The classification and prediction of T-cell receptors (TCRs) protein sequences are of significant interest in understanding the immune system and developing personalized immunotherapies. In this ...study, we propose a novel approach using Pseudo Amino Acid Composition (PseAAC) protein encoding for accurate TCR protein sequence classification. The PseAAC2Vec encoding method captures the physicochemical properties of amino acids and their local sequence information, enabling the representation of protein sequences as fixed-length feature vectors. By incorporating physicochemical properties such as hydrophobicity, polarity, charge, molecular weight, and solvent accessibility, PseAAC2Vec provides a comprehensive and informative characterization of TCR protein sequences. To evaluate the effectiveness of the proposed PseAAC2Vec encoding approach, we assembled a large dataset of TCR protein sequences with annotated classes. We applied the PseAAC2Vec encoding scheme to each sequence and generated feature vectors based on a specified window size. Subsequently, we employed state-of-the-art machine learning algorithms, such as support vector machines (SVM) and random forests (RF), to classify the TCR protein sequences. Experimental results on the benchmark dataset demonstrated the superior performance of the PseAAC2Vec-based approach compared to existing methods. The PseAAC2Vec encoding effectively captures the discriminative patterns in TCR protein sequences, leading to improved classification accuracy and robustness. Furthermore, the encoding scheme showed promising results across different window sizes, indicating its adaptability to varying sequence contexts.
•The classification and prediction of T-cell receptors (TCRs) protein sequences are essential for understanding the immune system and developing personalized immunotherapies.•However, applying machine learning algorithms to protein sequences could be challenging, as these algorithms typically require numerical embeddings.•We propose a novel approach using Pseudo Amino Acid Composition (PseAAC) protein encoding for accurate TCR protein sequence classification.•The PseAAC2Vec encoding method captures the physicochemical properties of amino acids and their local sequence information, enabling the representation of protein sequences as fixed-length feature vectors.
Reducing dietary crude protein (CP) concentration while maintaining adequate amino acid (AA) supply by free AA inclusion can contribute to attenuate the negative environmental effects of animal ...farming. This study investigated upper limits of dietary free AA inclusions without undesirable effects including the dependence on asparagine (Asn) and glutamine (Gln) supply. Ten broilers were allocated to sixty-three metabolism units each and offered nine experimental diets from day (d) 7–21 (n 7). One diet (167 g CP/kg) contained 80 g soya protein isolate (SPI)/kg. In the other diets, 25, 50, 75 and 100 % of the digestible AA from SPI were substituted with free AA. Digestible Asn+aspartic acid (Asp) and Gln+glutamic acid (Glu) were substituted with Asp/Glu or 50/50 mixes of Asp/Asn and Glu/Gln, respectively. Total excreta were collected from d 11–14 and from d 18–21. Growth and nitrogen accretion were unaffected by 25 and 50 % substitution without and with free Asn/Gln, respectively, but decreased at higher substitution (P ≤ 0·024). Circulating concentrations of Asp, Glu and Gln were unaffected by treatment, while Asn decreased at substitution higher than 50 % when Asn/Gln were not provided (P ≤ 0·005). Blood gas analysis on d 21 indicated a compensated metabolic acidosis at substitution higher than 50 and 75 % without and with free Asn/Gln, respectively (P ≤ 0·017). Results suggest that adding Asn/Gln increased an upper limit for proportion of dietary free AA from 10 to 19 % of dietary CP and enabled higher free AA inclusion without affecting the acid–base balance.
