Pharmacokinetics of L-theanine and the effect on amino acid composition in mice administered with L-theanine.

L-theanine, an amino acid component of the tea leaves of Camellia sinensis, is sold in Japan as a supplement for good sleep. Although several studies in humans and mice have reported the effects of L-theanine on brain function, only a few reports have comprehensively clarified the disposition of theanine administered to mice and its effects on concentrations of other blood amino acids. In this study, we aimed to determine the changes in the blood levels of L-theanine administered to mice and amino acid composition of the serum. L-theanine were administered to four-week-old Std-ddY male mice orally or via tail vein injection. L-theanine and other amino acids in serum prepared from blood collected at different time points post-dose were labeled with phenylisothiocyanate and quantified. The serum concentration of orally administered L-theanine peaked 15 min after administration. The area under the curve for tail vein injection revealed the bioavailability of L- theanine to be approximately 70%. L-theanine administration did not affect any amino acid levels in the serum, but a significant increase in the peak area overlapping the Glycine (Gly) peak was observed 30 min after administration. L-theanine administered to mice was rapidly absorbed and eliminated, suggesting that taking L-theanine as a supplement is safe without affecting its own levels or serum levels of other amino acids. However, considering that Gly, similar to L-theanine, is used as a dietary supplement for its anxiolytic effects and to improve sleep, determining the effects of L-theanine administration on Gly is important and needs further research.

In vitro antioxidant activity evaluation of pine nut peptides (Pinus koraiensis) fermented by Bacillus subtilis LS-45.

In this study, we utilized the remarkable capabilities of Bacillus subtilis ls-45 during the fermentation process to generate pine nut peptide. Through gene sequencing, we confirmed the proficiency of Bacillus subtilis ls-45 in producing protease, thereby serving as a valuable enzymatic source for protein hydrolysis. Our investigation focused on examining the variations in amino acid types and quantities between enzymatic pine nut protein peptide (EPP) and fermented pine nut protein polypeptide (FPP). Furthermore, we conducted a comprehensive assessment of the in vitro antioxidant activities of EPP and FPP, encompassing measurements of their Hydroxyl radical scavenging rate, Total reducing capacity, Superoxide anion scavenging rate, and ABTS+ radical scavenging rate. Notably, FPP exhibited superior antioxidant capacity compared to EPP. By employing semi-inhibitory mass concentration (IC50) analysis, we determined that FPP displayed enhanced efficacy in neutralizing hazardous free radicals when compared to EPP.

High moisture extrusion of plant proteins: advances, challenges, and opportunities.

High moisture extrusion is a widely used technology for producing fibrous meat analogues in an efficient and scalable manner. Extrusion of soy, wheat gluten, and pea is well-documented and related products are already available in the market. There has been growing interest to diversify the protein sources used for meat analogues due to concerns over food waste, monocropping and allergenicity. Optimizing the extrusion process for plant proteins (e.g., hemp, mung bean, fava bean) tends to be time consuming and relies on the operators' intuition and experience to control the process well. Simulating the extrusion process has been challenging so far due to the diverse inputs and configurations involved during extrusion. This review details the mechanism for fibrous structure formation and provides an overview of the extrusion parameters used for texturizing a broad range of plant protein sources. Referring to these data reduces the resources needed for optimizing the extrusion process for novel proteins and may be useful for future extrusion modeling efforts. The review also highlights potential challenges and opportunities for extruding plant proteins, which may help to accelerate the development and commercialization of related products.

Human milk extracellular vesicles enhance muscle growth and physical performance of immature mice associating with Akt/mTOR/p70s6k signaling pathway.

