Amino acid sequence and D/L-configuration determination methods for D-amino acid-containing peptides in living organisms

d-Amino acids in biological systems

Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.

Geometric basis of action potential of skeletal muscle cells and neurons

Although we know something about single-cell neuromuscular junctions, it is still unclear how multiple skeletal muscle cells coordinate to complete intricate spatial curve movement. Here, we hypothesize that skeletal muscle cell populations with action potentials are aligned according to curved manifolds in space (a curved shape in space). When a specific motor nerve impulse is transmitted, the skeletal muscle also moves according to the corresponding shape (manifolds). The action potential of motor nerve fibers has the characteristics of a time curve manifold, and this time-manifold curve of motor nerve fibers comes from the visual cortex in which spatial geometric manifolds are formed within the synaptic connection of neurons. This spatial geometric manifold of the synaptic connection of neurons originates from spatial geometric manifolds outside nature that are transmitted to the brain through the cone cells and ganglion cells of the retina. The essence of life is that life is an object that can move autonomously, and the essence of life's autonomous movement is the movement of proteins. Theoretically, because of the infinite diversity of geometric manifold shapes in nature, the arrangement and combination of 20 amino acids should have infinite diversity, and the geometric manifold formed by the protein three-dimensional spatial structure should also have infinite diversity.

Age estimation in humans through the analysis of aspartic acid racemization from teeth: A scoping review of methods, outcomes, and open research questions

Teeth are considered the most resistant structures in the human body. In forensic odontology, teeth are useful for human identification, especially when dental age estimation is necessary. Despite numerous studies, there is no consensus regarding the best methods for dental age estimation. The analysis of aspartic acid racemization, however, has shown promising results. This scoping review aimed to present a descriptive synthesis of the current literature regarding dental age estimation through aspartic acid racemization. Four electronic databases were screened: PubMed, Scielo, Web of Science, and Scopus. Cross-sectional studies published before April 2021 were selected. From 206 articles found, 26 met the eligibility criteria. Several experimental protocols and laboratory settings were detected, but the different protocols did not seem to significantly reduce error rates in dental age estimation. The analysis of aspartic acid racemization in human dental tissues produced accurate and potentially reliable results for age estimation. Aspartic acid racemization stands out especially in the adulthood - age category in which other methods struggle to deliver proper performances. Studies with larger samples, independent testing, and standardized laboratory procedures are necessary. Equator-like reporting guidelines are encouraged to enable future systematic reviews and meta-analyses.

A Biochemical Lanthanide-Encoding Approach Enables Quantitative Monitoring of the Bacterial Response to Vancomycin Treatment

A pathogenic bacterium has its own mechanisms for not only pathogenic attack but also exogenous invasion defense, in which the bacterial cell wall is the front line of attack and defense. We developed a biochemical lanthanide-encoding approach to quantify the uncanonical d-amino acid (d-X) that was edited in a small proportion into the terminal acyl-d-Ala-d-X of nascent peptidoglycan UDP-MurNAc-pentapeptides in the bacterial cell wall. This approach overcomes the difficulties regarding quantification and accuracy issues encountered by the popular optical imaging and traditional high-performance liquid chromatography-based methods. Newly synthesized azide-d-Leu and ketone-d-Met were used together with alkynyl-d-Ala for their metabolic assembly and then bioorthogonally encoded by the correspondingly fabricated DBCO-DOTA-Gd, H₂NO-DOTA-Eu, and azide-DOTA-Sm tags. This approach allows direct quantification of the d-X in situ in the cell wall using ¹⁵⁸Gd, ¹⁵³Eu, and ¹⁵⁴Sm species-unspecific isotope dilution inductively coupled plasma mass spectrometry, avoiding any tedious and complex "cell-broken" pretreatment procedures that might induce racemization of the d-X. The obtained site-specific and accurate in situ information about the d-X enables quantitative monitoring of the bacterial response when Staphylococcus aureus meets vancomycin, showing that the amounts of azide-d-Leu and ketone-d-Met assembled are more important after determining the structure- and composition-dependent bacterial antibiotic resistance mechanisms. In addition, we found that the combined use of vancomycin and d-Ala restores the efficacy of vancomycin and might be a wise and simple way to combat vancomycin intermediate-resistant S. aureus.

