Chain Amino Acids Research Articles

Riboflavin-mediated ultraviolet photosensitive oxidation of beef myofibrillar proteins with different storage times.

The study was designed to investigate the mechanism of Riboflavin (RF)-mediated UVA photosensitive oxidation on beef myofibrillar proteins (MP) oxidized at different storage times. To elucidate the direct relationship between RF and protein oxidation, the mechanism of action was analyzed in terms of amino acid and side chain residues, protein structure, and protein oxidative metabolism. Oxidation of MP resulted in significant changes in the levels of carbonyls, sulfhydryls, Lysine, Arginine, Threonin, and Histidine. The oxidized MP secondary structure was changed, fluorescence intensity decreased, and surface hydrophobicity increased. Metabolomics results revealed that RF-mediated UVA photosensitized oxidation is primarily mediated by Riboflavin metabolism and co-regulated with Phenylalanine metabolism. Moreover, with the increase of frozen storage time, Arginine and proline metabolism was inhibited, and the contents of creatine were significantly reduced, which exacerbated MP oxidative damage. The results provide a theoretical basis for unraveling the mechanism of RF-mediated UVA photosensitive oxidation of MP.

Management Thalassemia in Indonesia : A Literature Review

Thalassemia is a disease classified in the group of hereditary hemolytic anemia caused by the failure of the formation of one of the four amino acid chains forming Hb, causing incomplete Hb formation. Thalassemia carriers account for 7% of the world's population. At present, the cornerstone of treatment for β-TM in Indonesia remains supportive, including blood transfusions and iron chelation therapy. With a comprehensive discussion about thalassemia in Indonesia, it is hoped that the diagnosis and treatment of thalassemia will be more optimal and effective in future research.

Managing tomato bacterial wilt through pathogen suppression and host resistance augmentation using microbial peptide.

The increasing health and environmental risks associated with synthetic chemical pesticides necessitate the exploration of safer, sustainable alternatives for plant protection. This study investigates a novel biosynthesized antimicrobial peptide (AMP) from Lactiplantibacillus argentoratensis strain IT, identified as the amino acid chain PRKGSVAKDVLPDPVYNSKLVTRLINHLMIDGKRG, for its efficacy in controlling bacterial wilt (BW) disease in tomato (Solanum lycopersicum) caused by Ralstonia solanacearum. Our research demonstrates that foliar application of this AMP at a concentration of 200 ppm significantly reduces disease incidence by 49.3% and disease severity by 45.8%. Scanning electron microscopy revealed severe morphological disruptions in the bacterial cells upon exposure to the AMP. Additionally, the AMP enhanced host resistance by elevating defense enzyme activities, leading to notable improvements in plant morphology, including a 95.5% increase in plant length, a 20.1% increase in biomass, and a 96.69% increase in root length. This bifunctional AMP provides dual protection by exerting direct antimicrobial activity against the pathogen and eliciting plant defense mechanisms. These findings underscore the potential of this biologically sourced AMP as a natural agent for combating plant diseases and promoting growth in tomato crops. To the best of our knowledge, this is the first study to demonstrate the use of a foliar spray application of a biosynthesized microbial peptide as biocontrol agent against R. solanacearum. This interaction not only highlights its biocontrol efficacy but also its role in promoting the growth of Solanum lycopersicum thereby increasing overall agricultural yield.

Insights through molecular modeling into the structural requirement of Phenyl(6-phenylpyrazin-2-yl)methanone derivatives as aldose reductase inhibitors

Aldose reductase, play an important role in the pathogenesis of diabetic complications such as neuropathy, nephropathy and retinopathy. Therefore design of aldose reductase inhibitors has received considerable attention. In the present study molecular insights were explored through docking and QSAR. The quantification of the structural features of Phenyl(6-phenylpyrazin-2-yl)methanone analogs inferred that atomic Senderson electronegativity, van der Waals volume and charge distribution on the molecule are decisive for the aldose reductase inhibitory activity. Moreover, docking study depicted that benzonoid system of scaffold is crucial for - interaction with the side chain of key aromatic amino acids i.e. TRP111 and TRP20. These structural insights might provide significant roadmap for continuing search of potential ARIs prior to synthesis.