Extracellular vesicles (EVs) play an important role in human and bovine milk composition. According to excellent published studies, it also exerts various functions in the gut, bone, or immune system. However, the effects of milk-derived EVs on skeletal muscle growth and performance have yet to be fully explored. Firstly, the current study examined the amino acids profile in human milk EVs (HME) and bovine milk EVs (BME) using targeted metabolomics. Secondly, HME and BME were injected in the quadriceps of mice for four weeks (1 time/3 days). Then, related muscle performance, muscle growth markers/pathways, and amino acids profile were detected or measured by grip strength analysis, rotarod performance testing, Jenner-Giemsa/H&E staining, Western blotting, and targeted metabolomics, respectively. Finally, HME and BME were co-cultured with C2C12 cells to detect the above-related indexes and further testify relative phenomena. Our findings mainly demonstrated that HME and BME significantly increase the diameter of C2C12 myotubes. HME treatment demonstrates higher exercise performance and muscle fiber densities than BME treatment. Besides, after KEGG and correlation analyses with biological function after HME and BME treatment, results showed L-Ornithine acts as a "notable marker" after HME treatment to affect mouse skeletal muscle growth or functions. Otherwise, L-Ornithine also significantly positively correlates with the activation of the AKT/mTOR pathway and myogenic regulatory factors (MRFs) and can also be observed in muscle and C2C12 cells after HME treatment. Overall, our study not only provides a novel result for the amino acid composition of HME and BME, but the current study also indicates the advantage of human milk on skeletal muscle growth and performance.

Utilization of Yeast Extract as a Flavor Enhancer and Masking Agent in Sodium-Reduced Marinated Shrimp.

Deepwater pink shrimp (Parapenaus longirostris) has a significantly high catch yield and is a highly important food source for human nutrition in terms of its nutritional value. The reduction of salt content in seafood products while preserving taste poses a significant challenge. The aim of this study is to reduce the NaCl ratio used in the shrimp marination process by substituting it with KCl and masking the resulting bitterness from KCl using natural flavor enhancers, such as yeast extracts. The marinated shrimp were prepared using 50% KCl instead of 50% NaCl. In order to mask the bitter taste caused by KCl and enhance the flavor, two different types of yeast extracts obtained from Saccharomyces cerevisiae were utilized in the formulation. Nutritional composition, Na and K contents, amino acid composition, color measurement, bacteriological quality, pH changes, and sensory evaluations were conducted to assess the impact of salt reduction and yeast extracts on the sensory, chemical, and physical attributes of the products. L-glutamic acid, L-alanine, L-aspartic acid, L-leucine, L-valine, and L-lysine were found to be higher in samples with Levex Terra yeast extract. Despite a 50% reduction in NaCl content, the addition of yeast extract led to an increase in the umami taste due to the elevation of amino acids present. Yeast extracts can offer a promising solution for enhancing the sensory qualities of seafood products with reduced salt content by conducting more detailed sensory development examinations.

The Functional and Physicochemical Properties of Rice Protein Concentrate Subjected to Acetylation.

The aim of the present study was to increase the value of rice protein concentrate (RPC) by improving the functional properties of a preparation subjected to acetylation and analyze the impact of this chemical modification on chemical composition, digestibility, and protein patterning using SDS-PAGE electrophoresis and FT-IR spectroscopy. In the modified samples, the protein content increased (80.90-83.10 g/100 g cf. 74.20 g/100 g in the control). Electrophoresis revealed that the content of the main rice protein fractions (prolamin and glutelin) decreased as the concentration of the modifying reagent increased. Through spectroscopic analysis, wavenumbers, corresponding to the presence of proteins or lipids, aromatic systems, and carbohydrates, were observed. The use of acetic anhydride did not change the digestibility of the modified RPC significantly when compared to that of the control sample. The acetylation of the RPC caused a significant increase in its emulsifying properties at pH 8 (1.83-14.74%) and its water-binding capacity but did not have a statistically significant impact on the oil-absorption capacity. There was a slight increase in protein solubility and a decrease in foaming capacity in the modified RPC.

Slaughter performance of the main goose breeds raised commercially in China and nutritional value of the meats of the goose breeds: a systematic review.

