Age estimation based on aspartic acid racemization in elastin from the yellow ligaments

Molecular age estimation based on posttranslational protein modifications in bone: why the type of bone matters

Age-at-death estimation is of great relevance for the identification of unknown deceased individuals. In skeletonised corpses, teeth and bones are theoretically available for age estimation, but in many cases, only single bones or even only bone fragments are available for examination. In these cases, conventional morphological methods may not be applicable, and the application of molecular methods may be considered. Protein-based molecular methods based on the D-aspartic acid (D-Asp) or pentosidine (Pen) content have already been successfully applied to bone samples. However, the impact of the analysed type of bone has not yet been systematically investigated, and it is still unclear whether data from samples of one skeletal region (e.g. skull) can also be used for age estimation for samples of other regions (e.g. femur). To address this question, D-Asp and Pen were analysed in bone samples from three skeletal regions (skull, clavicle, and rib), each from the same individual. Differences between the bone types were tested by t-test, and correlation coefficients (ρ) were calculated according to Spearman. In all types of bone, an age-dependent accumulation of D-Asp and Pen was observed. However, both parameters (D-Asp and Pen) exhibited significant differences between bone samples from different anatomical regions. These differences can be explained by differences in structure and metabolism in the examined bone types and have to be addressed in age estimation based on D-Asp and Pen. In future studies, bone type-specific training and test data have to be collected, and bone type-specific models have to be established.

Immunohistochemical localization of d ‐ β ‐aspartic acid in congenital and acquired middle ear cholesteatoma

Objective/Hypothesis

Middle ear cholesteatoma is characterized by abnormal growth of the keratinizing squamous epithelium of the temporal bone. d‐β‐aspartic acid is the major isomer of d‐aspartic acid found in elderly tissue. We assessed the immunoreactivity to k‐β‐aspartic acid of congenital and acquired middle ear cholesteatomas.

Study Design

Case–control studies.

Material and Methods

Tissue samples were collected from 21 patients comprising 21 ears with congenital middle ear cholesteatoma and 26 patients comprising 29 ears with acquired type. Their clinical and histopathological features were investigated. We divided the middle ear cholesteatoma samples into three layers: the perimatrix, matrix, and cystic contents. The patterns of immunoreactivity to d‐β‐aspartic acid expression were then assessed immunohistochemically.

Results

Two patterns of immunoreactivity to d‐β‐aspartic acid were detected in middle ear cholesteatoma: infiltrative and diffuse. In congenital middle ear cholesteatoma, d‐β‐aspartic acid expression was observed throughout all the layers (perimatrix, matrix, and cystic contents), and immunoreactivity to d‐β‐aspartic acid was dramatically strong in all layers. The expression levels of d‐β‐aspartic acid to the cystic content and perimatrix were significantly higher in congenital middle ear cholesteatoma than in the acquired type.

Conclusions

This study showed the expression levels of d‐β‐aspartic acid in middle ear cholesteatoma to differ significantly between congenital and acquired middle ear cholesteatoma. Our results indicate that overexpression of d‐β‐aspartic acid is likely to be involved in the pathogenesis of cholesteatoma, and we speculate that d‐β‐aspartic acid could be a novel biomarker for, and a therapeutic target in, congenital and acquired middle ear cholesteatoma.

Level of Evidence

4

Predicting Reaction Mechanisms for the Threonine-Residue Stereoinversion Catalyzed by a Dihydrogen Phosphate Ion

