Exome-matched protein as the ideal dietary amino acid pattern: A narrative review.

Prebiotic cationic amino acids support formation of an ancient protein fold

Application of Analytical Techniques to Chiral Amino Acid Profiling in Clinical Samples: Bridging Chemistry and Disease Research.

Amino acids are the basic building blocks of proteins that are required to control various vital biological processes, including immune response, hormone regulation, metabolic control, and gene expression. Although L-amino acids are the primary components of protein synthesis, their mirror-image counterparts, D-amino acids, exhibit distinct pharmacological and biological characteristics. As a result, reliable identification and measurement of these enantiomers have become critical criteria in biology, chemistry, and medicine. Because changes in D-amino acid levels are closely related to the onset and progression of a variety of human disorders, the therapeutic utility of these amino acids as diagnostic biomarkers is gaining traction. This article investigates the vital role of chiral amino acids in clinical disorders, with a particular emphasis on their implications for neurological conditions. It also evaluates the several techniques and analytical systems used to identify enantiomeric amino acids in complex biological matrices, focusing on current technological breakthroughs that have increased the sensitivity and precision of these evaluations.

A Comprehensive Experimental and Theoretical Spectroscopic Study of Proteinogenic Amino Acids

Amino acids are essential building blocks of life, yet our understanding of their chemistry and electronic structure in the solid state remains limited. This is particularly important because amino acids in the solid state are relevant to biological and pharmaceutical processes. X-ray photoelectron spectroscopy provides a powerful experimental probe of chemical states and occupied electronic structure; however, most spectroscopy studies of amino acids focus on gas-phase species or surface adsorbates, while crystalline amino acids remain underexplored, largely because of experimental challenges associated with radiation damage. Additionally, the spectra are often complex and difficult to interpret, motivating a combined experimental-theoretical approach. This study combines X-ray photoelectron spectroscopy and density functional theory calculations to systematically investigate the core, semi-core, and valence states of 20 proteinogenic amino acids as well as selenomethionine which can be incorporated during protein synthesis and deliver the essential nutrient, Se, required by humans. Calculated relative core binding energies show excellent agreement with experiment and enable reliable assignments. Projections of the density of states provide insight into the influence of local coordination and extended crystal structure, yielding a systematic understanding of the electronic structure and bonding in solid-state AAs. The insights gained from this study enhance the understanding of crystalline amino acids and validate the robustness of an integrated experiment--theory framework.

Ideal Amino Acid Profiles in Diets for Broiler Chickens Remain Elusive Targets

Amino acids are the ‘building blocks’ of protein, including both feathers and whole-body protein, and serve numerous functional roles, including energy provision. Amino acid requirements for broiler chickens are expressed as ideal amino acid ratios relative to digestible lysine. However, ideal amino acid profiles in diets for broiler chickens are likely to remain elusive targets. This review considers the factors contributing to this situation. Just one complicating factor is that amino acids may be deposited as protein in either feathers or whole-body protein. However, in the partitioning of amino acids, it appears that preference may be given to feathering, which requires clarification. A second complicating factor is the transition of amino acids across enterocytes of the small intestinal gut mucosa, and small intestinal uptake of amino acids may be rate-limiting for growth performance. Protein-bound amino acids may be absorbed as oligopeptides or monomeric amino acids, and non-bound amino acids do not require digestion prior to their intestinal uptake. The transition of amino acids across the gut mucosa is involved because amino acids may be diverted into anabolic and/or catabolic pathways and are thereby denied entry to the portal circulation. The metabolic fate of amino acids in the gut mucosa may be subject to manipulation by nutritional strategies, but our comprehension of the relevant metabolism within avian enterocytes is inadequate. The post-enteral availability of twenty proteinogenic amino acids is complex with important implications for the efficiency of utilisation. Importantly, acceptably accurate amino acid profiles will be advantageous for sustainable chicken-meat production into the future.

