value of sago noodles favored by consumers. The method used is an experimental design using Completely Randomized (CRD) with 4 concentration levels of lead fish meal, namely, 4% without a lead fish meal (M0), 6% (M1), 8% (M2), and 10% (M3). The analysis of sago noodles was performed and proximate by the AOAC method; amino acids by HPLC; fatty acids by GC; and minerals by HPLC. The results of the showed that the study getting the best treatment was a concentration of 8% (M2) with the characteristics of whole sago noodles' appearance: attractive, grayish-white color; a distinctive aroma of sago noodles with a hint of fish; a specific taste typical of sago noodles and fish prickly taste; delicious; slightly chewy texture. Sensory evaluation with a taste value of 8.9, an aroma of 8.6, a visual value of 8.9, and a texture value of 8.8. Its nutritional content is 5.58% protein content, air 22.35%, ash 1.69%, fat 1.41%, and carbohydrates 68.29%. The proximate values are protein 5.58%, water content 22.35%, ash 1.69%, fat content 1.41%, and carbohydrates (different) 68.29%. The mineral content is Ca.P.I, Mg, Zn, and Fe. Amino acids consist of 8 types of essential amino acids, namely, histidine, arginine, threonine, valine, alanine, methionine, isoleucine, leucine, phenylalanine, and 7 types of nonessential amino acids, namely, aspartic acid, glutamic acid, serine, glycine, tyrosine. Its fatty acid profile has 13 components of unsaturated fatty acids and 17 components of saturated fatty acids.

The Importance of Metabolites in Modulating Insulin Sensitivity

BACKGROUND: Metabolism impairment in obese condition usually initially triggered by inflammation and insulin signaling impairment. The involvement of metabolites, including lipids, amino acids, and ketone bodies, in altering insulin sensitivity has been revealed after massive data sets were provided by the studies regarding metabolomics and lipidomics.CONTENT: Metabolites were now understood to serve more than just the metabolism products, but also as active signaling molecules including in insulin and immunological actions. Different lipid metabolites can serve as signaling molecules to induce insulin resistance of sensitivity through a similar pathway, and impact on the inflammation status. Branched Chain Amino Acids (BCAA) and many amino acids have been correlated with mitochondrial dysfunction and insulin impairment. Ketogenic diet, supplementation and microbiota transplantation become the current strategies to set a preferable metabolites composition to modulate insulin sensitivity.SUMMARY: Thousands of metabolites can now be measured using technical and bioinformatics developments. Different types of amino acids, fatty acids, and bile acids are being studied in relation to altered metabolic states, particularly obesity and type 2 diabetes mellitus. A thorough knowledge of the metabolic changes that contribute to insulin resistance might lead to the discovery of new targets for enhancing insulin sensitivity and preventing and treating many metabolic disorders.KEYWORDS: metabolites, insulin resistance, lipids, amino acids, ketone bodies

Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation.

In an effort to combat rising antimicrobial resistance, our labs have rationally designed cationic, helical, amphipathic antimicrobial peptides (AMPs) as alternatives to traditional antibiotics since AMPs incur bacterial resistance in weeks, rather than days. One highly positively charged AMP, WLBU2 (+13e), (RRWV RRVR RWVR RVVR VVRR WVRR), has been shown to be effective in killing both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria by directly perturbing the bacterial membrane nonspecifically. Previously, we used two equilibrium experimental methods: synchrotron X-ray diffuse scattering (XDS) providing lipid membrane thickness and neutron reflectometry (NR) providing WLBU2 depth of penetration into three lipid model membranes (LMMs). The purpose of the present study is to use the results from the scattering experiments to guide molecular dynamics (MD) simulations to investigate the detailed biophysics of the interactions of WLBU2 with LMMs of Gram-negative outer and inner membranes, and Gram-positive cell membranes, to elucidate the mechanisms of bacterial killing. Instead of coarse-graining, backmapping, or simulating without bias for several microseconds, all-atom (AA) simulations were guided by the experimental results and then equilibrated for ∼0.5 μs. Multiple replicas of the inserted peptide were run to probe stability and reach a combined time of at least 1.2 μs for G(-) and also 2.0 μs for G(+). The simulations with experimental comparisons help rule out certain structures and orientations and propose the most likely set of structures, orientations, and effects on the membrane. The simulations revealed that water, phosphates, and ions enter the hydrocarbon core when WLBU2 is positioned there. For an inserted peptide, the three types of amino acids, arginine, tryptophan, and valine (R, W, V), are arranged with the 13 Rs extending from the hydrocarbon core to the phosphate group, Ws are located at the interface, and Vs are more centrally located. For a surface state, R, W, and V are positioned relative to the bilayer interface as expected from their hydrophobicities, with Rs closest to the phosphate group, Ws close to the interface, and Vs in between. G(-) and G(+) LMMs are thinned ∼1 Å by the addition of WLBU2. Our results suggest a dual anchoring mechanism for WLBU2 both in the headgroup and in the hydrocarbon region that promotes a defect region where water and ions can flow across the slightly thinned bacterial cell membrane.