Molecular Structure of Paraoxonase-1 and Its Modifications in Relation to Enzyme Activity and Biological Functions-A Comprehensive Review.

PON1 is a Ca2+-dependent enzyme that indicates a hydrolytic activity towards a broad spectrum of substrates. The mechanism of hydrolysis catalyzed by this enzyme is poorly understood. It was shown that the active site of PON1 is highly dynamic. The catalytic center of this enzyme consists of side chains of amino acids binding two calcium ions, from which the first one performs a structural function and the other one is responsible for the catalytic properties of PON1. This review summarizes available information on the structure of PONs, the role of amino acids located in the active site in specificity, and multiple substrate affinity of enzymes for understanding and explaining the basis of the physiological function of PONs. Moreover, in this paper, we described the changes in the structure of PONs induced by environmental and genetic factors and their association with diseases. The detoxification efficiency depends on the polymorphism of the PON1 gene, especially Q192R. However, data on the association between single-nucleotide polymorphisms (SNPs) in the PON1 gene and cardiovascular or neurodegenerative diseases are insufficient. The reviewed papers may confirm that PON1 is a very promising tool for diagnostics, but further studies are required.

Peptides, Modern Technology for Plant Defense Response for Sustainable Green Agriculture for Increasing worldwide populations

Peptides are short chains of amino acids that are the building blocks of chosen proteins. Peptides are a secure and efficient alternative to existing synthetic pesticides and insecticides. A constant and reasonable food supply is critical to the foundation of economic prosperity and growth in several countries. Innovations in fertilizers, pesticides, plant breeding, trait development, and improved farming methods are the main drivers of productivity and growth. India's per capita food prices are among the lowest in the world among healthcare, pharmaceuticals, animal nutrition, and plant nutrition. In current years, peptides have become widespread research targets in crop protection as antibacterial agents, immune inducers, plant growth regulators, insecticides, and herbicides due to their rich raw material sources, excellent activity, and supreme environmental compatibility. The present manuscript briefly introduces the advances in peptide research, provides an overview of peptide research in crop protection, and summarizes the utilization of peptides in crop protection and the prospects of peptides as green pesticides for agriculture and sustainable development for increasing populations.

Antimicrobial Peptides: The Game-Changer in the Epic Battle Against Multidrug-Resistant Bacteria.

The rapid progress of antibiotic resistance among bacteria has prompted serious medical concerns regarding how to manage multidrug-resistant (MDR) bacterial infections. One emerging strategy to combat antibiotic resistance is the use of antimicrobial peptides (AMPs), which are amino acid chains that act as broad-spectrum antimicrobial molecules and are essential parts of the innate immune system in mammals, fungi, and plants. AMPs have unique antibacterial mechanisms that offer benefits over conventional antibiotics in combating drug-resistant bacterial infections. Currently, scientists have conducted multiple studies on AMPs for combating drug-resistant bacterial infections and found that AMPs are a promising alternative to conventional antibiotics. On the other hand, bacteria can develop several tactics to resist and bypass the effect of AMPs. Therefore, it is like a battle between the bacterial community and the AMPs, but who will win? This review provides thorough insights into the development of antibiotic resistance as well as detailed information about AMPs in terms of their history and classification. Furthermore, it addresses the unique antibacterial mechanisms of action of AMPs, how bacteria resist these mechanisms, and how to ensure AMPs win this battle. Finally, it provides updated information about FDA-approved AMPs and those that were still in clinical trials. This review provides vital information for researchers for the development and therapeutic application of novel AMPs for drug-resistant bacterial infections.