Resistance exercise and amino acids are two major factors that influence muscle protein turnover. Here, we examined the effects of resistance exercise and branched-chain amino acids (BCAA), ...individually and in combination, on the expression of anabolic and catabolic genes in human skeletal muscle. Seven subjects performed two sessions of unilateral leg press exercise with randomized supplementation with BCAA or flavored water. Biopsies were collected from the vastus lateralis muscle of both the resting and exercising legs before and repeatedly after exercise to determine levels of mRNA, protein phosphorylation, and amino acid concentrations. Intake of BCAA reduced (P < 0.05) MAFbx mRNA by 30 and 50% in the resting and exercising legs, respectively. The level of MuRF-1 mRNA was elevated (P < 0.05) in the exercising leg two- and threefold under the placebo and BCAA conditions, respectively, whereas MuRF-1 total protein increased by 20% (P < 0.05) only in the placebo condition. Phosphorylation of p70(S6k) increased to a larger extent (∼2-fold; P < 0.05) in the early recovery period with BCAA supplementation, whereas the expression of genes regulating mTOR activity was not influenced by BCAA. Muscle levels of phenylalanine and tyrosine were reduced (13-17%) throughout recovery (P < 0.05) in the placebo condition and to a greater extent (32-43%; P < 0.05) following BCAA supplementation in both resting and exercising muscle. In conclusion, BCAA ingestion reduced MAFbx mRNA and prevented the exercise-induced increase in MuRF-1 total protein in both resting and exercising leg. Further-more, resistance exercise differently influenced MAFbx and MuRF-1 mRNA expression, suggesting both common and divergent regulation of these two ubiquitin ligases.
Abstract
Ultraviolet-screening compounds from the cyanobacterium Lyngbya sp. CU2555 were partially characterized and investigated for their induction by UV radiation, stability under different ...abiotic factors, and free radical scavenging activity. Based on the high-performance liquid chromatography coupled with diode array detector and ion trap liquid chromatography/mass spectrometry analysis, the compounds were identified as palythine (UVλmax: 319 nm; m/z: 245), asterina (UVλmax: 330 nm; m/z: 289), scytonemin (UVλmax: 384 nm; mw: 544), and reduced scytonemin (UVλmax: 384 nm; m/z: 547). This is the first report for the occurrence of palythine, asterina, and an unknown mycosporine-like amino acids (MAA), M-312 (UVλmax: 312 ± 1 nm), in addition to scytonemin and reduced scytonemin in Lyngbya strains studied so far. Induction of MAAs and scytonemin was significantly more prominent upon exposure to UV-A + UV-B radiation. Both MAAs and scytonemin were highly resistant to some physicochemical factors such as UV-B, heat, and a strong oxidizing agent and exhibited strong antioxidant activity. These results indicate that the studied cyanobacterium may protect itself from deleterious short-wavelength radiation by synthesizing photoprotective compounds in response to harmful UV radiation.
Azoles have been applied widely to combat pathogenic fungi in medicine and agriculture and, consequently, loss of efficacy has occurred in populations of some species. Often, but not always, ...resistance was found to result from amino acid substitutions in the molecular target of azoles, 14α-sterol demethylase (CYP51 syn. ERG11). This review summarizes CYP51 function, evolution, and structure. Furthermore, we compare the occurrence and contribution of CYP51 substitutions to azole resistance in clinical and field isolates of important fungal pathogens. Although no crystal structure is available yet for any fungal CYP51, homology modeling using structures from other origins as template allowed deducing models for fungal orthologs. These models served to map amino acid changes known from clinical and field isolates. We conclude with describing the potential consequences of these changes on the topology of the protein to explain CYP51-based azole resistance. Knowledge gained from molecular modeling and resistance research will help to develop novel azole structures.
Tau is a scaffolding protein that serves multiple cellular functions that are perturbed in neurodegenerative diseases, including Alzheimer's disease (AD) and frontotemporal dementia (FTD). We have ...recently shown that amyloid‐β, the second hallmark of AD, induces de novo protein synthesis of tau. Importantly, this activation was found to be tau‐dependent, raising the question of whether FTD‐tau by itself affects protein synthesis. We therefore applied non‐canonical amino acid labelling to visualise and identify newly synthesised proteins in the K369I tau transgenic K3 mouse model of FTD. This revealed massively decreased protein synthesis in neurons containing pathologically phosphorylated tau, a finding confirmed in P301L mutant tau transgenic rTg4510 mice. Using quantitative SWATH‐MS proteomics, we identified changes in 247 proteins of the de novo proteome of K3 mice. These included decreased synthesis of the ribosomal proteins RPL23, RPLP0, RPL19 and RPS16, a finding that was validated in both K3 and rTg4510 mice. Together, our findings present a potential pathomechanism by which pathological tau interferes with cellular functions through the dysregulation of ribosomal protein synthesis.