Differential Post-Translational Amino Acid Isomerization Found among Neuropeptides in Aplysia californica

d-Amino acid-containing peptides (DAACPs) make up a class of post-translationally modified peptides in animals that play important roles as cell-to-cell signaling molecules. Despite the functional importance of l- to d-residue isomerization, little is known about its prevalence, mostly due to difficulties associated with detecting differences in peptide stereochemistry. Prior efforts to discover DAACPs have been largely focused on pursuing peptides based on homology to known DAACPs or DAACP-encoding precursors. Here, we used a combination of enzymatic screening, mass spectrometry, and chromatographic analysis to identify novel DAACPs in the central nervous system (CNS) of Aplysia californica. We identified five new DAACPs from the pleurin precursor and three DAACPs from previously uncharacterized proteins. In addition, two peptides from the pleurin precursor, Plrn2 and Plrn3, exist as DAACPs with the d-residue found at position 2 or 3. These differentially modified forms of Plrn2 and Plrn3 are located in specific regions of the animal's CNS. Plrn2 and Plrn3 appear to be the first animal DAACPs in which the d-residue is found at more than one position, and this suggests that l- to d-residue isomerization may be a more variable/dynamic modification than previously thought. Overall, this study demonstrates the utility of nontargeted DAACP discovery approaches for identifying new DAACPs and demonstrates that isomerization is prevalent throughout the CNS of A. californica.

Aspartic acid racemization of root dentin used for dental age estimation in a Polish population sample

Precise age determination of unidentified bodies and human remains is one of the essential tasks of forensic science. The aim of this study was to assess the applicability of using the enantiomeric composition of aspartic acid racemization in root and crown dentin for dental age estimation using a Polish population sample. Coronal and root dentin from four teeth groups from the mandible were studied using gas chromatography with mass spectrometry. The results demonstrated a very high correlation between the chronological age and enantiomeric composition in both of the dentin samples. Individual linear equations of root dentin with correlation coefficients between 0.96 and 0.98 and a standard estimation error of ±2.95–4.84 years validated the application of aspartic acid racemization as a significant practical contribution to everyday forensic medical practice. Discrepancies in methodological aspects and modifications that simplify the protocol are presented.

(+) or (-)-1-(9-fluorenyl)ethyl chloroformate as chiral derivatizing agent: A review

Over the last 30years, (±)-1-(9-fluorenyl)ethyl chloroformate ((±)-FLEC) was used as a chiral derivatizing agent in various analytical applications involving a wide range of endogenous, pharmaceutical and environmentally relevant molecules. This comprehensive review aims to present all the significant aspects related to the state of the art in FLEC labeling and subsequent chiral separation of the resulting diastereomers using LC, SFC and CE techniques.

Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality

D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conformational propensities of L- and D-amino acids are a reflection of one another due to the straightforward geometric inversion at the Cα atom. However, this presumption does not account for the directionality of the backbone dipole and the inverted propensities have never been definitively confirmed in this context. Furthermore, there is little known of how alternative side chain chirality affects the backbone conformations of isoleucine and threonine. Using a GGXGG host-guest pentapeptide system, we have completed exhaustive sampling of the conformational propensities of the D-amino acids, including D-allo-isoleucine and D-allo-threonine, using atomistic molecular dynamics simulations. Comparison of these simulations with the same systems hosting the cognate L-amino acids verifies that the intrinsic backbone conformational propensities of the D-amino acids are the inverse of their cognate L-enantiomers. Where amino acids have a chiral center in their side chain (Thr, Ile) the β-configuration affects the backbone sampling, which in turn can confer different biological properties.

Site-specific characterization of (D)-amino acid containing peptide epimers by ion mobility spectrometry

Traditionally, the d-amino acid containing peptide (DAACP) candidate can be discovered by observing the differences of biological activity and chromatographic retention time between the synthetic peptides and naturally occurring peptides. However, it is difficult to determine the exact position of d-amino acid in the DAACP candidates. Herein, we developed a novel site-specific strategy to rapidly and precisely localize d-amino acids in peptides by ion mobility spectrometry (IMS) analysis of mass spectrometry (MS)-generated epimeric fragment ions. Briefly, the d/l-peptide epimers were separated by online reversed-phase liquid chromatography and fragmented by collision-induced dissociation (CID), followed by IMS analysis. The epimeric fragment ions resulting from d/l-peptide epimers exhibit conformational differences, thus showing different mobilities in IMS. The arrival time shift between the epimeric fragment ions was used as criteria to localize the d-amino acid substitution. The utility of this strategy was demonstrated by analysis of peptide epimers with different molecular sizes, [d-Trp]-melanocyte-stimulating hormone, [d-Ala]-deltorphin, [d-Phe]-achatin-I, and their counterparts that contain all-l amino acids. Furthermore, the crustacean hyperglycemia hormones (CHHs, 8.5 kDa) were isolated from the American lobster Homarus americanus and identified by integration of MS-based bottom-up and top-down sequencing approaches. The IMS data acquired using our novel site-specific strategy localized the site of isomerization of l- to d-Phe at the third residue of the CHHs from the N-terminus. Collectively, this study demonstrates a new method for discovery of DAACPs using IMS technique with the ability to localize d-amino acid residues.

