Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.

The extant complex proteins must have evolved from ancient short and simple ancestors. The double-ψ ß-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.

Qualitative Nitrogen Malnutrition Damages Gut and Alters Microbiome in Adult Mice. A Preliminary Histopathological Study.

Amino-acids (AAs) are the exclusive source of nitrogen for cells. AAs result from the breakdown of food proteins and are absorbed by mucosa of the small intestine that act as a barrier to harmful materials. The quality of food proteins may differ, since it reflects content in Essential-AAs (EAAs) and digestibility but, until now, attention was paid mainly to the interaction between indigested proteins as a whole and microbiota. The link between microbiome and quality of proteins has been poorly studied, although these metabolic interactions are becoming more significant in different illnesses. We studied the effects of a special diet containing unbalanced EAAs/Non-EAAs ratio, providing excess of Non-EAAs, on the histopathology of gut epithelium and on the microbiome in adult mice, as model of qualitative malnutrition. Excess in Non-EAAs have unfavorable quick effect on body weight, gut cells, and microbiome, promoting weakening of the intestinal barrier. Re-feeding these animals with standard diet partially reversed the body alterations. The results prove that an unbalanced EAAs/Non-EAAs ratio is primarily responsible for microbiome modifications, not vice-versa. Therefore, treating microbiota independently by treating co-existing qualitative malnutrition does not make sense. This study also provides a reproducible model of sarcopenia-wasting cachexia like the human protein malnutrition.

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes.

Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.

Assessing the role of amino acids in systemic inflammation and organ failure in patients with ACLF.

BACKGROUND & AIMS: Systemic inflammation and organ failure(s) are the hallmarks of acute-on-chronic liver failure (ACLF), yet their pathogenesis remains uncertain. Herein, we aimed to assess the role of amino acids in these processes in patients with ACLF. METHODS: The blood metabolomic database of the CANONIC study (comprising 137 metabolites, with 43% related to amino acids) - obtained in 181 patients with ACLF and 650 with acute decompensation without ACLF (AD) - was reanalyzed with a focus on amino acids, in particular 9 modules of co-regulated metabolites. We also compared blood metabolite levels between ACLF and AD. RESULTS: The main findings in ACLF were: i) Metabolite modules were increased in parallel with increased levels of markers of systemic inflammation and oxidative stress. ii) Seventy percent of proteinogenic amino acids were present and most were increased. iii) A metabolic network, comprising the amino acids aspartate, glutamate, the serine-glycine one-carbon metabolism (folate cycle), and methionine cycle, was activated, suggesting increased purine and pyrimidine nucleotide synthesis. iv) Cystathionine, L-cystine, glutamate and pyroglutamate, which are involved in the transsulfuration pathway (a methionine cycle branch) were increased, consistent with increased synthesis of the antioxidant glutathione. v) Intermediates of the catabolism of 5 out of the 6 ketogenic amino acids were increased. vi) The levels of spermidine (a polyamine inducer of autophagy with anti-inflammatory effects) were decreased. CONCLUSIONS: In ACLF, blood amino acids fueled protein and nucleotide synthesis required for the intense systemic inflammatory response. Ketogenic amino acids were extensively catabolized to produce energy substrates in peripheral organs, an effect that was insufficient because organs failed. Finally, the decrease in spermidine levels may cause a defect in autophagy contributing to the proinflammatory phenotype in ACLF. LAY SUMMARY: Systemic inflammation and organ failures are hallmarks of acute-on-chronic liver failure (ACLF). Herein, we aimed to characterize the role of amino acids in these processes. The blood metabolome of patients with acutely decompensated cirrhosis, and particularly those with ACLF, reveals evidence of intense skeletal muscle catabolism. Importantly, amino acids (along with glucose), are used for intense anabolic, energy-consuming metabolism in patients with ACLF, presumably to support de novo nucleotide and protein synthesis in the activated innate immune system.