Synopsis
We demonstrate that protein synthesis is significantly decreased in the presence of frontotemporal dementia tau. Using SWATH‐MS de novo proteomics we reveal altered synthesis of distinct sets of proteins, including ribosomal proteins.
Global protein synthesis is decreased in transgenic mouse models of tauopathy and this decrease correlates with tau pathology.
SWATH‐MS de novo proteomics shows that distinct clusters of proteins are altered in synthesis in mice with pathological tau.
Ribosomal protein synthesis is decreased in two mouse models of tauopathy and this decrease is more pronounced as disease progresses.
Total abundance of the ribosomal subunit RPl23 is decreased in mouse models of tauopathy and in human FTD‐brain.
Analyses of brain samples from transgenic mice and human patients reveal that pathogenic tau alters de novo protein synthesis, suggesting a new mechanism underlying neurodegenerative disease pathology.
An unprecedented highly enantioselective Ru‐catalyzed direct asymmetric reductive amination of α‐keto amides with ammonium salts has been disclosed, efficiently offering valuable enantioenriched ...N‐unprotected unnatural α‐amino acid derivatives bearing a broad range of aryl or alkyl α‐substituents. This protocol features easily accessible substrates, good functional‐group tolerance and excellent enantiocontrol, making it a good complementary approach to the known methods. Moreover, this method is also applicable to the preparation of N‐unprotected unnatural α‐amino acid derivatives containing an additional stereogenic center at the β‐position through a dynamic kinetic resolution (DKR) process. Convenient transformations of the obtained products into chiral N‐unprotected unnatural α‐amino acids, drug intermediates, peptides, and organocatalysts/ligands further showcase the utility of this method.
An unprecedented Ru‐catalyzed direct asymmetric reductive amination of α‐keto amides with ammonium salts has been achieved. This protocol provides an efficient and practical way for the synthesis of diverse enantioenriched α‐aryl‐ or alkyl‐substituted N‐unprotected unnatural α‐amino acids and N‐unprotected β‐branched α‐amino acids. Further follow‐up transformations enable access to drug intermediates, peptides, and organocatalysts/ligands.
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins is an important tool for understanding biological function. Traditionally, each new ncAA targeted for incorporation ...requires a resource-consuming process of generating new ncAA aminoacyl tRNA synthetase/tRNACUA pairs. However, the discovery that some tRNA synthetases are "permissive", in that they can incorporate multiple ncAAs, means that it is no longer always necessary to develop a new synthetase for each newly desired ncAA. Developing a better understanding of what factors make ncAA synthetases more permissive would increase the utility of this new approach. Here, we characterized two synthetases selected for the same ncAA that have markedly different "permissivity profiles." Remarkably, the more permissive synthetase incorporated an ncAA for which we had not been able to generate a synthetase through de novo selection methods. Crystal structures revealed that the two synthetases recognize their parent ncAA through a conserved core of interactions, with the more permissive synthetase displaying a greater degree of flexibility in its interaction geometries. We also observed that intraprotein interactions not directly involved in ncAA binding can play a crucial role in synthetase permissivity and suggest that optimization of such interactions might provide an avenue to engineering synthetases with enhanced permissivity.
