Plant amino acid analogues as antimicrobial agents

Early Changes in Plasma Amino Acid Concentrations during Aggressive Nutritional Therapy in Extremely Low Birth Weight Infants

Phase shifts of the circadian rhythm of K(+) uptake by Lemna gibba G3, caused by pulse administration of various amino acids analogs, were examined and compared. The various phase shifts were not due to any disturbance in the biosynthesis of amino acids, since the effective time of day and direction of the phase shift caused by analogs were not correlated with the standard amino acid which was modified. Effective analogs could be classified into three groups. The first group was effective during the middle subjective day and caused both advances and delays in phase. The second group was effective early in the subjective night, causing large delays and small phase advance. Analogs in the third group shifted the phase as did cycloheximide and were effective at the subjective dawn. Since the analogs of the third group were known to inhibit protein synthesis, it is likely that they shift the phase by lowering the level of some protein(s) important for the clock. By contrast, since the analogs in groups 1 and 2 are known to generate abnormal proteins, the different phase-shifting patterns caused by analogs in groups 1 and 2 suggest that at least two other proteins are important for the circadian timing loop. The amino acid analogs shift the phase as a result of their incorporation into these proteins instead of the standard amino acid. This probably alters the structure and/or activities of these proteins.

Additivity of apparent and standardized ileal amino acid digestibility of corn and soybean meal in broiler diets.

To fulfil their function, nuclear pore complexes (NPCs) must discriminate between inert proteins and nuclear transport receptors (NTRs), admitting only the latter. This specific permeation is thought to depend on interactions between hydrophobic patches on NTRs and phenylalanine-glycine (FG) or related repeats that line the NPC. Here, we tested this premise directly by conjugating different hydrophobic amino-acid analogues to the surface of an inert protein and examining its ability to cross NPCs unassisted by NTRs. Conjugation of as few as four hydrophobic moieties was sufficient to enable passage of the protein through NPCs. Transport of the modified protein proceeded with rates comparable to those measured for the innate protein when bound to an NTR and was relatively insensitive both to the nature and density of the amino acids used to confer hydrophobicity. The latter observation suggests a non-specific, small, and plant interaction network between cargo and FG repeats.

The tip and hidden part of the iceberg: Proteinogenic and non-proteinogenic aliphatic amino acids

The peroxiredoxin‐1 (PRX1) of redox peroxidase reduces reactive oxygen and nitrogen species levels in human cells and can be regulated by its interacting partner sulfiredoxin‐1 (SRX1). A 9‐mer core peptide segment (termed CTTc) located in the C‐terminal tail of PRX1 was found previously to mediate the PRX1–SRX1 interaction, and proteinogenic amino acids were also examined for each residue of the CTTc peptide. However, only proteinogenic amino acids can guarantee sufficient exploitation of the structural diversity space of CTTc‐derived peptidic inhibitors targeting SRX1. In this study, the structural diversity space was further expanded by introducing 34 nonproteinogenic amino acids plus 20 proteinogenic amino acids as the building blocks of nonapeptides, and a systematic single‐position binding energy change (SSRBEC) profile of the nonapeptide against SRX1 was created computationally by performing machine learning scoring, molecular dynamics simulation, and binding energetics analysis. A reduced combinatorial peptide library consisting of over 500,000 nonproteinogenic amino acid‐containing nonapeptide candidates was designed using a rational computational peptidology strategy based on the SSRBEC profile, from which a variety of top‐scored hits were identified and their affinities to SRX1 were measured at the molecular level to substantiate the computational findings. Three nonproteinogenic amino acid‐containing peptides, CTTc[ut8], CTTc[ut3], and CTTc[ut6] possessed high potency, and their affinities were improved considerably relative to the native CTTc peptide. Structural analysis revealed that the SRX1‐binding peptide sequences can be divided into three sections, that is, amino‐terminal section N, middle section M, and carboxy‐terminal section C, in which section N and, secondarily, section C are primarily responsible for the peptide binding affinity and specificity to SRX1, while section M is exposed to solvent and does not directly interact with SRX1.

Domestic cats and dogs are carnivores that have evolved differentially in the nutrition and metabolism of amino acids. This article highlights both proteinogenic and nonproteinogenic amino acids. Dogs inadequately synthesize citrulline (the precursor of arginine) from glutamine, glutamate, and proline in the small intestine. Although most breeds of dogs have potential for adequately converting cysteine into taurine in the liver, a small proportion (1.3%–2.5%) of the Newfoundland dogs fed commercially available balanced diets exhibit a deficiency of taurine possibly due to gene mutations. Certain breeds of dogs (e.g., golden retrievers) are more prone to taurine deficiency possibly due to lower hepatic activities of cysteine dioxygenase and cysteine sulfinate decarboxylase. De novo synthesis of arginine and taurine is very limited in cats. Thus, concentrations of both taurine and arginine in feline milk are the greatest among domestic mammals. Compared with dogs, cats have greater endogenous nitrogen losses and higher dietary requirements for many amino acids (e.g., arginine, taurine, cysteine, and tyrosine), and are less sensitive to amino acid imbalances and antagonisms. Throughout adulthood, cats and dogs may lose 34% and 21% of their lean body mass, respectively. Adequate intakes of high-quality protein (i.e., 32% and 40% animal protein in diets of aging dogs and cats, respectively; dry matter basis) are recommended to alleviate aging-associated reductions in the mass and function of skeletal muscles and bones. Pet-food grade animal-sourced foodstuffs are excellent sources of both proteinogenic amino acids and taurine for cats and dogs, and can help to optimize their growth, development, and health.