The stereoinversion of amino acid residues in proteins is considered to trigger various age-related diseases. Serine (Ser) residues are relatively prone to stereoinversion. It is assumed that threonine (Thr) residues also undergo stereoinversion, which results in the formation of the d-allo-Thr residue, by the same mechanisms as those for Ser-residue stereoinversion; however, d-allo-Thr residues have not been detected in vivo. To date, although Ser-residue stereoinversion has been suggested to progress via enolization, plausible reaction mechanisms for Thr-residue stereoinversion have not been proposed. In this study, we investigated the pathway of Thr-residue enolization and successfully identified the three types of plausible reaction pathways of Thr-residue stereoinversion catalyzed by a dihydrogen phosphate ion. The geometries of reactant complexes, transition states, and enolized product complexes were optimized using B3LYP density functional methods, and single-point calculations were performed for all optimized geometries using Møller-Plesset perturbation theory to obtain reliable energies. As a result, the calculated activation energies of Thr-residue stereoinversion were 105-106 kJ mol^-1, which were comparable with those of Ser-residue stereoinversion reported previously. The infrequency of Thr-residue stereoinversion may be due to other factors, such as the hydrophobicity and/or the steric hindrance of the γ-methyl group, rather than the high activation energies.

Biochemical analyses for dental age estimation: a review

Background

For various legal and forensic scenarios, establishing an individual’s age, both living and dead, plays a crucial role. Various morphological, radiographic, and molecular methods can be used for age estimation. In children and adolescents, age estimation is based on the established developmental stages. However, in adults, where the development ceases into maturation, the degenerative changes play a role in determining the age.

Main body of the abstract

In the natural aging process, several molecular changes occur most commonly in the long-living proteins and hard tissues like the teeth and bone. These molecular changes gradually lead to alterations in several organs and organ systems, which can be quantified and correlated with age, including aspartic acid racemization, collagen crosslinks, advanced glycation-end products, and mitochondrial DNA mutations.

Short conclusion

Among the above methods, the racemization of aspartic acid can be considered as the most precise method. The main advantage of using aspartic acid racemization is that the sample can be collected from tissues (teeth) protected from various environmental and nutritional factors. If all the confounding factors are stable, the utilization of advanced glycation-end products can also be considered valuable. Environmental factors like lead accumulations may also help determine the age. However, further studies need to be conducted, focusing on providing a more standardized method. This review provides a concise summary of the biochemical techniques that can be used for estimation of age.

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.

Theoretical Studies on the Effect of Isomerized Aspartic Acid Residues on the Three-Dimensional Structures of Bovine Pancreatic Ribonucleases A

Isomerized aspartic acid (Asp) residues have previously been identified in various aging tissues, and are suspected to contribute to age-related diseases. Asp-residue isomerization occurs nonenzymatically under physiological conditions, resulting in the formation of three types of isomerized Asp (i.e., L-isoAsp, D-Asp, and D-isoAsp) residues. Asp-residue isomerization often accelerates protein aggregation and insolubilization, making structural biology analyses difficult. Recently, Sakaue et al. reported the synthesis of a ribonuclease A (RNase A) in which Asp121 was artificially replaced with different isomerized Asp residues, and experimentally demonstrated that the enzymatic activities of these artificial mutants were completely lost. However, their structural features have not yet been elucidated. In the present study, the three-dimensional (3D) structures of these artificial-mutant RNases A were predicted using molecular dynamics (MD) simulations. The 3D structures of wild-type and artificial-mutant RNases A were converged by 3000-ns MD simulations. Our computational data show that the structures of the active site and the formation frequencies of the appropriate catalytic dyad structures in the artificial-mutant RNases A were quite different from wild-type RNase A. These computational findings may provide an explanation for the experimental data which show that artificial-mutant RNases A lack enzymatic activity. Herein, MD simulations have been used to evaluate the influences of isomerized Asp residues on the 3D structures of proteins.

Nutzung von Altersinformationen aus posttranslationalen Proteinmodifikationen und DNA-Methylierung zur postmortalen Lebensaltersschätzung

Mit der Identifikation und Beschreibung „molekularer Uhren“ (posttranslationale Proteinmodifikationen, DNA-Methylierung) eröffnen sich neue Möglichkeiten zur Entwicklung von Verfahren zur postmortalen Lebensaltersschätzung. Bislang werden diese Ansätze aber nur unabhängig voneinander eingesetzt. Ihre Verknüpfung verspricht eine bessere Erfassung hochkomplexer Alterungsprozesse und damit die Möglichkeit zur Entwicklung optimierter Verfahren zur Altersschätzung für verschiedenste Szenarien der forensischen Praxis.