Determination of amino acid profile for argininosuccinic aciduria disorder using High-Performance Liquid Chromatography with fluorescence detection.

Argininosuccinic aciduria is an autosomal, recessive amino acid disorder that is caused by a deficiency of the argininosuccinate lyase enzyme. Citrulline is the most significant marker to detect this disorder. We used the High-performance liquid chromatography with fluorescence detection with 450 nm emission and 330 nm excitation wavelengths, 15 mmol/L potassium dihydrogen phosphate and 5 mmol/L dipotassium hydrogen phosphate as Mobile Phase A, and 50 mL water, 250 mL acetonitrile, and 200 mL methanol as Mobile Phase B in gradient mode with flow rate of 1.2 mL/min. The citrulline concentration was 22 µmol/L in healthy infants and 220 µmol/L in infants suffering from the disorder.

A novel method for achieving an optimal classification of the proteinogenic amino acids.

The classification of proteinogenic amino acids is crucial for understanding their commonalities as well as their differences to provide a hint for why life settled on the usage of precisely those amino acids. It is also crucial for predicting electrostatic, hydrophobic, stacking and other interactions, for assessing conservation in multiple alignments and many other applications. While several methods have been proposed to find "the" optimal classification, they have several shortcomings, such as the lack of efficiency and interpretability or an unnecessarily high number of discriminating features. In this study, we propose a novel method involving a repeated binary separation via a minimum amount of five features (such as hydrophobicity or volume) expressed by numerical values for amino acid characteristics. The features are extracted from the AAindex database. By simple separation at the medians, we successfully derive the five properties volume, electron-ion-interaction potential, hydrophobicity, α-helix propensity, and π-helix propensity. We extend our analysis to separations other than by the median. We further score our combinations based on how natural the separations are.

Revealing Metabolic Perturbation Following Heavy Methamphetamine Abuse by Human Hair Metabolomics and Network Analysis.

Methamphetamine (MA) is a highly addictive central nervous system stimulant. Drug addiction is not a static condition but rather a chronically relapsing disorder. Hair is a valuable and stable specimen for chronic toxicological monitoring as it retains toxicants and metabolites. The primary focus of this study was to discover the metabolic effects encompassing diverse pathological symptoms of MA addiction. Therefore, metabolic alterations were investigated in human hair following heavy MA abuse using both targeted and untargeted mass spectrometry and through integrated network analysis. The statistical analyses (t-test, variable importance on projection score, and receiver-operator characteristic curve) demonstrated that 32 metabolites (in targeted metabolomics) as well as 417 and 224 ion features (in positive and negative ionization modes of untargeted metabolomics, respectively) were critically dysregulated. The network analysis showed that the biosynthesis or metabolism of lipids, such as glycosphingolipids, sphingolipids, glycerophospholipids, and ether lipids, as well as the metabolism of amino acids (glycine, serine and threonine; cysteine and methionine) is affected by heavy MA abuse. These findings reveal crucial metabolic effects caused by MA addiction, with emphasis on the value of human hair as a diagnostic specimen for determining drug addiction, and will aid in identifying robust diagnostic markers and therapeutic targets.

Prediction of High-Risk Types of Human Papillomaviruses Using Reduced Amino Acid Modes.

A human papillomavirus type plays an important role in the early diagnosis of cervical cancer. Most of the prediction methods use protein sequence and structure information, but the reduced amino acid modes have not been used until now. In this paper, we introduced the modes of reduced amino acids to predict high-risk HPV. We first reduced 20 amino acids into several nonoverlapping groups and calculated their structure and physicochemical modes for high-risk HPV prediction, which was tested and compared with the existing methods on 68 samples of known HPV types. The experiment result indicates that the proposed method achieved better performance with an accuracy of 96.49%, indicating that the reduced amino acid modes might be used to improve the prediction of high-risk HPV types.

A comprehensive metabolic profiling of the metabolically healthy obesity phenotype.