Topoisomerase Enzyme Inhibitors as Potential Drugs Against Cancer: What Makes Them Selective or Dual? - A Review.

Topoisomerase inhibitors are extensively used in cancer chemotherapy. In the process of identifying novel anticancer compounds, biological evaluations are crucial and include, among others, the use of in silico and in vitro approaches. This work aimed to present recent research involving the obtainment and in silico and in vitro evaluation of topoisomerase I, II, and double inhibitors, of synthetic and natural origin, as potential compounds against tumor cells, in addition to proposing the construction of a desirable enzyme catalytic site. Therefore, it was observed that most Topoisomerase I inhibitors presented medium to large structures, with a rigid portion and a flexible region. In contrast, Topoisomerase IIα inhibitors showed medium and large structural characteristics, in addition to the planarity of the aromatic rings, which are mitigated due to flexible rings but may also present elements that restrict conformation. Most compounds that exhibit dual inhibitory activity had relatively long chains, in addition to a flat and rigid portion suggestive of affinity for Topo I and a flexible region characteristic of selective drugs for Topo II. Besides, it is noticed that most compounds that exhibit dual inhibitory showed similarities in the types of interactions and amino acids when compared to the selective compounds of Topo I and II. For instance, selective Topoisomerase I inhibitors interact with Arginine364 residues, and selective Topoisomerase II inhibitors interact with Arginine487 residues, as both residues are targets for dual compounds.

Galacto-oligosaccharides and xylo-oligosaccharides affect meat flavor by altering the cecal microbiome, metabolome, and transcriptome of chickens

Studies have shown that prebiotics can affect meat quality; however, the underlying mechanisms remain poorly understood. This study aimed to investigate whether prebiotics affect the flavor of chicken meat via the gut microbiome and metabolome. The gut content was collected from chickens fed with or without prebiotics (galacto-oligosaccharides or xylo-oligosaccharides) and subjected to microbiome and metabolome analyses, whereas transcriptome sequencing was performed using chicken breast. Prebiotic supplementation yielded a slight improvement that was not statistically significant in the growth and production performance of chickens. Moreover, treatment with prebiotics promoted fat synthesis and starch hydrolysis, thus increasing meat flavor by enhancing lipase and α-amylase activity in the blood of broiler chickens. The prebiotics altered the proportions of microbiota in the gut at different levels, especially microbiota in the phyla Bacteroidetes and Firmicutes, such as members of the Alistipes, Bacteroides, and Faecalibacterium genera. Furthermore, the prebiotics altered the content of cecal metabolites related to flavor substances, including 8 types of lysophosphatidylcholine (lysoPC) and 4 types of amino acid. Differentially expressed genes (DEGs) induced by prebiotics were significantly involved in fatty acid accumulation processes, such as lipolysis in adipocytes and the adipocytokine signaling pathway. Changes in gut microbiota were correlated with metabolites, for example, Bacteroidetes and Firmicutes were positively and negatively correlated with lysoPC, respectively. Finally, DEGs interacted with cecal metabolites, especially meat-flavor-related amino acids and their derivatives. The findings of this study integrated and incorporated associations among the gut microbiota, metabolites, and transcriptome, which suggests that prebiotics affect the flavor of chicken meat.

