Types Of Amino Acids Research Articles

Synthesis and Identification of New Heterocyclic Compounds from Isatin by Schiff Base Reaction

Heterocyclic compounds possess a cyclic structure with two or more different kinds of atoms in the ring. The history of heterocyclic chemistry began in the 1800s, in step with the development of organic chemistry. Since rings can be of any size, from three-membered upwards, and since the heteroatoms can be drawn in almost any combination from a large number of the elements (though nitrogen, oxygen, and sulfur are still by far the most common), the number of possible heterocyclic systems is almost limitless. An enormous number of heterocyclic compounds are known and this number continues to increase very rapidly. This work is divided into two different parts: First part: Synthesis of imines by Schiff base reaction, this part involves synthesis three of imines by treatment isatin with a variety of cyclo primary amines. Second part: [3 + 2] Cycloaddition reaction, this part includes reacting each product of the first part with two types of amino acids. All steps of reactions followed by TLC– papers. All synthesized compounds were confirmed through the use of different spectroscopic techniques (IR and NMR), melting points.

Nilai Proksimat dan Profil Asam Amino Ikan Sembilang (Paraplotosus albilabris) dari Perairan Bintan, Kepulauan Riau

Eeltail catfish (Paraplotosus albilabris) is a type of marine fish that has high nutritional content but is still rarely used further. In this study, we examined the proximate content and types of amino acids found in the flesh and skin of eeltail fish (Paraplotosus albilabris). The method used in this research is measurment of morphometric, proximate content and amino acids contained in flesh and skin of eeltail catfish The result of this study showed flesh contained 16.98% protein, 1.36% ash, 79.95% water, 1.12% fat, and 0.59% carbohydrates, respectively. On the skin, there was 33.49% protein, 1.41% ash, 64.26% water, 0.36% fat, and 0.48% carbohydrates. Meat had an essential amino acid yield of 84,222.14 mg/kg (52.97%) and skin had 76,429 mg/kg (30.45%), The amount of non-essential amino acids was 74,795.7 mg/kg (47.03%), and the amount of skin was 174.669 mg/kg (69.57%).

A versatile technique based on surface-enhanced Raman spectroscopy for label-free detection of amino acids and peptide formation in body fluids.

As an effective analytical method, surface-enhanced Raman spectroscopy (SERS) is widely used in the detection of nucleic acids, amino acids, and other biomolecules. However, obtaining the SERS signal of nonaromatic amino acids is still a challenge. In this work, excess sodium borohydride was used as a reducing agent to prevent the surface of silver nanoparticles from being coated with AgO to enable amino acid molecules to reach the surface of silver nano-substrates. Calcium ions were used as aggregators for silver nano-substrates to successfully achieve the label-free and accurate fingerprint determination of various nonaromatic amino acids. Different types of amino acids were distinguished based on the changes in their peak intensity that were obtainedusing colorless and transparent organic dichloromethane (DCM) as the internal standard. A Raman signal for low-concentration amino acids in body fluids was detected, and the detection limit for tyrosine was 5 ng/mL. Moreover, the physical and chemical properties of peptides and the formation of peptide chains were further analyzed. The proposed method can potentially be applied to protein sequencing.

Fermented meat and digestive tract of snail as amino acid supplements for functional feed of native chickens

Sources of amino acids and lactic acid bacteria have been developed from the hydrolysis of snail meat and its digestive tract through a fermentation process using a consortium of microorganisms present in cow’s milk whey, which is fermented by microorganisms from rice washing water with internal microorganisms from snails. The fermentation process used the Submerged Fermentation (SmF) method. The fermentation process was carried out using Lactic Acid Bacteria (LAB) inoculants contained in rice washing water. This product was researched and developed with the aim of being a feed supplement to reduce the use of fish meal or other protein sources such as concentrates in the preparation of feed for poultry. Product development studies were carried out on the LAB content in rice washing water and fermented snail meat and its digestive tract, as well as their amino acid content. The results of the study showed that at the dilution of rice washing water, approximately 3 different colonies of LAB were found, the dilution of 10-1 to 10-4 could not be counted but at the dilution of 10-5, 50 colonies of LAB were obtained with an amount of 5 x 107 CFU/ml. The fermented snail meat and its digestive tract contained approximately 4 different LAB colonies and found 3 x 104 CFU/ml at a dilution of 10-3, and contained 6 types of amino acids, namely; alanine, glycine, cysteine, arginine, lysine, and proline. The conclusion of this research is that fermented snail meat and digestive tract have potential as an amino acid supplement for functional feed for native chickens.