Experimental strategies for the analysis of D-amino acid containing peptides in crustaceans: a review

Detection of D-amino acids in natural peptides has been, and remains a challenging task, as peptidyl isomerization is a peculiar and subtle posttranslational modification that does not induce any change in primary sequence or in physicochemical properties of the molecule such as molecular mass or pI. Therefore, the presence of a D-amino acid residue in a peptide chain is generally transparent to classical methods of peptide analysis (electrophoresis, chromatography, mass spectrometry, molecular biology). In this article, we will review the various experimental strategies and analytical techniques, which have been used to characterize and to study D-amino acid containing peptides in crustaceans.

Analysis of Endogenous D-Amino Acid-Containing Peptides in Metazoa

Peptides are chiral molecules with their structure determined by the composition and configuration of their amino acid building blocks. The naturally occurring amino acids, except glycine, possess two chiral forms. This allows the formation of multiple peptide diastereomers that have the same sequence. Although living organisms use L-amino acids to make proteins, a group of D-amino acid-containing peptides (DAACPs) has been discovered in animals that have at least one of their residues isomerized to the D-form via an enzyme-catalyzed process. In many cases, the biological functions of these peptides are enhanced due to this structural conversion. These DAACPs are different from those known to occur in bacterial cell wall and antibiotic peptides, the latter of which are synthesized in a ribosome-independent manner. DAACPs have now also been identified in a number of distinct groups throughout the Metazoa. Their serendipitous discovery has often resulted from discrepancies observed in bioassays or in chromatographic behavior between natural peptide fractions and peptides synthesized according to a presumed all-L sequence. Because this L-to-D post-translational modification is subtle and not detectable by most sequence determination approaches, it is reasonable to suspect that many studies have overlooked this change; accordingly, DAACPs may be more prevalent than currently thought. Although diastereomer separation techniques developed with synthetic peptides in recent years have greatly aided in the discovery of natural DAACPs, there is a need for new, more robust methods for naturally complex samples. In this review, a brief history of DAACPs in animals is presented, followed by discussion of a variety of analytical methods that have been used for diastereomeric separation and detection of peptides.

Detecting D-amino acid-containing neuropeptides using selective enzymatic digestion

Neuropeptides, gene products that undergo extensive post-translational modification (PTM), are frequently characterized using mass spectrometry (MS). One PTM in particular, the conversion of an L-amino acid to a D-amino acid, has no associated mass shift. Therefore, this PTM is difficult to evaluate using MS alone, especially in complex peptide mixtures. Here, enzymatic digestion using microsomal alanyl aminopeptidase is combined with MS characterization. This enzyme selectively degrades peptides lacking a D-amino acid in the second position from the N-terminus. By comparing a sample before and after digestion, D-amino acid-containing peptides (DAACPs) present in small quantities in a complex mixture can be identified, even among much larger quantities of other non-DAACPs. Protocols that use microsomal alanyl aminopeptidase as a discovery-enabling agent are described and validated by identifying a known DAACP from the Aplysia californica abdominal ganglion.

An improved sample preparation for an LC method used in the age estimation based on aspartic acid racemization from human dentin

The determination of age on the basis of aspartic acid (Asp) racemization in teeth is one of the most reliable and accurate methods to date. In this paper, the usefulness of HPLC coupled with fluorescence detection for determination of Asp racemization was evaluated. A modified sample preparation is proposed for better stability of o-phthaldialdehyde-N-acetyl-L-cysteine derivatives of D/L-Asp (due to the instability below pH 7). To ensure the accuracy of the method, the validation parameters' specificity, precision, linearity, and LOD were determined. Three dentin samples of premolar teeth, extracted from living individuals (bucco-lingual longitudinal sections of 1 mm thickness), were analyzed and quantitative results are discussed.