A number of goose breeds are raised commercially in China. However, the data on the slaughter performance of the goose breeds and the nutritional value of their meats lack a thorough comparative analysis. In this systematic review, the slaughter performance of the goose breeds and nutritional value of their meats were comparatively analyzed to provide an overview of the characteristics of the goose breeds raised commercially in China. Fifteen goose breeds were selected from 27 research articles published up to January 2022 on the slaughter performance of the goose breeds raised commercially in China and their nutrient composition after literature searching, literature screening, variety selection, and data collation. The slaughter indexes of the goose breeds and the basic nutrient composition, amino acid composition, and fatty acid composition of the meats of the goose breeds were standardized using min-max normalization and compared. The results suggest that the slaughter indexes and nutritional indicators of the meats of Yangzhou white goose, Xupu goose, Landaise geese, and Sichuan white goose are more balanced than those of the meats of the other goose breeds. The results of this review can lay the foundation for optimizing the breeding methods of the commercially raised goose breeds and processing methods of the meats of the geese. © 2022 Society of Chemical Industry.

HGDTI: predicting drug-target interaction by using information aggregation based on heterogeneous graph neural network.

BACKGROUND: In research on new drug discovery, the traditional wet experiment has a long period. Predicting drug-target interaction (DTI) in silico can greatly narrow the scope of search of candidate medications. Excellent algorithm model may be more effective in revealing the potential connection between drug and target in the bioinformatics network composed of drugs, proteins and other related data. RESULTS: In this work, we have developed a heterogeneous graph neural network model, named as HGDTI, which includes a learning phase of network node embedding and a training phase of DTI classification. This method first obtains the molecular fingerprint information of drugs and the pseudo amino acid composition information of proteins, then extracts the initial features of nodes through Bi-LSTM, and uses the attention mechanism to aggregate heterogeneous neighbors. In several comparative experiments, the overall performance of HGDTI significantly outperforms other state-of-the-art DTI prediction models, and the negative sampling technology is employed to further optimize the prediction power of model. In addition, we have proved the robustness of HGDTI through heterogeneous network content reduction tests, and proved the rationality of HGDTI through other comparative experiments. These results indicate that HGDTI can utilize heterogeneous information to capture the embedding of drugs and targets, and provide assistance for drug development. CONCLUSIONS: The HGDTI based on heterogeneous graph neural network model, can utilize heterogeneous information to capture the embedding of drugs and targets, and provide assistance for drug development. For the convenience of related researchers, a user-friendly web-server has been established at http://bioinfo.jcu.edu.cn/hgdti .

Classifying COVID-19 based on amino acids encoding with machine learning algorithms.

COVID-19 disease causes serious respiratory illnesses. Therefore, accurate identification of the viral infection cycle plays a key role in designing appropriate vaccines. The risk of this disease depends on proteins that interact with human receptors. In this paper, we formulate a novel model for COVID-19 named "amino acid encoding based prediction" (AAPred). This model is accurate, classifies the various coronavirus types, and distinguishes SARS-CoV-2 from other coronaviruses. With the AAPred model, we reduce the number of features to enhance its performance by selecting the most important ones employing statistical criteria. The protein sequence of SARS-CoV-2 for understanding the viral infection cycle is analyzed. Six machine learning classifiers related to decision trees, k-nearest neighbors, random forest, support vector machine, bagging ensemble, and gradient boosting are used to evaluate the model in terms of accuracy, precision, sensitivity, and specificity. We implement the obtained results computationally and apply them to real data from the National Genomics Data Center. The experimental results report that the AAPred model reduces the features to seven of them. The average accuracy of the 10-fold cross-validation is 98.69%, precision is 98.72%, sensitivity is 96.81%, and specificity is 97.72%. The features are selected utilizing information gain and classified with random forest. The proposed model predicts the type of Coronavirus and reduces the number of extracted features. We identify that SARS-CoV-2 has similar physicochemical characteristics in some regions of SARS-CoV. Also, we report that SARS-CoV-2 has similar infection cycles and sequences in some regions of SARS CoV indicating the affectedness of vaccines on SARS-CoV-2. A comparison with deep learning shows similar results with our method.

ACP-ADA: A Boosting Method with Data Augmentation for Improved Prediction of Anticancer Peptides.