BACKGROUND: The ever-increasing prevalence of obesity constitutes a major health problem worldwide. A subgroup of obese individuals has been described as "metabolically healthy obese" (MHO). In contrast to metabolically unhealthy obese (MUO), the MHO phenotype has a favorable risk profile. Despite this, the MHO phenotype is still sub-optimally characterized with respect to a comprehensive risk assessment. Our aim was to increase the understanding of metabolic alterations associated with healthy and unhealthy obesity. METHODS: In this cross-sectional study, men and women (18-70 years) with obesity (body mass index (BMI) ≥ 30 kg/m2) or normal weight (NW) (BMI ≤ 25 kg/m2) were classified with MHO (n = 9), MUO (n = 10) or NW (n = 11) according to weight, lipid profile and glycemic regulation. We characterized individuals by comprehensive metabolic profiling using a commercial available high-throughput proton NMR metabolomics platform. Plasma fatty acid profile, including short chain fatty acids, was measured using gas chromatography. RESULTS: The concentrations of very low density lipoprotein (VLDL), intermediate density lipoprotein (IDL) and low density lipoprotein (LDL) subclasses were overall significantly higher, and high density lipoprotein (HDL) subclasses lower in MUO compared with MHO. VLDL and IDL subclasses were significantly lower and HDL subclasses were higher in NW compared with MHO. The concentration of isoleucine, leucine and valine was significantly higher in MUO compared with MHO, and the concentration phenylalanine was lower in NW subjects compared with MHO. The fatty acid profile in MHO was overall more favorable compared with MUO. CONCLUSIONS: Comprehensive metabolic profiling supports that MHO subjects have intermediate-stage cardiovascular disease risk marker profile compared with NW and MUO subjects. CLINICAL TRIAL REGISTRATION NUMBER: NCT01034436, Fatty acid quality and overweight (FO-study).

Distribution, Contents, and Types of Mycosporine-Like Amino Acids (MAAs) in Marine Macroalgae and a Database for MAAs Based on These Characteristics.

Mycosporine-like amino acids (MAAs), maximally absorbed in the wavelength region of 310-360 nm, are widely distributed in algae, phytoplankton and microorganisms, as a class of possible multi-functional compounds. In this work, based on the Web of Science, Springer, Google Scholar, and China national knowledge infrastructure (CNKI), we have summarized and analyzed the studies related to MAAs in marine macroalgae over the past 30 years (1990-2019), mainly focused on MAAs distribution, contents, and types. It was confirmed that 572 species marine macroalgae contained MAAs, namely in 45 species of Chlorophytes, 41 species of Phaeophytes, and 486 species of Rhodophytes, and they respectively belonged to 28 orders. On this basis, we established an open online database to quickly retrieve MAAs in 501 species of marine macroalgae. Furthermore, research concerning MAAs in marine macroalgae were analyzed using CiteSpace. It could easily be seen that the preparation and purification of MAAs in marine macroalgae have not been intensively studied during the past 10 years, and therefore it is necessary to strengthen the research in the preparation and purification of MAA purified standards from marine macroalgae in the future. We agreed that this process is not only interesting, but important due to the potential use of MAAs as food and cosmetics, as well as within the medicine industry.

A General Strategy for Engineering Noncanonical Amino Acid Dependent Bacterial Growth.

Synthetic auxotrophy in which bacterial viability depends on the presence of a synthetic amino acid provides a robust strategy for the containment of genetically modified organisms and the development of safe, live vaccines. However, a simple, general strategy to evolve essential proteins to be dependent on synthetic amino acids is lacking. Using a temperature-sensitive selection system, we evolved an Escherichia coli (E. coli) sliding clamp variant with an orthogonal protein-protein interface, which contains a Leu273 to p-benzoylphenyl alanine (pBzF) mutation. The E. coli strain with this variant DNA clamp has a very low escape frequency (<10-10), and its growth is strictly dependent on the presence of pBzF. This selection strategy can be generally applied to create ncAA dependence of other organisms with DNA clamp homologues.