The non-protein amino acid β-methylamino-L-alanine (BMAA) has been linked to neurodegenerative disease and reported throughout the environment. Proposed mechanisms of bioaccumulation, trophic ...transfer and chronic toxicity of BMAA rely on the hypothesis of protein misincorporation. Poorly selective methods for BMAA analysis have led to controversy. Here, a recently reported highly selective method for BMAA quantitation using hydrophilic interaction liquid chromatography-differential mobility spectrometry-tandem mass spectrometry (HILIC-DMS-MS/MS) is expanded to include proteinogenic amino acids from hydrolyzed biological samples. For BMAA quantitation, we present a double spiking isotope dilution approach using D
-BMAA and
C
N
-BMAA. These methods were applied to study release of BMAA during acid hydrolysis under a variety of conditions, revealing that the majority of BMAA can be extracted along with only a small proportion of protein. A time course hydrolysis of BMAA from mussel tissue was carried out to assess the recovery of BMAA during sample preparation. The majority of BMAA measured by typical methods was released before a significant proportion of protein was hydrolyzed. Little change was observed in protein hydrolysis beyond typical hydrolysis times but the concentration of BMAA increased linearly. These findings demonstrate protein misincorporation is not the predominant form of BMAA in cycad and shellfish.
Bushen Zhichan decoction (BSZCF) is derived from Liuwei Dihuang Pill, a famous Chinese herbal formula recorded in the book Key to Therapeutics of Children's Diseases. It has been widely used as a ...basic prescription for nourishing and tonifying the liver and kidneys to treat Parkinson's disease (PD), but its mechanism remains to be explored.
BSZCF, a Chinese herbal formula comprising five herbs: Rehmannia glutinosa (Gaertn.) DC., Dioscorea oppositifolia L., Cornus officinalis Siebold & Zucc., Fallopia multiflora (Thunb.) Haraldson and Cistanche tubulosa (Schenk) Wight, is used clinically to treat PD. In vivo and in vitro experiments were designed to elucidate the mechanism of BSZCF in the protection of dopamine (DA) neurons and the treatment of PD. The toxicity of excitatory amino acids (EAA) may be attenuated by inhibiting the transcription factor Yin Yang 1 (YY1) and up-regulating the expression of excitatory amino acid transporter 1 (EAAT1).
After 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was intraperitoneally injected into specific pathogen free (SPF) C57BL/6J mice, model mice were intragastrically given adamantane hydrochloride tablets (AHT) or different doses of BSZCF for 14 days. Both open field and pole-climbing tests were conducted to assess behavioral changes. In vitro: 1-Methyl-4-phe-nylpyridiniumiodide (MPP+)-injured human neuroblastoma cells (SH-SY5Y) were utilized to construct PD cell models. Primary astrocytes were transfected with EAAT1 and YY1 lentiviruses for EAAT1 gene knockout and YY1 gene knockout astrocytes, respectively. The high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis of BSZCF was performed to control the quality of blood drugs. The optimal concentration and time of PD cell models treated by BSZCF were determined by the use of Cell Counting Kit-8 (CCK8). Enzyme-linked immunosorbent assay (ELISA) was used for measuring glutamate (Glu) in the peripheral blood and cells of each group. Western blotting (WB) and real-time quantitative polymerase chain reaction (qPCR) were used to detect tyrosine hydroxylase (TH), dopamine transporters (DAT), EAAT1 and YY1 protein and mRNA. After the blockade of EAAT1, immunofluorescence (IF) assay was used to detect the TH protein in each group.
In vivo research showed that BSZCF improved the behavioral symptoms of PD mice, and reduced the death of DA neurons and the level of Glu. The mechanism may be related to the decrease of YY1 expression and the increase of EAAT1 levels. In vitro experiments showed that the anti-excitatory amino acid toxicity of BSZCF was achieved by inhibiting YY1 expression and regulating EAAT1.
By inhibiting YY1 to increase the expression of EAAT1 and attenuating the toxicity of Glu, BSZCF exerts the effect of protecting DA neurons and treating PD-like symptoms in mice.
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•A Chinese herbal compound (Bushen Zhichan decoction, BSZCF) may slow the progression of Parkinson's disease.•BSZCF had a dopamine neuron protective effect associated with reduced glutamate (Glu) accumulation.•BSZCF reduced Glu accumulation primarily involved an increase in EAAT1 being transcriptionally regulated by YY1.•Knockdown experiments validated YY1 as a major target for BSZCF to exert neuroprotective effects.
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