Cancer is the second-leading cause of death worldwide, and therapeutic peptides that target and destroy cancer cells have received a great deal of interest in recent years. Traditional wet experiments are expensive and inefficient for identifying novel anticancer peptides; therefore, the development of an effective computational approach is essential to recognize ACP candidates before experimental methods are used. In this study, we proposed an Ada-boosting algorithm with the base learner random forest called ACP-ADA, which integrates binary profile feature, amino acid index, and amino acid composition with a 210-dimensional feature space vector to represent the peptides. Training samples in the feature space were augmented to increase the sample size and further improve the performance of the model in the case of insufficient samples. Furthermore, we used five-fold cross-validation to find model parameters, and the cross-validation results showed that ACP-ADA outperforms existing methods for this feature combination with data augmentation in terms of performance metrics. Specifically, ACP-ADA recorded an average accuracy of 86.4% and a Mathew's correlation coefficient of 74.01% for dataset ACP740 and 90.83% and 81.65% for dataset ACP240; consequently, it can be a very useful tool in drug development and biomedical research.

Influence of Enzymatic Hydrolysis and Molecular Weight Fractionation on the Antioxidant and Lipase / α-Amylase Inhibitory Activities In Vitro of Watermelon Seed Protein Hydrolysates.

This study aims to evaluate the potential in vitro antioxidant and anti-obesity activities of watermelon seed protein hydrolysates (WSPH) obtained using different combinations of enzymes alcalase−proteinase K (ALC-PK) and alcalase−actinidin (ALC-ACT). There was a direct relationship between the degree of hydrolysis (DH) and the biological activities of the WSPH, with the highest DPPH (approximately 85%) and lipase inhibitory activities (≈59%) appreciated at DH of 36−37% and 33−35% when using ALC-PK and ALC-ACT, respectively. Following molecular weight fractionation, the ALC-PK WSPH < 3 kDa (F1) assayed at 1 mg.mL−1 had the highest DPPH-radical scavenging (89.22%), ferrous chelating (FC) (79.83%), reducing power (RP) (A 0.51), lipase inhibitory (71.36%), and α-amylase inhibitory (62.08%) activities. The amino acid analysis of ALC-PK WSPH and its fractions revealed a relationship between the biological activity of the extracts and their composition. High contents of hydrophobic amino acids, arginine, and aromatic amino acids were related to high antioxidant, lipase inhibitory, and α-amylase inhibitory activities in the extracts, respectively. Overall, this study revealed that underutilized protein sources such as WSPH, using the appropriate combination of enzymes, could result in the generation of new ingredients and compounds with powerful antioxidant and anti-obesity activities with promising applications as nutraceuticals or functional foods.

Process Optimization, Amino Acid Composition, and Antioxidant Activities of Protein and Polypeptide Extracted from Waste Beer Yeast.

Repurposing of waste beer yeast (WBY) that a main by-product of brewing industry has attracted considerable attention in recent years. In this study, the protein and polypeptide were extracted by ultrasonic-assisted extraction and enzymatic hydrolysis with process optimization, which resulted in a maximum yield of 73.94% and 61.24%, respectively. Both protein and polypeptide of WBY were composed of 17 Amino acids (AA) that included seven essential amino acids (EAA), and typically rich in glutamic acid (Glu) (6.46% and 6.13%) and glycine (Gly) (5.26% and 6.02%). AA score (AAS) revealed that the threonine (Thr) and SAA (methionine + cysteine) were the limiting AA of WBY protein and polypeptide. Furthermore, the antioxidant activities of WBY polypeptide that lower than 10 kDa against hydroxyl radical, DPPH radical, and ABTS radical were 95.10%, 98.37%, and 69.41%, respectively, which was significantly higher than that of WBY protein (25-50 kDa). Therefore, the protein and polypeptide extracted from WBY can be a source of high-quality AA applying in food and feed industry. Due to small molecular weight, abundant AA, and great antioxidant activity, WBY polypeptide can be promisingly used as functional additives in the pharmaceutical and healthcare industry.

Physicochemical and Functional Properties of 2S, 7S, and 11S Enriched Hemp Seed Protein Fractions.