Interfacial rheological properties of cholesteryl-oligopeptide surfactants: Effects of hydrophilic group structure

Surfactants derived from natural compounds have a wide variety of molecular structures and exhibit various functions. In the present work, 5 surfactants were synthesized by linking a cholesteryl group to different amino acid/oligopeptides. The enhanced intermolecular van der Waals interactions between the cholesteryl group provided a strong driving force for the ordered assembly of surfactants at interface. The interfacial properties of these surfactants were also influenced significantly by the number and type of amino acids in the oligopeptides. As the number of amino acids in the oligopeptides increased, the number of hydrogen bonding sites increased, which in turn enhanced the interfacial activity as well as the intermolecular interactions between the derived surfactants. Meanwhile, because of the synergy of multiple hydrogen bonds and strong van der Waals forces between kalium cholesteryl triglycine (Chol-GGG-K) molecules, the interfacial relaxation processes were greatly inhibited and the interfacial film was less viscoelastic. The functional groups in kalium cholesteryl glycyl-L-valine (Chol-GT-K) and kalium cholesteryl glycyl-L-tyrosine (Chol-GV-K) hindered hydrogen bond formation between the oligopeptides and also slowed the relaxation processes at the interface, which decreased the interfacial viscoelasticity of the Chol-GT-K and Chol-GV-K films. The obtained results provide new insights into the relationships between the molecular structure and interfacial behaviors of cholesteryl-oligopeptide surfactants and provide a framework for surfactant design and further application in the food, pharmaceutical, cosmetic, and material industries.

Met/Val129 polymorphism of the full-length human prion protein dictates distinct pathways of amyloid formation

Methionine/valine polymorphism at position 129 of the human prion protein, huPrP, is tightly associated with the pathogenic phenotype, disease progress, and age of onset of neurodegenerative diseases such as Creutzfeldt–Jakob disease or Fatal Familial Insomnia. This raises the question of whether and how the amino acid type at position 129 influences the structural properties of huPrP, affecting its folding, stability, and amyloid formation behavior. Here, our detailed biophysical characterization of the 129M and 129V variants of recombinant full-length huPrP(23–230) by amyloid formation kinetics, CD spectroscopy, molecular dynamics simulations, and sedimentation velocity analysis reveals differences in their aggregation propensity and oligomer content, leading to deviating pathways for the conversion into amyloid at acidic pH. We determined that the 129M variant exhibits less secondary structure content before amyloid formation and higher resistance to thermal denaturation compared to the 129V variant, whereas the amyloid conformation of both variants shows similar thermal stability. Additionally, our molecular dynamics simulations and rigidity analyses at the atomistic level identify intramolecular interactions responsible for the enhanced monomer stability of the 129M variant, involving more frequent minimum distances between E196 and R156, forming a salt bridge. Removal of the N-terminal half of the 129M full-length variant diminishes its differences compared to the 129V full-length variant and highlights the relevance of the flexible N terminus in huPrP. Taken together, our findings provide insight into structural properties of huPrP and the effects of the amino acid identity at position 129 on amyloid formation behavior.

Analysis of Aspergillus versicolor exudate composition.

Aspergillus versicolor, a widely distributed fungus, is associated with pollution and carcinogenic hazards. This study aimed to examine the functions of the A. versicolor exudate and laid a scientific foundation for improving our understanding, utilization, and control of A. versicolor. The A. versicolor exudate proteome, ion content, and amino acid components were determined using label-free quantitation, atomic absorption spectrophotometry, and high-performance liquid chromatography, respectively. In total, 502 proteins were identified in the A. versicolor exudate. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and cluster of orthologous group analyses were used to annotate the functional classification and pathways of the aligned proteins. Proteins identified in the exudate were mainly enriched in carbohydrate metabolic process, translation, oxidoreductase activity, oxidoreductase activity, hydrolase activity, cell wall-related processes, catalytic activity, and unknown functions. The exudate comprised Na, K, Ca, Fe, and Mg cations. Among the 17 types of amino acids detected in the exudate, 7 were essential and 10 were nonessential. The exudate may be involved in the vital processes of A. versicolor. Additionally, the exudate may play an important role in the growth, development, reproduction, homeostasis, nutrient supply for regrowth, and virulence of A. versicolor.

Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered.

There is increasing evidence that many intrinsically disordered regions (IDRs) in proteins play key functional roles through interactions with other proteins or nucleic acids. These interactions often exhibit a context-dependent structural behavior. We hypothesize that low complexity regions (LCRs), often found within IDRs, could have a role in inducing local structure in IDRs. To test this, we predicted IDRs in the human proteome and analyzed their structures or those of homologous sequences in the Protein Data Bank (PDB). We then identified two types of simple LCRs within IDRs: regions with only one (polyX or homorepeats) or with only two types of amino acids (polyXY). We were able to assign structural information from the PDB more often to these LCRs than to the surrounding IDRs (polyX 61.8% > polyXY 50.5% > IDRs 39.7%). The most frequently observed polyX and polyXY within IDRs contained E (Glu) or G (Gly). Structural analyses of these sequences and of homologs indicate that polyEK regions induce helical conformations, while the other most frequent LCRs induce coil structures. Our work proposes bioinformatics methods to help in the study of the structural behavior of IDRs and provides a solid basis suggesting a structuring role of LCRs within them.

Karakteristik Kimia Dan Fisik Telur Burung Gosong Filipina (Megapodius cumingii) Dari Pulau Toroguso, Kabupaten Banggai, Sulawesi Tengah, Indonesia

This research was conducted to examine the physical characteristics, chemical composition of the eggs of the filipina gosong bird (Megapodius cumingii) obtained from nesting sites on the coast of Poat Island, Pagimana District, Banggai Regency, Central Sulawesi Province. Measurement of the physical characteristics of eggs (weight, diameter, length and egg index) were carried out at the Laboratory of Biology Study Program, Tadulako University. Besides, observation on egg color, shape and egg texture were also conducted. Measurements of water and fat content, protein, carbohydrates, ash, crude fiber and egg antioxidants (Proxymate analysis) were carried out at the Chemistry Laboratory, Faculty of Mathematics and Natural Sciences, Tadulako University. Amino acid analysis was carried out at the Integrated Laboratory of IPB by using HPLC (High Performance Liquid Chromatography). The results showed that the eggs of the Filipina charred bird had an oval shape with two shell colors, dark brown and light brown, and the texture was smooth. The average size of egg weight, length, diameter and egg index were 99.35 g, 7.31 cm, 5.5 cm and 72.43%, respectively. The results of the chemical analysis of filipino gosong eggs revealed that water and fat content, protein, carbohydrates, ash, crude fiber and egg antioxidants were 50.45%, 18.75%, 13.40%, 0.02%, 375.98% and 1.82% respectively. The result showed a higher protein content compared to fat content. The 17 types of amino acids included essential and non-essential amino acids. Glutamate was the highest concentration of 2.10%, while cysteine was the lowest concentration of 0.15%.

Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.

Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions characterized by high diversity of amino acid composition. Similarity between regions of protein sequences frequently reflect functional similarity between them. In this article, we discuss strengths and weaknesses of the similarity analysis of low complexity regions using BLAST, HHblits and CD-HIT. These methods are considered to be the gold standard in protein similarity analysis and were designed for comparison of high complexity regions. However, we lack specialized methods that could be used to compare the similarity of low complexity regions. Therefore, we investigated the existing methods in order to understand how they can be applied to compare such regions. Our results are supported by exploratory study, discussion of amino acid composition and biological roles of selected examples. We show that existing methods need improvements to efficiently search for similar low complexity regions. We suggest features that have to be re-designed specifically for comparing low complexity regions: scoring matrix, multiple sequence alignment, e-value, local alignment and clustering based on a set of representative sequences. Results of this analysis can either be used to improve existing methods or to create new methods for the similarity analysis of low complexity regions.