Nonessential amino acid usage for protein replenishment in humans: a method of estimation.

BACKGROUND: Essential amino acids (EAAs) are key factors in determining dietary protein quality. Their RDAs have been estimated. However, although nonessential amino acids (NEAAs) are utilized for protein synthesis too, no estimates of their usage for body protein replenishment have been proposed so far. OBJECTIVE: The aim of this study was to provide minimum, approximate estimates of NEAA usage for body protein replenishment/conservation in humans. METHODS: A correlation between the pattern of both EAAs and NEAAs in body proteins, and their usage, was assumed. In order to reconstruct an "average" amino acid pattern/composition of total body proteins (as grams of amino acid per gram of protein), published data of relevant human organs/tissues (skeletal muscle, liver, kidney, gut, and collagen, making up ∼74% of total proteins) were retrieved. The (unknown) amino acid composition of residual proteins (∼26% of total proteins) was assumed to be the same as for the sum of the aforementioned organs excluding collagen. Using international EAA RDA values, an average ratio of EAA RDA to the calculated whole-body EAA composition was derived. This ratio was then used to back-calculate NEAA usage for protein replenishment. The data were calculated also using estimated organ/tissue amino acid turnover. RESULTS: The individual ratios of World Health Organization/Food and Agriculture Organization/United Nations University RDA to EAA content ranged between 1.35 (phenylalanine + tyrosine) and 3.68 (leucine), with a mean ± SD value of 2.72 ± 0.81. In a reference 70-kg subject, calculated NEAA usage for body protein replenishment ranged from 0.73 g/d for asparagine to 3.61 g/d for proline. Use of amino acid turnover data yielded similar results. Total NEAA usage for body protein replenishment was ∼19 g/d (45% of total NEAA intake), whereas ∼24 g/d was used for other routes. CONCLUSION: This method may provide indirect minimum estimates of the usage of NEAAs for body protein replacement in humans.

Plasma metabolomic profiling of amino acids and polar lipids in Iranian obese adults.

BACKGROUND: Obesity, widely recognized as a serious health concern, is characterized by profoundly altered metabolism. However, the intermediate metabolites involved in this change remain largely unknown. OBJECTIVE: We conducted targeted metabolomics profiling to identify moieties associated with adult obesity. METHODS: In this case-control study of Iranian adults, 200 obese patients were compared with 100 controls based on 104 metabolites profiled by a targeted metabolomic approach using liquid chromatography coupled to triple quadrupole mass spectrometry (LC-MS/MS). The analysis comprised acylcarnitines, diacyl-phosphatidylcholines (PCaa), acyl-alkyl-phosphatidylcholines (PCae), sphingomyelins (SM), lyso-phospholipids (LPC) and amino acids. We performed multivariable linear regression to identify metabolites associated with obesity, adjusting for age, sex, total energy intake, total physical activity, smoking, and alcohol consumption. The Bonferroni correction was used to adjust for multiple testing. RESULTS: A pattern of 19 metabolites was significantly associated with obesity. Branched chain amino acids, alanine, glutamic acid, proline, tyrosine LPCa C16:1, PCaa C32:1, PCaa C32:2 and PCaa C38:3 were positively, while serine, asparagine, LPCa C18:1, LPCa C18:2, LPCe C18:0, PCae C34:3, PCae C38:4 and PCae C40:6 were negatively associated with obesity (all p < 0.00048). CONCLUSIONS: A metabolomic profile containing 9 amino acids and 10 polar lipids may serve as a potential biomarker of adult obesity. Further studies are warranted to replicate these findings as well as investigate potential changes in this profile after weight reduction.

Detecting Amino Acid Coevolution with Bayesian Graphical Models.