The hemp seed contains protein fractions that could serve as useful ingredients for food product development. However, utilization of hemp seed protein fractions in the food industry can only be successful if there is sufficient information on their levels and functional properties. Therefore, this work provides a comparative evaluation of the structural and functional properties of hemp seed protein isolate (HPI) and fractions that contain 2S, 7S, or 11S proteins. HPI and protein fractions were isolated at pH values of least solubility. Results showed that the dominant protein was 11S, with a yield of 72.70 ± 2.30%, while 7S and 2S had values of 1.29 ± 0.11% and 3.92 ± 0.15%, respectively. The 2S contained significantly (p < 0.05) higher contents of sulfhydryl groups at 3.69 µmol/g when compared to 7S (1.51 µmol/g), 11S (1.55 µmol/g), and HPI (1.97 µmol/g). The in vitro protein digestibility of the 2S (72.54 ± 0.52%) was significantly (p < 0.05) lower than those of the other isolated proteins. The intrinsic fluorescence showed that the 11S had a more rigid structure at pH 3.0, which was lost at higher pH values. We conclude that the 2S fraction has superior solubility, foaming capacity, and emulsifying activity when compared to the 7S, 11S, and HPI.

IMPACT OF NUTRITIONAL CORRECTION OF PROTEIN METABOLISM DISORDERS ON THE CLINICAL COURSE OF PULMONARY TUBERCULOSIS.

OBJECTIVE: The aim: To study the impact of nutritional correction of protein metabolism disorders on the clinical course of pulmonary tuberculosis. PATIENTS AND METHODS: Materials and methods: The study involved 67 patients with pulmonary tuberculosis, which were divided into two groups: group I - 35 patients who underwent nutritional correction of protein metabolism disorders against the background of antimycobacterial therapy (AMBT) and group II - 32 patients who received standard AMBT. An assessment of clinical indicators and the condition of protein metabolism (PM) was conducted by determining the concentration of individual non-essential, essential amino acids and their total amount. RESULTS: Results: The proposed correction scheme includes food products containing essential nutrients and biologically active compounds that have a positive impact on the corresponding links of pathogenesis and can be used throughout all phases of treatment. Its application had a positive impact on the indicators of PM (significant (p<0.05) increase in total amount of essential amino acids (TAEAA), total amount of non-essential amino acids (TANEAA) and total amount of amino acids (TAAA) in blood serum and the concentration of individual essential and non-essential amino acids (significantly reached the level of indicators in healthy individuals) and clinical course of tuberculosis (intoxication syndrome disappeared earlier by 10.8 ± 0.97 days, and respiratory one by 8.95 ± 1.68 days), there was an increase in the frequency of healing of decay cavities at the time of completion of treatment by 34.0% and a significant (p<0.05) reduction in the average duration of treatment by 21.1±2.91 days. CONCLUSION: Conclusions: The application of nutritional correction of protein metabolism in the complex treatment of patients with pulmonary tuberculosis made it possible to obtain a pronounced positive impact on the clinical course of the disease and the condition of protein metabolism, which contributed to an increase in the effectiveness of treatment and rehabilitation.

[Amaranth grain proteins: prospects for use in specialized food products].