Legumes, a dietary staple for centuries, have seen an influx of conventional and unconventional varieties to cater to human care conscious consumers. These legumes often undergo pretreatments like baking, soaking, or boiling to mitigate the presence of non-proteinogenic amino acids (NPAAs) and reduce associated health risks. The recent tara flour health scare, linked to the NPAA baikiain, emphasizes the need for robust analytical methods to ensure the safety and quality of both traditional and novel plant-based protein alternatives. While traditional techniques provide insights into protein and non-proteinogenic amino acid profiles, modern liquid chromatography-mass spectrometry (LC-MS) offers superior sensitivity and specificity for NPAA detection. This study employed an LC-QToF method with MS/MS analysis to comprehensively map the distribution of free NPAAs and proteinogenic amino acids (PAAs) in various legume samples. A total of 47 NPAAs and 20 PAAs were identified across the legume samples, with at least 7–14 NPAAs detected in each sample. Sulfur-containing NPAAs, such as S-methyl-L-cysteine, γ-glutamyl-S-methyl cysteine, and S-methyl homoglutathione, were predominantly found in Phaseolus and Vigna species. Cysteine and methionine were the sulfur-containing PAAs identified. Gel electrophoresis and soluble protein quantification were also conducted to understand legume protein composition holistically. This orthogonal approach provides a valuable tool for ensuring the overall quality of plant-based proteins and may aid in investigating food poisoning or outbreaks related to such products.

Natural amino acids as potential chelators for soil remediation

Four new complementation groups of mutations which confer resistance to several amino acid analogs in Saccharomyces cerevisiae are described. These mutants were isolated on medium containing urea as the nitrogen source, in contrast to previous studies that had used medium containing proline. All four resistance to amino acid analog (raa) complementation groups appear to confer resistance by reducing amino acid analog and amino acid uptake. In some genetic backgrounds, raa leu2 and raa thr4 double mutants are inviable, even on rich medium. The raa4 mutation may affect multiple amino acid transport systems, since raa4 mutants are unable to use proline as a nitrogen source. raa4 is, however, unlinked to a previously described amino acid analog resistance and proline uptake mutant, aap1, or to the general amino acid permease mutant gap1. Both raa4 and gap1 prevent uptake of [3H]leucine in liquid cultures. The raa1, raa2, and raa3 mutants affect only a subset of the amino acid analogs and amino acids affected by raa4. The phenotypes of raa1, -2, and -3 mutants are readily observed on agar plates but are not seen in uptake and incorporation of amino acids measured in liquid media.

Four new complementation groups of mutations which confer resistance to several amino acid analogs in Saccharomyces cerevisiae are described. These mutants were isolated on medium containing urea as the nitrogen source, in contrast to previous studies that had used medium containing proline. All four resistance to amino acid analog (raa) complementation groups appear to confer resistance by reducing amino acid analog and amino acid uptake. In some genetic backgrounds, raa leu2 and raa thr4 double mutants are inviable, even on rich medium. The raa4 mutation may affect multiple amino acid transport systems, since raa4 mutants are unable to use proline as a nitrogen source. raa4 is, however, unlinked to a previously described amino acid analog resistance and proline uptake mutant, aap1, or to the general amino acid permease mutant gap1. Both raa4 and gap1 prevent uptake of [3H]leucine in liquid cultures. The raa1, raa2, and raa3 mutants affect only a subset of the amino acid analogs and amino acids affected by raa4. The phenotypes of raa1, -2, and -3 mutants are readily observed on agar plates but are not seen in uptake and incorporation of amino acids measured in liquid media.