Enzyme-driven oxygen-fuelled pathway selectivity of tyrosine-containing peptide oxidation evolution

The pathway selectivity of chemical evolution controlled by enzymes, with proteins and peptides as substrates, is of critical significance to determine biological processes and functions. In nature, organisms utilize tyrosinase to catalyse oxidation reactions of tyrosine to produce multifunctional compounds in different pathways. However, it remains a great challenge to manipulate the pathway selection of tyrosinase-guided chemical evolution for achieving biomaterials with on-demand functions. We herein report that controlling oxygen concentration is effective in regulating the evolution of tyrosinase-catalysed oxygenation pathways of tyrosine-containing peptides and even proteins. The melanin formation pathway predominates under oxygen-enriched conditions, while fluorescent compounds are preferentially generated under hypoxic conditions. The chemical evolution of tyrosine-containing peptides, regardless of their neighbouring amino acid types and sequences, tends to be governed by these two competitive pathways. These competitive pathways are manipulated by conformational transformation of tyrosinase active centre that is determined by oxygen concentration. Moreover, the oxygen-controlled chemical evolution of tyrosine-containing biomolecules can be broadly realized by tyrosinase to obtain melanin-based photothermal materials or multicolour fluorescent materials. This work reveals the plausible role of oxygen in the pathway selectivity of enzyme-controlled chemical evolution of tyrosine-containing peptides and verifies the possibility of fluorescent detection in living cultured melanoma cells, which provides a versatile strategy for precise design and engineering of tyrosine-involved multifunctional biomaterials.

Improvement of an Automated Sample Injection System for Pillar Array Columns to Increase Analytical Reproducibility.

In our previous study, we developed an automatic sample injection system for pillar array columns for quantitative analysis. An autosampler was used to maintain a constant sample injection volume. However, the sample was diluted during injection using the autosampler, thus deteriorating the analytical reproducibility. In this study, we have substituted the autosampler with a syringe pump to overcome the abovementioned problem and improve the system. Sample dilution was avoided by filling the entire capillary with the sample at a constant rate. This improved system also increased the analytical reproducibility. In the previous system, the relative standard deviation (RSD) exceeded 17% of the peak height for coumarin dyes. In contrast, the improved system decreased the RSD to the range 1.2–1.8%. The analytical reproducibility was evaluated by using five types of amino acids. The RSD of each peak height was within 3.0%, confirming good reproducibility. These results indicate that the sample injection method developed in this study can be applied to biological sample analyses as a simple quantitative analysis method for pillar array columns.

Widely targeted metabolomic profiling combined with transcriptome analysis provides new insights into amino acid biosynthesis in green and red pepper fruits

The type and content of amino acids in pepper are important indicators to reflect its nutritional value, largely affecting the purchasing behavior of consumers. Understanding the biosynthesis of amino acids in pepper fruit is beneficial to the development of pepper functional food. Widely targeted metabolomics, transcriptome analysis, correlation analysis, weighted gene co-expression network analysis (WGCNA), and canonical correlation analysis (CCA) were used to evaluate the quality characteristics of green and red pepper amino acids. The results showed 78 kinds of amino acids and their derivatives in the fruit of pepper. The essential amino acids were comprehensive and abundant. Especially, the contents of lysine and tryptophan were high. However, significant differences were found in the ratio of essential amino acids to total amino acids in green and red pepper. The ratio of essential amino acids to total amino acids in red pepper was up to 28.88%, while that in green pepper was up to 17.69%. WGCNA and CCA analyses were performed in combination with amino acid metabolism profiling and transcriptome analysis to further identify the main contributors to amino acid synthesis in green and red pepper. The results showed PK and PFK were the genes in the backbone of the amino acid biosynthesis pathway, which had a direct impact on the synthesis of various amino acids, and were the main genes for amino acid synthesis in pepper fruit. In this study, the amino acid biosynthesis rules for two kinds of pepper were analyzed by amino acid metabolism profiling and transcriptome analysis, which provided the basis for the development of amino acid nutritional supplements and pepper functional food.