Biochemistry of amino acid racemization and clinical application to musculoskeletal disease

During aging, proteins are subject to numerous forms of damage. Several types of non-enzymatic post-translational modifications have been described in aging proteins, including oxidation, nitration, glycation, and racemization. Racemization of amino acids is the spontaneous conversion of L-enantiomers to the D-form, which is dependent on temperature, pH, and time. Because of the time-dependent nature of racemization, it can be used to determine the relative age and turnover rates of long-lived proteins. There are many such long-lived proteins within the body; they are found in the brain, eye, and heart, but are particularly abundant in proteins found in musculoskeletal tissues such as bone and cartilage. During disease, musculoskeletal tissues have pathologically altered turnover rates. Because turnover rates can be estimated from levels of racemization, racemized musculoskeletal protein fragments may serve as useful biomarkers of disease. This review discusses the biochemistry of amino acid racemization in proteins and its clinical application to musculoskeletal disease.

Racemization of aspartic acid from human dentin in the estimation of chronological age

The estimation of chronological age in cadavers, human remains and in living human beings by various methods is discussed. These methods, which are based on the age dependent non-enzymatic changes of l-form amino acids to d-form amino acids, mainly aspartic acid, are among the most reliable and accurate methods to date. Most of these methods use gas chromatography (GC). In this review, results of aspartic acid racemization in dentin at different targets are discussed. In addition, pre-considerations and guidelines are given for the selection of dentin from teeth. A pilot project was run to evaluate the efficiency of high performance liquid chromatography (HPLC) coupled with fluorescence detection. New buffer conditions were found to obtain stable derivatives of aspartic acid enantiomers for the estimation of racemization.

Measuring D-amino acid-containing neuropeptides with capillary electrophoresis

Neuropeptides are heavily posttranslationally modified (PTM) gene products that are often characterized by a variety of mass spectrometric approaches. Recently, the occurrence of amino acids in the D-form has been documented in several neuropeptides. As this modification has no associated mass shift, this particular PTM is difficult to evaluate using mass spectrometry (MS) alone. Here we demonstrate several approaches using capillary electrophoresis (CE) with absorbance and laser-induced fluorescence (LIF) for the separation of native and derivatized molluscan peptides containing D-amino acids. The combination of peptide derivatization followed by CE/LIF is well suited for single cell measurements because of its ability to characterize the peptides in such small samples. In order to verify this approach, the D-Trp-containing peptide NdWFa (NH2-Asn-D-Trp-Phe-CONH2), present in individual neurons from the marine mollusk Aplysia californica, has been characterized. The mass spectra show that NdWFa and/or NWFa are present in specific neurons; CE/LIF analysis of these cells demonstrates that NdWFa is the dominant form of the peptide.

Stereoselective peptide analysis

The stereochemistry of a peptide determines its spatial features and can profoundly influence its chemical properties and biological activity. Thus, the analysis of the stereochemical properties of a peptide is an important aspect of its characterisation. For such investigations a "selector" that engages in stereoselective interactions with the peptide analytes is often used. A substantiated knowledge of the underlying molecular recognition mechanism will therefore be helpful in understanding existing and developing new stereoselective analysis systems. After a short introduction concerning the fundamentals of peptide stereoisomers and their biological implications, the stereoselective peptide analysis methods described in the literature are comprehensively reviewed. The characteristics and applications of the employed methods based on various techniques including chromatography (pressure- and electrokinetically driven), capillary electrophoresis, nuclear magnetic resonance spectroscopy and mass spectrometry are discussed. The various selectors that have been utilised to discriminate peptide enantiomers and/or diastereomers are described concurrently. The review concludes with an overview of combinations and comparisons of techniques that have been applied to the analysis of peptide stereoisomers and constitute a trend for further developments.

Recent progress in derivatization methods for LC and CE analysis

The derivatization procedure with a suitable fluorescence or chemiluminescence reagent is performed for the purpose of increasing the detection sensitivity and selectivity, in high-performance liquid chromatography (HPLC) and/or capillary electrophoresis (CE). In this article, recent derivatization methods and their applications to biosamples are described. In HPLC, femto mol order of mass detection limits are obtained by derivatization. Regarding the fluorescence reagents, the use of water-soluble reagents has been effective to avoid an undesired adsorption in the process of determination of peptides. In CE, the advantages of having extremely low mass detection limits (ranging from atto to yocto mol level) and requiring only a very short analysis time (less than a few minutes) are made possible by using laser-induced fluorescence or near infra-red detections.