Hemoglobin targeting potential of aminocarb pesticide: Investigation into dynamics, conformational stability, and energetics in solvent environment

Aminocarb (AMC), a carbamate pesticide, due to its prevalent usage exhibits increased accumulation in the environment affecting both insects and humans. It enters the human body via food grains and be transported through bloodstream. AMC's chemical structure, containing specific molecular frameworks and functional groups, enables it to bind with proteins like albumin and hemoglobin. Given that molecules with similar architecture are known to bind with hemoglobin, we aimed to explore Aminocarb's binding capability and the potential mechanism or mode of its interaction with hemoglobin. Hb being a tetramer with a profound interface between amino acid chains offers multiple binding sites. It is therefore important to investigate the structural aspects of binding of AMC by employing various spectroscopic and in-silico methods. The surface of the α1 chain near the α1β2 interface emerges as the preferred binding site for AMC, primarily due to its conformational restrictions. In its bound state, AMC tends to maintain a relaxed conformation, closely resembling its globally optimized geometry, and resides in close proximity to the α1 chain via multiple hydrophobic contacts and water bridge as observed in molecular dynamics (MD) simulations. Fluorescence quenching experiments showed moderate binding strength (7.7 × 10⁴ L M⁻1 at 288 K, 7.8 × 10⁴ L M⁻1 at 298 K, 7.9 × 10⁴ L M⁻1 at 308 K) and spontaneous binding, driven by hydrophobic and van der Waals interactions, as indicated by enthalpy (0.80–0.91 kJ mol⁻1), entropy (0.0970–0.0974 kJ mol⁻1), and Gibbs free energy (−27.13 to - 29.08 kJ mol⁻1). Circular dichroism experiments reveal no major structural changes in Hb. Quantum chemical calculations and MD simulations reveal conformation-dependent energy differences, enhancing our understanding of AMC's binding mechanism to Hb.

Bioactive Peptides from Fermented Foods: Production Approaches, Sources, and Potential Health Benefits.

Microbial fermentation is a well-known strategy for enhancing the nutraceutical attributes of foods. Among the fermentation outcomes, bioactive peptides (BAPs), short chains of amino acids resulting from proteolytic activity, are emerging as promising components thanks to their bioactivities. Indeed, BAPs offer numerous health benefits, including antimicrobial, antioxidant, antihypertensive, and anti-inflammatory properties. This review focuses on the production of bioactive peptides during the fermentation process, emphasizing how different microbial strains and fermentation conditions influence the quantity and quality of these peptides. Furthermore, it examines the health benefits of BAPs from fermented foods, highlighting their potential in disease prevention and overall health promotion. Additionally, this review addresses the challenges and future directions in this field. This comprehensive overview underscores the promise of fermented foods as sustainable and potent sources of bioactive peptides, with significant implications for developing functional foods and nutraceuticals.

Conductance Channels in a Single-Entity Enzyme.

For a long time, the prevailing view in the scientific community was that proteins, being complex macromolecules composed of amino acid chains linked by peptide bonds, adopt folded structure with insulating or semiconducting properties, with high bandgaps. However, recent discoveries of unexpectedly high conductance levels, reaching values in the range of dozens of nanosiemens (nS) in proteins, have challenged this conventional understanding. In this study, we used scanning tunneling microscopy (STM) to explore the single-entity conductance properties of enzymatic channels, focusing on bilirubin oxidase (BOD) as a model metalloprotein. By immobilizing BOD on a conductive carbon surface, we discern its preferred orientation, facilitating the formation of electronic and ionic channels. These channels show efficient electron transport (ETp), with apparent conductance up to the 15 nS range. Notably, these conductance pathways are localized, minimizing electron transport barriers due to solvents and ions, underscoring BOD's redox versatility. Furthermore, electron transfer (ET) within the BOD occurs via preferential pathways. The alignment of the conductance channels with hydrophilicity maps, molecular vacancies, and regions accessible to electrolytes explains the observed conductance values. Additionally, BOD exhibits redox activity, with its active center playing a critical role in the ETp process. These findings significantly advance our understanding of the intricate mechanisms that govern ETp processes in proteins, offering new insights into the conductance of metalloproteins.