In Vorbereitung umfangreicher Untersuchungen zur Überprüfung dieser Hypothese wurden verschiedene molekulare Uhren (Akkumulation von D‑Asparaginsäure, Akkumulation von Pentosidin und DNA-Methylierungsmarker [RPA2, ZYG11A, F5, HOXC4, NKIRAS2, TRIM59, ELOVL2, DDO, KLF14 und PDE4C]) in 4 fäulnisresistenten Geweben (Knochen, Sehne, Bandscheibe, Epiglottis) von 15 Individuen untersucht.

In allen untersuchten Geweben fand sich eine starke Korrelation beider Proteinmarker sowie jeweils mehrerer DNA-Methylierungsmarker mit dem Lebensalter. Dabei zeigten die untersuchten Parameter gewebsspezifische Veränderungen mit dem Alter.

Die Ergebnisse der Pilotstudie belegen das Potenzial der Verknüpfung molekularer Verfahren für die postmortale Altersschätzung. Weitere Untersuchungen werden zeigen, wie genau postmortale Altersschätzungen sein können, wenn Altersinformationen aus posttranslationalen Proteinmodifikationen und DNA-Methylierung aus verschiedenen Geweben in multivariaten Modellen verknüpft werden.

Molecular Mechanisms of Succinimide Formation from Aspartic Acid Residues Catalyzed by Two Water Molecules in the Aqueous Phase

Aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. The formation of isomerized Asp residues is considered to be associated with various age-related diseases, such as cataracts and Alzheimer’s disease. In the present paper, we describe the reaction pathway of Suc residue formation from Asp residues catalyzed by two water molecules using the B3LYP/6-31+G(d,p) level of theory. Single-point energies were calculated using the MP2/6-311+G(d,p) level of theory. For these calculations, we used a model compound in which an Asp residue was capped with acetyl and methylamino groups on the N- and C-termini, respectively. In the aqueous phase, Suc residue formation from an Asp residue was roughly divided into three steps, namely, iminolization, cyclization, and dehydration, with the activation energy estimated to be 109 kJ mol⁻¹. Some optimized geometries and reaction modes in the aqueous phase were observed that differed from those in the gas phase.

Simultaneous and Rapid Detection of Multiple Epimers and Isomers of Aspartyl Residues in Lens Proteins Using an LC-MS-MRM Method

Traditionally, studies of post translational modifications (PTMs) by mass analysis have been limited to modifications such as deamidation and oxidation that have a mass shift. Although Asp isomerization is an important PTM, the selective detection of Asp isomers by mass spectrometry was originally thought to be impossible due to the identical mass of the isomers. The recent development of an LC-MS-based method has facilitated rapid and accurate quantitative analysis of Asp isomers in long-lived proteins; however, because the quantification is based on the extracted ion chromatogram acquired by an MS1 scan, this methodology is not always efficient for detecting extremely low-abundance peptides in complex biological samples. In this paper, we evaluated Asp isomer-containing peptides of αA-crystallin present in tryptic digests of human lens samples with different degrees of protein aggregation and different ages using LC coupled with multiple reaction monitoring (MRM). In a single analysis, the LC-MRM method enabled three tryptic peptides containing isomers of Asp58, Asp91/92, and Asp151 to be detected simultaneously. The extent of isomerization and epimerization of these specific Asp sites in αA-crystallin increased with the progress of α-crystallin aggregation. For the analysis of samples known to isomerize at specific Asp residues, MRM gives a more rapid, less laborious, and high-quality separation of Asp isomer-containing peptides relative to the previous MS1-based quantitative method.