The comparative study of homologous proteins can provide abundant information about the functional and structural constraints on protein evolution. For example, an amino acid substitution that is deleterious may become permissive in the presence of another substitution at a second site of the protein. A popular approach for detecting coevolving residues is by looking for correlated substitution events on branches of the molecular phylogeny relating the protein-coding sequences. Here we describe a machine learning method (Bayesian graphical models) implemented in the open-source phylogenetic software package HyPhy, http://hyphy.org , for extracting a network of coevolving residues from a sequence alignment.

Alterations in serum amino-acid profile in the progression of colorectal cancer: associations with systemic inflammation, tumour stage and patient survival.

BACKGROUND: Cancer cachexia is a complex wasting syndrome affecting patients with advanced cancer, with systemic inflammation as a key component in pathogenesis. Protein degradation and release of amino acids (AAs) in skeletal muscle are stimulated in cachexia. Here, we define factors contributing to serum AA levels in colorectal cancer (CRC). METHODS: Serum levels of nine AAs were characterised in 336 CRC patients and their relationships with 20 markers of systemic inflammatory reaction, clinicopathological features of cancers and patient survival were analysed. RESULTS: Low serum glutamine and histidine levels and high phenylalanine levels associated with indicators of systemic inflammation, including high modified Glasgow Prognostic Score, high blood neutrophil/lymphocyte ratio and high serum levels of CRP, IL-6 and IL-8. Low levels of serum glutamine, histidine, alanine and high glycine levels also associated with advanced cancer stage and with poor cancer-specific survival in univariate analysis. CONCLUSIONS: In CRC, serum AA levels are associated with systemic inflammation and disease stage. These findings may reflect muscle catabolism induced by systemic inflammation in CRC.

Amino Acid Transport Across the Mammalian Intestine.

The small intestine mediates the absorption of amino acids after ingestion of protein and sustains the supply of amino acids to all tissues. The small intestine is an important contributor to plasma amino acid homeostasis, while amino acid transport in the large intestine is more relevant for bacterial metabolites and fluid secretion. A number of rare inherited disorders have contributed to the identification of amino acid transporters in epithelial cells of the small intestine, in particular cystinuria, lysinuric protein intolerance, Hartnup disorder, iminoglycinuria, and dicarboxylic aminoaciduria. These are most readily detected by analysis of urine amino acids, but typically also affect intestinal transport. The genes underlying these disorders have all been identified. The remaining transporters were identified through molecular cloning techniques to the extent that a comprehensive portrait of functional cooperation among transporters of intestinal epithelial cells is now available for both the basolateral and apical membranes. Mouse models of most intestinal transporters illustrate their contribution to amino acid homeostasis and systemic physiology. Intestinal amino acid transport activities can vary between species, but these can now be explained as differences of amino acid transporter distribution along the intestine. © 2019 American Physiological Society. Compr Physiol 9:343-373, 2019.

1H NMR Metabolomics Identifies Underlying Inflammatory Pathology in Osteoarthritis and Rheumatoid Arthritis Synovial Joints.

Despite osteoarthritis (OA) and rheumatoid arthritis (RA) being typically age-related, their underlying etiologies are markedly different. We used 1H nuclear magnetic resonance (NMR) spectroscopy to identify differences in metabolite profiles in low volumes of OA and RA synovial fluid (SF). SF was aspirated from knee joints of 10 OA and 14 RA patients. 100 µL SF was analyzed using a 700 MHz Avance IIIHD Bruker NMR spectrometer with a TCI cryoprobe. Spectra were analyzed by Chenomx, Bruker TopSpin and AMIX software. Statistical analysis was undertaken using Metaboanalyst. 50 metabolites were annotated, including amino acids, saccharides, nucleotides and soluble lipids. Discriminant analysis identified group separation between OA and RA cohorts, with 32 metabolites significantly different between OA and RA SF (false discovery rate (FDR) < 0.05). Metabolites of glycolysis and the tricarboxylic acid cycle were lower in RA compared to OA; these results concur with higher levels of inflammation, synovial proliferation and hypoxia found in RA compared to OA. Elevated taurine in OA may indicate increased subchondral bone sclerosis. We demonstrate that quantifiable differences in metabolite abundance can be measured in low volumes of SF by 1H NMR spectroscopy, which may be clinically useful to aid diagnosis and improve understanding of disease pathogenesis.