Una mirada a los D-aminoácidos en los seres vivos

The predominance of L-amino acids in biological systems has long been considered a defining feature of life. However, accumulating evidence over the past decades has demonstrated that D-amino acids are not merely biochemical anomalies, but biologically relevant molecules with diverse and essential functions across all domains of life. This review summarizes current knowledge on the distribution, biosynthesis, metabolism, and physiological roles of D-amino acids, highlighting their significance in microbial, animal, and evolutionary contexts. In bacteria, D-amino acids such as D-alanine and D-glutamate are integral components of peptidoglycan, contributing to cell wall integrity and resistance to proteolytic degradation. Beyond structural roles, several noncanonical D-amino acids act as signaling molecules to biofilm formation and microbial community dynamics. In eukaryotes, particularly in mammals, D-serine and D-aspartate have emerged as key neuromodulators involved in synaptic plasticity, neurodevelopment, and endocrine regulation, with growing implications in neurological and psychiatric disorders. Furthermore, the coexistence of functional D-amino acids with the largely L-based proteome raises fundamental questions about the origin and maintenance of biological homochirality. Mechanisms such as stereospecific aminoacyl-tRNA synthetases and D-aminoacyl-tRNA deacylases actively preserve proteomic homochirality while allowing selective utilization of D-amino acids in specialized pathways. Overall, D-amino acids represent a crucial yet historically underappreciated dimension of biological chemistry, with implications ranging from microbial physiology to neuroscience and the origin of life.

The quantitative amino acid economy of yeast reveals public versus private goods and guides syntrophic community design

ABSTRACT The biosynthetic capacity of a cell governs the production and exchange of amino acids. Given the distinct metabolic origins and intracellular requirements for amino acids, it is essential to establish quantitative amounts of internal amino acid pools and how these change across growth phases. Using Saccharomyces cerevisiae, here we establish an absolute, quantitative blueprint of the intracellular and extracellular amino acid economy, defining the fluxes of production, secretion, and consumption across 24 hours of cell growth. While the intracellular pool is dominated by a group of amino acids, their relative proportions continuously change over time. The extracellular pool is notably distinct in terms of composition and amounts. Only select amino acids are public goods secreted in significant amounts, and a subset of these (Ala, Val, Gln, Trp, and Phe) are subsequently re-consumed. Five amino acids, Asp, Lys, His, Arg, and Met, remain “privatized” even in nutrient abundance. We demonstrate that the strictly privatized amino acid Asp continuously sustains diverse carbon metabolism, while the public Ala is utilized following carbon depletion. Furthermore, nitrogen limitation triggers a significant shift toward storage, privatizing otherwise abundant nitrogen-rich compounds like Gln, Asn, and Pro. We thereby rationally establish pairs of stable synthetic communities of paired public good auxotrophs that show effective growth. Our results identify frameworks for feasible amino acid trade and provide a basis for engineering stable, synthetic communities of amino acid auxotrophs. IMPORTANCE Amino acids are central to a metabolic economy and are extensively exchanged between cells; yet, the scale of this economy remains unknown even in model microbes. This study establishes a quantitative blueprint of the amino acid economy in Saccharomyces cerevisiae by mapping production, secretion, and consumption fluxes. The findings reveal a distinction between public goods—such as alanine, which is secreted and re-consumed—and privatized resources, such as aspartate, which cells retain to sustain carbon metabolism. These pools shift across growth phases and move toward privatization during nitrogen limitation. By defining these frameworks, this study enables the rational design of stable, synthetic communities of auxotrophs. Amino acids are central to a metabolic economy and are extensively exchanged between cells; yet, the scale of this economy remains unknown even in model microbes. This study establishes a quantitative blueprint of the amino acid economy in Saccharomyces cerevisiae by mapping production, secretion, and consumption fluxes. The findings reveal a distinction between public goods—such as alanine, which is secreted and re-consumed—and privatized resources, such as aspartate, which cells retain to sustain carbon metabolism. These pools shift across growth phases and move toward privatization during nitrogen limitation. By defining these frameworks, this study enables the rational design of stable, synthetic communities of auxotrophs.