Influence of the conformations of αA-crystallin peptides on the isomerization rates of aspartic acid residues

The isomerization rate of aspartic acid (Asp) residue is known to be affected by the three-dimensional structures of peptides and proteins. Although the isomerized Asp residues were experimentally observed, structural features which affect the isomerization cannot be elucidated sufficiently because of protein denaturation and aggregation. In this study, molecular dynamics (MD) simulations were conducted on three αA-crystallin peptides (T6, T10, and T18), each containing a single Asp residue with different isomerization rate (T18 > T6 > T10) to clarify the structural factors of Asp isomerization tendency. For MD trajectories, distances between side-chain carboxyl carbon of Asp and main-chain amide nitrogen of (n + 1) residue (C_γ-N distances), root mean square fluctuations (RMSFs), and polar surface areas for main-chain amide nitrogen of (n + 1) residues (PSA_N) were calculated, because these structural features are considered to relate to the formations of cyclic imide intermediates. RMSFs and PSA_N are indexes of peptide backbone flexibilities and solvent exposure of the amide nitrogen, respectively. The average C_γ-N distances of T10 was longer than those of the other two peptides. In addition, the peptide containing Asp residue with a higher isomerization rate showed higher flexibility of the peptide backbone around the Asp residue. PSA_N for amide nitrogen in T18 were much larger than those of other two peptides. The computational results suggest that Asp-residue isomerization rates are affected by these factors.

Computational studies on nonenzymatic succinimide-formation mechanisms of the aspartic acid residues catalyzed by two water molecules

In the biological proteins, aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. Asp-residue isomerization causes the aggregation and the insolubilization of proteins, and is considered to be involved in various age-related diseases. Although Suc intermediate was considered to be formed by nucleophilic attack of the main-chain amide nitrogen of N-terminal side adjacent residue to the side-chain carboxyl carbon of Asp residue, previous studies have shown that the nucleophilic attack is more likely to proceed via iminol tautomer when the water molecules act as catalysts. However, the full pathway to Suc-intermediate formation has not been investigated, and the experimental analyses for the Asp-residue isomerization mechanism at atomic and molecular levels, such as the analysis of the transition state geometry, are difficult. In the present study, we computationally explored the full pathways for Suc-intermediate formation from Asp residues. The calculations were performed two types of reactant complexes, and all energy minima and TS geometries were optimized using B3LYP density functional methods. As a result, the SI-intermediate formation was divided into three processes, i.e., iminolization, cyclization, and dehydration processes, and the activation energies were calculated to be 26.1 or 28.4 kcal mol^-1. These values reproduce the experimental data. The computational results show that abundant water molecules in living organisms are effective catalysts for the Asp-residue isomerization.

Computational Studies on Water-Catalyzed Mechanisms for Stereoinversion of Glutarimide Intermediates Formed from Glutamic Acid Residues in Aqueous Phase

Aspartic acid (Asp) residues are prone to non-enzymatic stereoinversion, and Asp-residue stereoinversion is believed to be mediated via a succinimide (SI) intermediate. The stereoinverted Asp residues are believed to cause several age-related diseases. However, in peptides and proteins, few studies have reported the stereoinversion of glutamic acid (Glu) residues whose structures are similar to that of Asp. We previously presumed that Glu-residue stereoinversion proceeds via a glutarimide (GI) intermediate and showed that the calculated activation barriers of SI- and GI-intermediate stereoinversion are almost equivalent in the gas phase. In this study, we investigated the stereoinversion pathways of the l-GI intermediate in the aqueous phase using B3LYP density functional methods. The calculated activation barrier of l-GI-intermediate stereoinversion in the aqueous phase was approximately 36 kcal·mol-1, which was much higher than that in the gas phase. Additionally, as this activation barrier exceeded that of Asp-residue stereoinversion, it is presumed that Glu-residue stereoinversion has a lower probability of proceeding under physiological conditions than Asp-residue stereoinversion.

Age estimation based on aspartic acid racemization in dentine: what about caries-affected teeth?