Amaranth is a widespread genus of predominantly annual herbaceous plants belonging to the Amaranthaceae family, which is one of the most widely used pseudocereals along with quinoa and buckwheat in nutrition. The aim of the research was to review and analyze the results of the studies on the characteristics of amaranth grain proteins, the effect of various food processing methods on their quality, and the prospects for using amaranth protein hydrolysates in therapeutic nutrition. Material and methods. For the main search for the literature, the PubMed bibliographic database was used, which covers about 75% of the world's medical publications. In addition, Scopus and Web of Science databases and non-commercial search engine Google Scholar were used. The depth of the search was 15 years. Results. The paper presents a brief review of modern approaches for obtaining amaranth protein isolates and concentrates, including the use of a complex of physicochemical methods: grinding, sifting, extraction at high pH values, defatting, ultrafiltration, centrifugation, isoelectric precipitation, and drying of the protein product. A comparative characteristic of amino acid content of protein fractions of pseudocereals is presented. Basically, leucine, isoleucine, and valine are limiting amino acids for the grain protein of various varieties of amaranth. When substantiating and developing modern effective food technologies for processing amaranth grain, the studies dedicated to the evaluation of their impact on the biological value of amaranth protein deserve special attention. Methods of grain fermentation, sprouting, steaming, malting, boiling can be used to increase the bioavailability and digestibility of its ingredients. The results of in vitro and in vivo studies indicate the presence of hypotensive, hypolipidemic and antioxidant activity of the amaranth protein and its hydrolysates what determines the prospects for their use as part of foods for special dietary uses and therapeutic nutrition. An analysis of the scientific publications presented in the review indicates an increase in demand for high-quality gluten-free products and an increase in the range of mass-consumption foods, such as bakery, pasta, flour confectionery, with pseudo-cereals in their composition, including amaranth. Conclusion. The high biological value and technological properties of amaranth protein concentrates/isolates determine the prospects for their use to create a wide range of specialized foods for various purposes.

Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features.

BACKGROUND: Antimicrobial peptides (AMPs) are oligopeptides that act as crucial components of innate immunity, naturally occur in all multicellular organisms, and are involved in the first line of defense function. Recent studies showed that AMPs perpetuate great potential that is not limited to antimicrobial activity. They are also crucial regulators of host immune responses that can modulate a wide range of activities, such as immune regulation, wound healing, and apoptosis. However, a microorganism's ability to adapt and to resist existing antibiotics triggered the scientific community to develop alternatives to conventional antibiotics. Therefore, to address this issue, we proposed Co-AMPpred, an in silico-aided AMP prediction method based on compositional features of amino acid residues to classify AMPs and non-AMPs. RESULTS: In our study, we developed a prediction method that incorporates composition-based sequence and physicochemical features into various machine-learning algorithms. Then, the boruta feature-selection algorithm was used to identify discriminative biological features. Furthermore, we only used discriminative biological features to develop our model. Additionally, we performed a stratified tenfold cross-validation technique to validate the predictive performance of our AMP prediction model and evaluated on the independent holdout test dataset. A benchmark dataset was collected from previous studies to evaluate the predictive performance of our model. CONCLUSIONS: Experimental results show that combining composition-based and physicochemical features outperformed existing methods on both the benchmark training dataset and a reduced training dataset. Finally, our proposed method achieved 80.8% accuracies and 0.871 area under the receiver operating characteristic curve by evaluating on independent test set. Our code and datasets are available at https://github.com/onkarS23/CoAMPpred .

Physiological Limitations of Protein Foods Ounce Equivalents and the Underappreciated Role of Essential Amino Acid Density in Healthy Dietary Patterns.

Protein quality is an important component of protein intake to support growth, development, and maintenance of essential body tissues and functions. Therefore, protein quality should be emphasized as a key characteristic during protein food selection within the larger context of healthy dietary patterns, especially when considering the wide variance of protein quality across animal- and plant-based foods. However, the USDA Dietary Guidelines for Americans (DGA) do not address specific protein quality recommendations within their protein foods ounce equivalents guidance or as a component of Healthy U.S. Style, Healthy Vegetarian, and Healthy Mediterranean Style dietary patterns. In addition, the protein foods ounce equivalents within the DGA are not established on any obvious metabolic equivalency characteristic [i.e., energy, protein, or essential amino acid (EAA) content], which creates misleading messaging of equivalent functional and metabolic benefit across protein foods. EAA content is a key characteristic of protein quality and can be a practical focal point for protein intake recommendations and achieving healthy dietary patterns. This review discusses the importance of protein quality, the state of messaging within DGA recommendations, and proposes EAA density (i.e., EAA content relative to total energy) as one practical approach to improve current dietary recommendations. Two recent publications that evaluated the DGA protein foods ounce equivalents based on metabolic effect and their application within DGA recommended dietary patterns are discussed.