Probing sequence space to uncover molecular interactions driving FUS liquid-liquid phase separation

Fused in Sarcoma (FUS) is an essential RNA-processing protein functioning via self-assembly including through Liquid-Liquid Phase Separation (LLPS) and implicated in amyotrophic lateral sclerosis and frontotemporal dementia pathologies through aberrant subsequent neurodegeneration. However, the biomolecular interactions driving LLPS have not been thoroughly characterized. In this work, we probe in detail the role of each of the enriched residues types in FUS in LLPS. We present a number of mutagenic and biochemical-derived systems that refine our understanding of the roles of individual amino acid types beyond tyrosine and arginine in FUS phase separation.

Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote

Extant organisms commonly use 20 amino acids in protein synthesis. In the translation system, aminoacyl-tRNA synthetase (ARS) selectively binds an amino acid and transfers it to the cognate tRNA. It is postulated that the amino acid repertoire of ARS expanded during the development of the translation system. In this study we generated composite phylogenetic trees for seven ARSs (SerRS, ProRS, ThrRS, GlyRS-1, HisRS, AspRS, and LysRS) which are thought to have diverged by gene duplication followed by mutation, before the evolution of the last universal common ancestor. The composite phylogenetic tree shows that the AspRS/LysRS branch diverged from the other five ARSs at the deepest node, with the GlyRS/HisRS branch and the other three ARSs (ThrRS, ProRS and SerRS) diverging at the second deepest node. ThrRS diverged next, and finally ProRS and SerRS diverged from each other. Based on the phylogenetic tree, sequences of the ancestral ARSs prior to the evolution of the last universal common ancestor were predicted. The amino acid specificity of each ancestral ARS was then postulated by comparison with amino acid recognition sites of ARSs of extant organisms. Our predictions demonstrate that ancestral ARSs had substantial specificity and that the number of amino acid types amino-acylated by proteinaceous ARSs was limited before the appearance of a fuller range of proteinaceous ARS species. From an assumption that 10 amino acid species are required for folding and function, proteinaceous ARS possibly evolved in a translation system composed of preexisting ribozyme ARSs, before the evolution of the last universal common ancestor.

Effects of MPUV/chlorine oxidation and coexisting bromide, ammonia, and nitrate on DBP formation potential of five typical amino acids

Disinfection byproduct (DBP) formation is a potential concern with regard to MPUV/Cl2 application in water treatment. In this study, five typical amino acids (AAs) were selected to investigate their DBP alteration during short-term medium pressure (MP) UV/chlorine oxidation following post-chlorination relative to parallel dark controls. The five selected AAs include two potent DBP precursors (aspartic acid and tryptophan), one modest precursor (asparagine) and two poor precursors (phenylalanine and proline). MPUV/chlorine increased the total DBP formation and DBP-associated cytotoxicity of the two poor precursors phenylalanine (Phe) and proline (Pro) as well as their chlorine demands. Conversely, DBP formation and DBP-associated cytotoxicity of the three modest-to-potent DBP precursors showed the opposite changing trends due to MPUV/Cl2 oxidation. The two aromatic AAs (tryptophan and phenylalanine) were more readily to be affected by MPUV/Cl2 oxidation especially at acidic pH condition. Conversely, DBP formation and DBP-associated cytotoxicity of the three modest-to-potent precursors showed the opposite changing trends due to MPUV/Cl2 oxidation. Among the measured DBPs, the absolute formation potential changes of haloacetic acids and haloacetonitriles were the most prominent. Presence of bromide increased the trihalomethane formation potential of five AAs. Ammonia-spiked samples resulted in notably higher chlorine demands but slightly reduced DBPFP. Photonitration caused increased haloacetonitrile and trichloronitromethane formation but lower overall DBP formation potential and DBP-associated cytotoxicity. Results indicated that increased DBP formation of unreactive aromatic AAs may be problematic with respect to MPUV/Cl2 application, while the presence of inorganic ions may not contribute to further increase in calculated cytotoxicity of measured DBPs.