Synthesis, spectroscopy, solvation effect, topology and molecular docking studies on 2,2′-((1,2 phenylenebis (azaneylylidene)) bis (methaneylylidene)) bis(4-bromophenol)

The 2,2′-((1,2 phenylenebis (azaneylylidene)) bis (methaneylylidene)) bis(4-bromophenol) (5BSOP) Schiff base was synthesized, characterized using different spectroscopic techniques, and the data are compared with predictions from DFT computations. The calculated energy values are -8.65 eV (HOMO) and -6.66 eV (LUMO), and the energy gap was found to be 1.99 eV. The reactive atom sites in the chemical are identified by MEP analysis. The locations of localized and delocalized orbitals are revealed through ELF and LOL surface maps. The sites of non-covalent interactions are exposed by RDG and NCI analysis. The possible inter and intra-molecular interactions were determined by NBO analysis and the highest stabilization energy observed was 40.07 kcal/mol. Biological performance as a HMGCS2 expression enhancer was predicted by Pass online studies. Molecular docking simulation with protein 706I having HMGCS2 expression inhibition characteristics revealed a stable receptor-ligand interaction pose at a binding energy of -4.74 kcal/mol. The interaction of the Phe61 amino acid chain of 706I with 5BSOP through conventional H-bond expressed a bond distance of 3.24 Å.

Anti-Obesity Effects of a Collagen with Low Digestibility and High Swelling Capacity: A Human Randomized Control Trial.

Collagen is a protein formed by very long amino acid chains. When conveniently treated, it can incorporate water into the net, thus increasing its volume and mass. The present work aimed to evaluate the potential anti-obesity effects of bovine collagen that has been technologically treated to increase its water retention capacity in an acid pH medium, with the objective of inducing satiation. Collagen's digestibility was tested with a pepsin digestion test. Its swelling capacity was tested in an acid pH medium simulating gastric conditions. Postprandial levels of ghrelin in response to collagen supplementation were tested in rats. In a randomized control trial, 64 subjects with overweight/obesity were allocated in two groups: supplemented daily with two protein bars enriched with collagen (20 g per day) for 12 weeks, or control group. Anthropometric and biochemical measurements were assessed in all the participants. This collagen showed a low digestibility (<60%) and high swelling capacity (>1900%) in vitro. In humans with overweight and obesity, this collagen significantly reduced body weight, body mass index (BMI), systolic blood pressure (SBP), and fatty liver index (FLI) and increased fat-free mass when compared with the control group. A significant reduction in the sarcopenic index; total, troncular, and visceral fat (measured by DEXA); and serum leptin levels were observed in the collagen group at the end of the intervention, with no differences with respect to controls. Collagen reduced the sensation of hunger and increased fullness and satisfaction. In male Wistar rats, collagen decreased postprandial blood ghrelin levels. Collagen supplementation (20 g per day for 12 weeks) reduced body weight, BMI, waist circumference, fat mass, FLI, and SBP in humans with overweight and obesity, which might be related to the increased sensation of fullness and satisfaction reported by the volunteers after the intake.

Changes in Texture and Collagen Properties of Pork Skin during Salt-Enzyme-Alkali Tenderization Treatment.