Protein and amino acid digestibility of 15N Spirulina in rats.

PURPOSE: Spirulina is often used as dietary supplement for its protein content and quality. However, in vivo data on protein digestibility are lacking. This study aims to determine nitrogen and amino acid digestibility in rats. A secondary objective was to test the effect of sonication prior to ingestion to break cell walls. METHODS: Wistar rats were fed a single test meal containing 15N Spirulina that was either sonicated (n = 11) or not (control, n = 13). Rats were euthanized 6 h after the meal ingestion. Spirulina nitrogen digestibility was measured by assessment of 15N recovery in digestive contents. Amino acid digestibility was measured by quantification of the caecal amino acid content and their 15N enrichment. RESULTS: Real fecal nitrogen digestibility was 86.0 ± 0.7%, without any differences between groups. Mean 15N amino acid caecal digestibility was 82.8 ± 1.3%, and values ranged between 77.9 ± 1.9% for serine and 89.4 ± 1.0% for methionine. No effect of sonication was observed. The most limiting AA was histidine, with a chemical score of 0.98 and a PD-CAAS of 0.84. Lysine was also limiting in a lesser extent. CONCLUSION: The nitrogen and amino acid digestibility of Spirulina is relatively low, and showed no effect of prior sonication. Its amino acid composition is relatively well balanced but not enough to compensate for the poor digestibility.

Codon selection reduces GC content bias in nucleic acids encoding for intrinsically disordered proteins.

Protein-coding nucleic acids exhibit composition and codon biases between sequences coding for intrinsically disordered regions (IDRs) and those coding for structured regions. IDRs are regions of proteins that are folding self-insufficient and which function without the prerequisite of folded structure. Several authors have investigated composition bias or codon selection in regions encoding for IDRs, primarily in Eukaryota, and concluded that elevated GC content is the result of the biased amino acid composition of IDRs. We substantively extend previous work by examining GC content in regions encoding IDRs, from 44 species in Eukaryota, Archaea, and Bacteria, spanning a wide range of GC content. We confirm that regions coding for IDRs show a significantly elevated GC content, even across all domains of life. Although this is largely attributable to the amino acid composition bias of IDRs, we show that this bias is independent of the overall GC content and, most importantly, we are the first to observe that GC content bias in IDRs is significantly different than expected from IDR amino acid composition alone. We empirically find compensatory codon selection that reduces the observed GC content bias in IDRs. This selection is dependent on the overall GC content of the organism. The codon selection bias manifests as use of infrequent, AT-rich codons in encoding IDRs. Further, we find these relationships to be independent of the intrinsic disorder prediction method used, and independent of estimated translation efficiency. These observations are consistent with the previous work, and we speculate on whether the observed biases are causal or symptomatic of other driving forces.

An In-Silico Comparative Study of Lipases from the Antarctic Psychrophilic Ciliate Euplotes focardii and the Mesophilic Congeneric Species Euplotes crassus: Insight into Molecular Cold-Adaptation.

Cold-adapted enzymes produced by psychrophilic organisms have elevated catalytic activities at low temperatures compared to their mesophilic counterparts. This is largely due to amino acids changes in the protein sequence that often confer increased molecular flexibility in the cold. Comparison of structural changes between psychrophilic and mesophilic enzymes often reveal molecular cold adaptation. In the present study, we performed an in-silico comparative analysis of 104 hydrolytic enzymes belonging to the family of lipases from two evolutionary close marine ciliate species: The Antarctic psychrophilic Euplotes focardii and the mesophilic Euplotes crassus. By applying bioinformatics approaches, we compared amino acid composition and predicted secondary and tertiary structures of these lipases to extract relevant information relative to cold adaptation. Our results not only confirm the importance of several previous recognized amino acid substitutions for cold adaptation, as the preference for small amino acid, but also identify some new factors correlated with the secondary structure possibly responsible for enhanced enzyme activity at low temperatures. This study emphasizes the subtle sequence and structural modifications that may help to transform mesophilic into psychrophilic enzymes for industrial applications by protein engineering.