Evaluation of antibacterial activity induced by Staphylococcus aureus and Ent A in the hemolymph of Spodoptera littoralis

The problem of antibiotic resistance considers one of the most dangerous challenges facing the medical field. So, it is necessary to find substitutions to conventional antibiotics. Antimicrobial peptides (AMPs) are a bio-functional derivative that have been observed as one of the important solutions to such upcoming crisis. Owing to their role as the first line of defense against bacteria, fungi, and viruses. This study was conducted to induce the immune response of Spodoptera littoralis larvae by inoculation of sub lethal doses of Staphylococcus aureus and its enterotoxin. Since Staphylococcal enterotoxin A (SEA) considers the major causative agents of Staphylococcal food poisoning, our study oriented to purify and characterize this toxin to provoke its role in yielding AMPs with broad spectrum antimicrobial activity. A great fluctuation was recorded in the biochemical properties of immunized hemolymph not only in the total protein content but also protein banding pattern. Protein bands of ∼22 kDa (attacin-like) and ∼15 kDa (lysozyme-like) were found to be common between the AMPs induced as a result of both treatments. While protein bands of molecular weight ∼70 kDa (phenoloxidase-like) and ∼14 kDa (gloverin-like) were found specific for SEA treatment. Chromatographic analysis using HPLC for the induced AMPs showed different types of amino acids appeared with differences in their quantities and velocities. These peptides exhibited noticeable antimicrobial activity against certain Gram-positive and Gram-negative bacteria. In conclusion, the antimicrobial potential of the antimicrobial peptides (AMP) induced in the larval hemolymph of S. littoralis will be a promising molecule for the development of new therapeutic alternatives.

Structure-activity trends analysis between amino acid compositions and minimal inhibitory concentrations of antimicrobial peptides.

Antimicrobial peptides (AMPs) provide large structural libraries of molecules with high variability of constitutional amino acids (AAs). Highlighting structural organization and structure-activity trends in such molecular systems provides key information on structural associations and functional conditions that could usefully help for drug design. This work presents link analyses between minimal inhibitory concentration (MIC) and different types of constitutional AAs of anti-Pseudomonas aeruginosa AMPs. This scope was based on a dataset of 328 published molecules. Regulation levels of AAs in AMPs were statistically ordinated by correspondence analysis helping for classification of the 328 AMPs into nine structurally homogeneous peptide clusters (PCs 1-9) characterized by high/low relative occurrences of different AAs. Within each PC, negative trends between MIC and AAs were highlighted by iterated multiple linear regression models built by bootstrap processes (bagging). MIC decrease was linked to different AAs that varied with PCs: alcohol-type AAs (Thr, Ser) in Cys-rich and low Arg PCs (PCs 1-3); basic AAs (Lys, Arg) in Pro-rich and low Val PCs (PCs 4-8); Trp (heterocyclic AA) in Arg-rich PCs (PCs 6, 7, 9). Aliphatic AAs (more particularly Gly) showed MIC reduction effects in different PCs essentially under interactive forms.

Effective prediction of short hydrogen bonds in proteins via machine learning method

Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.

Multifunctional amino acids empowering bifunctional biosensing platform for depression study

Poor availability of objective approaches hinders effective diagnosis and treatment for depression. Biosensors provide a promising platform for the development of quantitative and practical methods for disease detection, as well as for drug discovery. Here, we developed an electrochemical biosensor has been established with the ability to simply and accurately detect the trace glucocorticoid receptor alpha (GRα), as a key biomarker of depression, in both hippocampus and blood cells. The integration of amino-ion graphene oxide (IL-rGO) and amino acid-coated gold nanoparticles (AA-AuNPs) via green synthesis remarkably magnifies the electrochemical signals, where amino acids play multiple roles as reducing agents, stabilizers, and bridging agents. After the optimization among AA-AuNPs@IL-rGO nanocomposites based on five typical amino acids, a biosensing surface has been constructed to implement analysis in real samples as a bifunctional platform. The obtained biosensor exhibited a remarkably low limit of detection (0.283 pg mL−1) and could thus sensitively identify the GRα differences in healthy and depressive rats with and without fluoxetine. The electrochemical biosensor developed herein was not only outstandingly sensitive but also simple to use and labor-saving, making it a promising all-in-one platform for depression diagnosis and drug discovery.

Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape

Low complexity regions (LCRs) differ in amino acid composition from the background provided by the corresponding proteomes. The simplest LCRs are homorepeats (or polyX), regions composed of mostly-one amino acid type. Extensive research has been done to characterize homorepeats, and their taxonomic, functional and structural features depend on the amino acid type and sequence context. From them, the next step towards the study of LCRs are the regions composed of two types of amino acids, which we call polyXY. We classify polyXY in three categories based on the arrangement of the two amino acid types ‘X’ and ‘Y’: direpeats (e.g. ‘XYXYXY’), joined (e.g. ‘XXXYYY’) and shuffled (e.g. ‘XYYXXY’). We developed a script to search for polyXY, and located them in a comprehensive set of 20,340 reference proteomes. These results are available in a dedicated web server called XYs, in which the user can also submit their own protein datasets to detect polyXY. We studied the distribution of polyXY types by amino acid pair XY and category, and show that polyXY in Eukaryota are mainly located within intrinsically disordered regions. Our study provides a first step towards the characterization of polyXY as protein motifs.

Profile of amino acids and fatty acids of some Indonesia tall coconut varieties

The main content of coconut kernels are fats and fatty acids as well as protein and amino acids, and these contents vary among the varieties. This variation of amino acids and fatty acids also occurs in Indonesian tall coconut varieties. The objective of this study was to characterize amino and fatty acids content of Indonesian tall coconut varieties, namely Mapanget Tall, Palu Tall, Bali Tall, Tenga Tall, Selayar Tall, OdeskaLobu Tall, Babasal Tall, and Mastutin Tall. This study was conducted in Manado and Bogor from 2014 - 2019 by using an observational method. The results showed that the coconut kernel has eight types of non-essential amino acids and eight types of essential amino acids. Palu Tall has the highest amino acid content: alanine, arginine, aspartate, glutamate, glycine, serine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, and valine. Mapanget Tall has the highest contents of caprylic, capric, and lauric fatty acids, each with 9.04, 6.71, and 53.67 %, respectively. The result of this study can be used to develop varieties to obtain coconuts with high essential amino acids and fatty acids for the production of VCO, desiccated coconut, and other raw food materials.

Theoretical Investigation of Racemization of Amino Acid using Organic Catalysts

Racemization of amino acid catalyzed by aldehyde and carboxylic acid has been proposed and widely used. Herein, we investigated the detailed racemization mechanism of alanine catalyzed by salicylaldehyde and acetic acid. Quantum chemistry calculations based on the density functional theory demonstrated that the dehydration reaction is the rate-determining step, and this dehydration step is enhanced by surrounding water molecules. We also discussed the dependence of the reaction rates on the type of amino acid.

Prediction of protein pK a with representation learning.

The behavior of proteins is closely related to the protonation states of the residues. Therefore, prediction and measurement of pKa are essential to understand the basic functions of proteins. In this work, we develop a new empirical scheme for protein pKa prediction that is based on deep representation learning. It combines machine learning with atomic environment vector (AEV) and learned quantum mechanical representation from ANI-2x neural network potential (J. Chem. Theory Comput. 2020, 16, 4192). The scheme requires only the coordinate information of a protein as the input and separately estimates the pKa for all five titratable amino acid types. The accuracy of the approach was analyzed with both cross-validation and an external test set of proteins. Obtained results were compared with the widely used empirical approach PROPKA. The new empirical model provides accuracy with MAEs below 0.5 for all amino acid types. It surpasses the accuracy of PROPKA and performs significantly better than the null model. Our model is also sensitive to the local conformational changes and molecular interactions.