The effects of salt-enzyme-alkali progressive tenderization treatments on porcine cortical conformation and collagen properties were investigated, and their effectiveness and mechanisms were analyzed. The tenderization treatment comprised three treatment stages: CaCl2 (25 °C/0-30 min), papain (35 °C/30-78 min), and Na2CO3 (25 °C/78-120 min). The textural, microscopic, and collagenous properties (content, solubility, and structure) of pork skin were determined at the 0th, 30th, 60th, 90th, and 120th min of the treatment process. The results showed that the shear force, hardness, and chewability of the skin decreased significantly (p < 0.05), and the elasticity exhibited a gradual increase with the progression of tenderization. The content and solubility of collagen showed no significant change at the CaCl2 treatment stage. However, the soluble collagen content increased, the insoluble collagen content decreased, and the collagen solubility increased by 18.04% during the subsequent treatment with papain and Na2CO3. Meanwhile, the scanning electron microscopy results revealed that the regular, wavy structure of the pig skin collagen fibers gradually disappeared during the CaCl2 treatment stage, the overall structure revealed expansion, and the surface microscopic pores gradually increased during the papain and Na2CO3 treatment stages. The findings of the Fourier transform infrared spectroscopy analysis indicated that the hydrogen bonding interactions between the collagen molecules and the C=O, N-H and C-N bonds in the subunit structure of collagen were substantially altered during treatment and that the breakage of amino acid chains and reduction in structural ordering became more pronounced with prolonged treatment. In the tertiary structure, the maximum emission wavelength was blue-shifted and then red-shifted, and the fluorescence intensity was gradually weakened. The surface hydrophobicity was slowly increased. The salt-enzyme-alkali tenderization treatment considerably improved the physical properties and texture of edible pork skins by dissolving collagen fibers and destroying the structure of collagen and its interaction force.

The evolution of amino acids under asteroidal aqueous alteration

Carbonaceous chondrites contain amino acids, with variable abundances and isotope compositions between and within carbonaceous chondrites. The parent body processes, and the presence of clay minerals may explain those differences. Here, we experimentally investigate the evolution of 6 amino acids (glycine, β-alanine, α-alanine, 2-aminoisobutyric acid, γ-aminobutyric acid, and isovaline) exposed to hydrothermal conditions in the presence or absence of silicates. We determined the chemical nature and isotopic composition of the organic compounds of the soluble and solid fractions of the residues using X-ray diffraction, spectroscopy, and mass-spectrometry methods. Glycine and α-alanine exhibit a rather high stability, which is consistent with the measured abundances of α-alanine and glycine in chondrites having experienced various degrees of aqueous alteration. In the meantime, the evolution of β-alanine under hydrothermal conditions leads to the formation of a new compound, which likely results from the decarboxylation and deamination of β-alanine followed by recombination. More than 95 % of γ-ABA was transformed into 2-pyrrolidione though self-cyclization during the aqueous alteration. The solid residues of the experiments conducted in the presence of clay minerals contain organic material, with abundances varying depending on the amino acid used for the experiments (TOC isovaline > 2-aminoisobutyric acid > γ-aminobutyric acid > glycine > α-alanine > β-alanine). Clay minerals thus preferentially trap branched amino acids over chained amino acids, likely within their interlayer spaces as suggested by XRD data. The δ13C values of amino acids have not changed significantly during the experiments, even with the presence of silicates. Thus, the δ13C values of amino acids reported in CR and CM chondrites likely relate to synthetic conditions or the origin of their precursors (i.e. inherited from the pre-accretion processes).

Sub-nanometer size level regulation of biomimetic channels in porous membrane for high-capacity removal of toxic dye contaminants

Organic dyes are an important chemical with a market demand of millions of tons. However, their massive emissions, especially alkaline dye contaminants, have caused serious disruption of the ecosystem and even cancers. Inspired by bionic mass transfer, several amino acid fragments (carboxylic acid, γ-aminobutyric acid, and glutamic acid) are introduced into the 2.5 nm-pore size cavity through in-situ polymerization. The flexible amino acid chains facilitate the transport of guest molecules into the channels, accelerating their movement within the porous framework. These flexible chains are implanted into a 2.5 nm pore cavity, forming a 0.8–1.5 nano-meter-sized confinement space, bringing about the strong absorption capability for alkaline contaminants. Notably, LNU-74-glutamic acid achieves an ultra-fast absorption rate for toxic dye contaminants (4.74 g g−1h−1), as well as the highest capacity per unit area among all reported porous adsorbents, including porous carbons, metal–organic frameworks, porous polymers. After encapsulation in commercial polymer, the mixed-matrix membrane reveals (LNU-74-glutamic acid@MMM) a rejection rate greater than 98 % in various real water environments at permeation flux of ∼320 L m−2h−1, including strong acid/alkali, river water, and seawater.