Amino acids (AAs) are important biomolecules responsible for plethora of functions in both prokaryotic and eukaryotic systems. There are 22 naturally occurring amino acids, among which 20 common amino acids appear in the genetic code and known as proteinogenic amino acids, which are the building blocks of proteins. Proteinogenic amino acids exist in two isomeric forms (except glycine) and the biological activity is often attributed to a specific stereoisomer. Most of the amino acids found in protein is predominantly L-AAs. A few D-amino acids can be found in bacterial cell wall, some marine invertebrates and higher organisms including frog, snail, spider, rat, chicken and human. Besides their role in protein synthesis, different proteinogenic amino acid stereoisomers have found to perform important biological roles either by functioning as precursors of a myriad of other bioactive molecules or by indicating several biological phenomena i.e. acting as markers for different physiological conditions. Given the biological importance of L- and D-amino acids (AAs), improved analytical methods for their resolution and accurate quantification remain of keen interest. Chiral analysis of amino acids in complex biological matrices poses numerous analytical challenges that are exacerbated by broad differences in polarity and ionization efficiencies of the proteinogenic amino acid stereoisomers. To date, various analytical methods are reported for chiral amino acid analysis including chromatographic, spectrometric, enzymatic, fluidic, electrophoretic and microbiological techniques. Advances in stationary phase, derivatization chemistry and instrumentation contributed to achieving baseline separation and accurate detection of trace levels of proteinogenic amino acids stereoisomers in different matrices. However, liquid and gas chromatography coupled to mass spectrometry based analytical methods remain the most popular platform in chiral amino acid analysis in terms of feasibility and performance. This review discusses different physicochemical and biological features and functions of proteinogenic amino acid stereoisomers and lists a variety of established chromatography and mass spectrometry based analytical methods for their analysis reported to date.

The growing interest in proteins, both in fundamental research and in drug discovery, has fuelled demand for efficient synthetic methods to access these biomolecules. Although solid-phase synthesis serves as the workhorse for accessing peptides up to 50 amino acids in length, ligation technologies have underpinned protein synthesis. Native chemical ligation (NCL) represents the most widely used method and relies on the reaction of a peptide bearing an N-terminal cysteine residue with a peptide thioester. While the seminal methodology was limited to reaction at N-terminal cysteine residues, the NCL concept has recently been extended with a view to improving reaction efficiency and scope. Specifically, the discovery that cysteine residues can be desulfurized to alanine has led to the development of a range of thiol-derived variants of the proteinogenic amino acids that can be employed in protein synthesis under a ligation–desulfurization manifold. Furthermore, a number of important technologies have been developed to access larger targets via multi-fragment assembly, including methods for latent thioester activation and orthogonal protecting group strategies. Very recently, the amino acid selenocysteine, together with selenylated proteinogenic amino acid variants, has been shown to facilitate rapid ligation with peptide selenoesters. The large rate accelerations of these ligations have enabled access to proteins on unprecedented timescales, while chemoselective deselenization chemistry renders hitherto unobtainable targets accessible. This Review highlights innovative developments that have greatly expanded the NCL concept, allowing it to serve as a rapid and efficient means of conquering more challenging synthetic protein targets in the near future. Native chemical ligation (NCL) has revolutionized the field of chemical protein synthesis. This Review discusses milestones such as desulfurization, the development of thiol and selenol analogues of proteinogenic amino acids and novel acyl donors for multi-component iterative ligations. These have greatly expanded the NCL concept and enabled the synthesis of hitherto inaccessible protein targets.

Here we describe the application of photochemical decarboxylative arylation as a late-stage functionalization reaction for peptides. The reaction uses redox-active esters of aspartic acid and glutamic acid on the solid phase to provide analogues of aromatic amino acids. By using aryl bromides as arylation reagents, a wide variety of amino acids can be accessed without having to synthesize them individually in solution. The reaction is compatible with proteinogenic amino acids and was used to perform a structure-activity relationship study of a PRMT5 binding peptide.

Herpesviral capsids are assembled in the host cell nucleus and are subsequently translocated to the cytoplasm. During this process it has been demonstrated that the human cytomegalovirus proteins pUL50 and pUL53 interact and form, together with other viral and cellular proteins, the nuclear egress complex at the nuclear envelope. In this study we provide evidence that specific residues of a conserved N-terminal region of pUL50 determine its intranuclear interaction with pUL53. In silico evaluation and biophysical analyses suggested that the conserved region forms a regular secondary structure adopting a globular fold. Importantly, site-directed replacement of individual amino acids by alanine indicated a strong functional influence of specific residues inside this globular domain. In particular, mutation of the widely conserved residues Glu-56 or Tyr-57 led to a loss of interaction with pUL53. Consistent with the loss of binding properties, mutants E56A and Y57A showed a defective function in the recruitment of pUL53 to the nuclear envelope in expression plasmid-transfected and human cytomegalovirus-infected cells. In addition, in silico analysis suggested that residues 3-20 form an amphipathic α-helix that appears to be conserved among Herpesviridae. Point mutants revealed a structural role of this N-terminal α-helix for pUL50 stability rather than a direct role in the binding of pUL53. In contrast, the central part of the globular domain including Glu-56 and Tyr-57 is directly responsible for the functional interaction with pUL53 and thus determines formation of the basic nuclear egress complex.