Reconstruction of the ancient beta-barrel with seven amino acid types

Reconstruction of the ancient beta-barrel with seven amino acid types

Nutrition Value and Growth Ability of Aquatic Weed Wolffia globosa as Alternative Feed Sources for Aquaculture System

One of the problems of aquaculture is the high cost of feed. Therefore, how to minimize the feed cost is of the main goals. It is necessary to find out natural sources that can be used as alternative feed. Wolffia globosa is an aquatic weed that is presumed to be used as an alternative feed source. Study the nutritional content of the Wolffia was conducted in June 2019, while the growth ability was conducted both outdoors and indoors in July 2019 at Research Center for Limnology Laboratory, LIPI. The W. globosa (percentage in dry weight) contained protein: 45.54%, fat: 5.33%, crude fiber: 9.98%, ash: 20.43%, and Nitrogen Free Extract:19.21%. It also contains 15 types of amino acids as much as 1.51 %w/w. At the outdoor system culture, the Wolffia has daily growth rate/GR (g/day) was 64.62−120.6, specific growth rate/SGR (%/day) was 14.622-15.333, and the daily productivity/P (g/m2/day) was 97.757−176.659. While at the indoor system culture the value of GR (g/day), SGR (%/day), and P (g/m2/day) were 0.675−1.50; 9.889−12.643; and 25.883−64.564 respectively. It is indicated that this Wolffia is very potential to be an alternative natural feed source for aquaculture or another purpose and needs further research.

IL-22 and its interaction with amino acid and glycolipid metabolite in polycystic ovary syndrome (PCOS) patients

IL-22 and its interaction with amino acid and glycolipid metabolite in polycystic ovary syndrome (PCOS) patients

Gamma-Ray Attenuation Characteristics of Some Essential Amino Acids for 57Co, 192Ir, 18F, and 116mIn Sources

Purpose: In different tissues of the body, proteins are important parts that are made up of building blocks called amino acids. Considering the wide applications of radioactive sources in industry and medicine, the need to study the attenuation characteristics of amino acids is determined. Materials and Methods: To study the attenuation characteristics of five types of amino acids, MCNPX Monte Carlo code and XMuDat program were used. Linear and mass attenuation coefficients, half and tenth value layers, mean free path, effective atomic and electronic cross-sections, effective atomic numbers and effective electron densities were calculated. 57Co, 192Ir, 18F, and 116mIn gamma sources were considered for this study. To validate the theoretical results, the obtained values were compared with the available experimental data. Results: The difference between the theoretical and experimental results was less than 11%. The results showed that with increasing photon energy, the linear and mass attenuation coefficients and effective atomic and electronic cross-sections decreased, while the half and tenth value layers and mean free path quantities increased. Furthermore, the linear attenuation coefficients, the effective atomic and electronic cross-sections, as well as the effective atomic number values increased with increasing amino acid density, while the effective electron density behaves independently of the amino acid density. Conclusion: The presented theoretical methods produced data similar to experimental results with fair accuracy, so by using these methods, attenuation properties of other amino acids can be obtained over a wide range of energies.

Chiral Nematic Cellulose Nanocrystal Films Cooperated with Amino Acids for Tunable Optical Properties.

The exploration of functional materials relies greatly on the understanding of material structures and nanotechnologies. In the present work, chiral nematic cellulose nanocrystal (CNC) films were prepared by incorporation with four types of amino acids (AAs, glycine, histidine, phenylalanine, and serine) via evaporation-induced self-assembly. The films present ideal iridescence and birefringence that can be tuned by the amount of AAs added. The intercalation of AAs enlarged the pitch values, contributing to the red-shift trend of the reflective wavelength. Among the AAs, serine presented the most compatible intercalation into cellulose crystals. Interestingly, histidine and phenylalanine composite films showed high shielding capabilities of UV light in diverse wavelength regions, exhibiting multi-optical functions. The sustainable preparation of chiral nematic CNC films may provide new strategies for materials production from biocompatible lignocellulose.