N-terminal domain of androgen receptor is a major therapeutic barrier and potential pharmacological target for treating castration resistant prostate cancer: a comprehensive review.

The incidence rate of prostate cancer (PCa) has risen by 3% per year from 2014 through 2019 in the United States. An estimated 34,700 people will die from PCa in 2023, corresponding to 95 deaths per day. Castration resistant prostate cancer (CRPC) is the leading cause of deaths among men with PCa. Androgen receptor (AR) plays a critical role in the development of CRPC. N-terminal domain (NTD) is the essential functional domain for AR transcriptional activation, in which modular activation function-1 (AF-1) is important for gene regulation and protein interactions. Over last 2decades drug discovery against NTD has attracted interest for CRPC treatment. However, NTD is an intrinsically disordered domain without stable three-dimensional structure, which has so far hampered the development of drugs targeting this highly dynamic structure. Employing high throughput cell-based assays, small-molecule NTD inhibitors exhibit a variety of unexpected properties, ranging from specific binding to NTD, blocking AR transactivation, and suppressing oncogenic proliferation, which prompts its evaluation in clinical trials. Furthermore, molecular dynamics simulations reveal that compounds can induce the formation of collapsed helical states. Nevertheless, our knowledge of NTD structure has been limited to the primary sequence of amino acid chain and a few secondary structure motif, acting as a barrier for computational and pharmaceutical analysis to decipher dynamic conformation and drug-target interaction. In this review, we provide an overview on the sequence-structure-function relationships of NTD, including the polymorphism of mono-amino acid repeats, functional elements for transcription regulation, and modeled tertiary structure of NTD. Moreover, we summarize the activities and therapeutic potential of current NTD-targeting inhibitors and outline different experimental methods contributing to screening novel compounds. Finally, we discuss current directions for structure-based drug design and potential breakthroughs for exploring pharmacological motifs and pockets in NTD, which could contribute to the discovery of new NTD inhibitors.

Low-temperature plasma jet treatment generates reactive oxygen species in solution that leads to peptide oxidation and protein aggregation

Abstract Low-temperature plasma (LTPs) jets are FDA-approved medical devices to remove cancerous tissue and aid in wound healing. However, reports on their reaction with proteins are conflicting, ranging from fragmentation, oxidation, aggregation, or a combination thereof. In this study we bridge the gap between plasma-treatment of short peptides to proteins at physiologically relevant concentrations. The LTP in this study is based on a helium dielectric barrier discharge (DBD) that forms a plasma-jet, which is directed at the solution without direct contact with the plasma, and results in the formation of reactive oxygen species (ROS) OH• and O2•- in solution. The longer the solution is treated, the more solution-phase ROS form. Treating peptide- and protein-containing solutions leads to extensive oxidation. The ROS led to the same oxidative modifications for peptide M with increasing chain length (9, 18, 37, 76 amino acids), which could be identified with high-resolution mass spectrometry. Oxidized species M+xO led to conformational changes such as compaction and elongation, while the unmodified peptide M remained unaltered, as found by ion mobility spectrometry and size exclusion chromatography. For proteins at high concentration, insoluble aggregates formed and could be identified by UV/Vis light scattering and atomic force microscopy. The formation of aggregates is dependent on the amino acid chain length, the peptide concentration, and the time for aggregate formation. These findings highlight the importance of both peptide chain length and concentration in determining the fate of peptides following the exposure to LTP, while also offering valuable insights for the field of plasma medicine. &amp;#xD;

Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation.