Predicting structural classes of proteins by incorporating their global and local physicochemical and conformational properties into general Chou's PseAAC.

In this study, I introduce novel global and local 0D-protein descriptors based on a statistical quantity named Total Sum of Squares (TSS). This quantity represents the sum of the squares differences of amino acid properties from the arithmetic mean property. As an extension, the amino acid-types and amino acid-groups formalisms are used for describing zones of interest in proteins. To assess the effectiveness of the proposed descriptors, a Nearest Neighbor model for predicting the major four protein structural classes was built. This model has a success rate of 98.53% on the jackknife cross-validation test; this performance being superior to other reported methods despite the simplicity of the predictor. Additionally, this predictor has an average success rate of 98.35% in different cross-validation tests performed. A value of 0.98 for the Kappa statistic clearly discriminates this model from a random predictor. The results obtained by the Nearest Neighbor model demonstrated the ability of the proposed descriptors not only to reflect relevant biochemical information related to the structural classes of proteins but also to allow appropriate interpretability. It can thus be expected that the current method may play a supplementary role to other existing approaches for protein structural class prediction and other protein attributes.

Flavor Compounds in Pixian Broad-Bean Paste: Non-Volatile Organic Acids and Amino Acids.

Non-volatile organic acids and amino acids are important flavor compounds in Pixian broad-bean paste, which is a traditional Chinese seasoning product. In this study, non-volatile organic acids, formed in the broad-bean paste due to the metabolism of large molecular compounds, are qualitatively and quantitatively determined by high-performance liquid chromatography (HPLC). Amino acids, mainly produced by hydrolysis of soybean proteins, were determined by the amino acid automatic analyzer. Results indicated that seven common organic acids and eighteen common amino acids were found in six Pixian broad-bean paste samples. The content of citric acid was found to be the highest in each sample, between 4.1 mg/g to 6.3 mg/g, and malic acid were between 2.1 mg/g to 3.6 mg/g ranked as the second. Moreover, fumaric acid was first detected in fermented bean pastes albeit with a low content. For amino acids, savory with lower sour taste including glutamine (Gln), glutamic acid (Glu), aspartic acid (Asp) and asparagines (Asn) were the most abundant, noted to be 6.5 mg/g, 4.0 mg/g, 6.4 mg/g, 4.9 mg/g, 6.2 mg/g and 10.2 mg/g, and bitter taste amino acids followed. More importantly, as important flavor materials in Pixian broad-bean paste, these two groups of substances are expected to be used to evaluate and represent the flavor quality of Pixian broad-bean paste. Moreover, the results revealed that citric acid, glutamic acid, methionine and proline were the most important flavor compounds. These findings are agreat contribution for evaluating the quality and further assessment of Pixian broad-bean paste.

Where Informatics Lags Chemistry Leads.

The fact that amino acid sequences dictate the tertiary structures of proteins has been known for more than five decades. While the molecular pathways to tertiary structure are still being worked out, with the axiom that similar sequences adopt similar structures, computational methods are being developed continually in parallel, utilizing the Protein Data Bank structural repository and homologue detection strategies to predict structures of sequences of interest. The success of this approach is limited by the ability to unravel the hidden similarities among amino acid sequences. We consider here the 20 amino acids as a complete set of chemical templates in the physicochemical space of proteins and propose a new structural and chemical classification of amino acids. An integration of this perspective into the conventional evolutionary methods of similarity detection leads to an unprecedented increase in the accuracy in homologue detection, resulting in improved protein structure prediction. The performance is validated on a large data set of 11716 unique proteins, and the results are benchmarked against conventional methods. The availability of good quality protein structures helps in structure-based drug design endeavors and in establishing protein structure-function correlations.