The convergence of biotechnology and artificial intelligence has the potential to transform drug development, especially in the field of therapeutic peptide design. Peptides are short chains of amino acids with diverse therapeutic applications that offer several advantages over small molecular drugs, such as targeted therapy and minimal side effects. However, limited oral bioavailability and enzymatic degradation have limited their effectiveness. With advances in deep learning techniques, innovative approaches to peptide design have become possible. In this work, we demonstrate HYDRA, a hybrid deep learning approach that leverages the distribution modeling capabilities of a diffusion model and combines it with a binding affinity maximization algorithm that can be used for de novo design of peptide binders for various target receptors. As an application, we have used our approach to design therapeutic peptides targeting proteins expressed by Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) genes. The ability of HYDRA to generate peptides conditioned on the target receptor's binding sites makes it a promising approach for developing effective therapies for malaria and other diseases.

Toxicity of antimony to plants: Effects on metabolism of N and S in a rice plant

Excess antimony (Sb) has been shown to damage plant growth. Rice plants readily absorb a large amount of Sb after a long period of flooding, yet the mechanisms underlying Sb toxicity in plants have not been solved. This study was conducted to explore the effects of Sb on the uptake of N and S, and monitor the concentrations of reduced glutathione (GSH) and enzymes associated with these processes. In addition, we analyzed differentially expressed metabolites (DEMs) correlated with amino acids (AAs) and oligopeptides, specifically DEMs containing sulfur (S), GSH and indole–3–acetic acid (IAA). The results showed that antimonite [Sb(III)] inhibited shoot growth whereas antimonate [Sb(V)] stimulated shoot growth. Interestingly, Sb(III)5/10 enhanced shoot concentrations of total nitrogen (N), NH4+–N [only at Sb(III)10] and S; but reduced the shoot concentrations of NO3–N and soluble protein. Sb(III)5/10 addition significantly increased oxidized glutathione (GSSG) concentration and activities of glutathione peroxidase (GSH–Px) and glutathione S-transferase (GST) but non–significantly affected concentration of reduced glutathione (GSH) and activities of γ-glutamylcysteine synthetase (GCL) and glutathione reductase (GR), suggesting Sb(III) restricted GSH recycling. Addition of Sb (1) increased the abundance of DEMs associated with lignins, Ca uptake, toxicity/detoxification, and branched chain AAs; (2) decreased the abundance of AAs inclcuding isoleucine (Ile), leucine (Leu), tryptophan (Trp), tyrosine (Tyr) and histidine (His); (3) increased the abundance of arginine (Arg), putrescine (Put) and spermidine (Spd); and (4) affected methylation and acetylation of many AAs, especially acetylation.

ACP-ESM: A novel framework for classification of anticancer peptides using protein-oriented transformer approach

Anticancer peptides (ACPs) are a class of molecules that have gained significant attention in the field of cancer research and therapy. ACPs are short chains of amino acids, the building blocks of proteins, and they possess the ability to selectively target and kill cancer cells. One of the key advantages of ACPs is their ability to selectively target cancer cells while sparing healthy cells to a greater extent. This selectivity is often attributed to differences in the surface properties of cancer cells compared to normal cells. That is why ACPs are being investigated as potential candidates for cancer therapy. ACPs may be used alone or in combination with other treatment modalities like chemotherapy and radiation therapy. While ACPs hold promise as a novel approach to cancer treatment, there are challenges to overcome, including optimizing their stability, improving selectivity, and enhancing their delivery to cancer cells, continuous increasing in number of peptide sequences, developing a reliable and precise prediction model. In this work, we propose an efficient transformer-based framework to identify ACPs for by performing accurate a reliable and precise prediction model. For this purpose, four different transformer models, namely ESM, ProtBERT, BioBERT, and SciBERT are employed to detect ACPs from amino acid sequences. To demonstrate the contribution of the proposed framework, extensive experiments are carried on widely-used datasets in the literature, two versions of AntiCp2, cACP-DeepGram, ACP-740. Experiment results show the usage of proposed model enhances classification accuracy when compared to the literature studies. The proposed framework, ESM, exhibits 96.45% of accuracy for AntiCp2 dataset, 97.66% of accuracy for cACP-DeepGram dataset, and 88.51% of accuracy for ACP-740 dataset, thence determining new state-of-the-art. The code of proposed framework is publicly available at github (https://github.com/mstf-yalcin/acp-esm).