Age estimation based on aspartic acid racemization (AAR) in dentine is one of the most precise methods in adult age. Caries induces protein degradation and may have an impact on the kinetics of AAR in dentine. We systematically examined standardized prepared dentine samples from caries-affected teeth to clarify the question, if caries-affected teeth should not be used for age estimation based on AAR at all, or if the analysis of dentine samples from such teeth may be useful after removal of the caries-affected tissue according to clinical standards. Our results suggest that caries may lead to an extensive protein degradation even in macroscopically healthy-appearing dentine samples from caries-affected teeth and may significantly affect the precision of age estimation. To ensure the quality of age estimation based on AAR in forensic practice, we recommend using dentine samples from healthy teeth. If only caries-affected teeth are available, dentine samples from at least two teeth from the same individual should be analyzed as it seems unlikely that caries-induced protein degradation occurred with identical kinetics in two different teeth. In any case, results of the analysis of caries-affected teeth must be interpreted with caution.

Kinetics of the competitive reactions of isomerization and peptide bond cleavage at l-α- and d-β-aspartyl residues in an αA-crystallin fragment

d-β-aspartyl (Asp) residue has been found in a living body such as aged lens crystallin, although l-α-amino acids are constituents in natural proteins. Isomerization from l-α- to d-β-Asp probably modulates structures to affect biochemical reactions. At Asp residue, isomerization and peptide bond cleavage compete with each other. To gain insight into how fast each reaction proceeds, the analysis requires the consideration of both pathways simultaneously and independently. No information has been provided, however, about these competitive processes because each reaction has been studied separately. The contribution of Asp isomers to the respective pathways has still been veiled. In this work, the two competitive reactions, isomerization and spontaneous peptide bond cleavage at Asp residue, were simultaneously observed and compared in an αA-crystallin fragment, S⁵¹ LFRTVLD⁵⁸ SG⁶⁰ containing l-α- and d-β-Asp58 isomers. The kinetics showed that the formation of l- and d-succinimide (Suc) intermediate, as a first step of isomerization, was comparable at l-α- and d-β-Asp. Although l-Suc was converted to l-β-Asp, d-Suc was liable to return to the original d-β-Asp, the reverse reaction marked enough to consider d-β-Asp as apparently stable. d-β-Asp was also resistant to the peptide bond cleavage. Such apparent less reactivity is probably the reason for gradual and abnormal accumulation of d-β-Asp in a living body under physiological conditions. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

D-β-aspartyl residue exhibiting uncommon high resistance to spontaneous peptide bond cleavage

Although L-amino acids were selected as main constituents of peptides and proteins during chemical evolution, D-aspartyl (Asp) residue is found in a variety of living tissues. In particular, D-β-Asp is thought to be stable than any other Asp isomers, and this could be a reason for gradual accumulation in abnormal proteins and peptides to modify their structures and functions. It is predicted that D-β-Asp shows high resistance to biomolecular reactions. For instance, less reactivity of D-β-Asp is expected to bond cleavage, although such information has not been provided yet. In this work, the spontaneous peptide bond cleavage was compared between Asp isomers, by applying real-time solution-state NMR to eye lens αΑ-crystallin 51–60 fragment, S⁵¹LFRTVLD⁵⁸SG⁶⁰ and αΒ-crystallin 61–67 analog, F⁶¹D⁶²TGLSG⁶⁷ consisting of L-α- and D-β-Asp 58 and 62, respectively. Kinetic analysis showed how tough the uncommon D-β-Asp residue was against the peptide bond cleavage as compared to natural L-α-Asp. Differences in pK_a and conformation between L-α- and D-β-Asp side chains were plausible factors to determine reactivity of Asp isomers. The present study, for the first time, provides a rationale to explain less reactivity of D-β-Asp to allow abnormal accumulation.

Biophysical chemistry of the ageing eye lens

This review examines both recent and historical literature related to the biophysical chemistry of the proteins in the ageing eye, with a particular focus on cataract development. The lens is a vital component of the eye, acting as an optical focusing device to form clear images on the retina. The lens maintains the necessary high transparency and refractive index by expressing crystallin proteins in high concentration and eliminating all large cellular structures that may cause light scattering. This has the consequence of eliminating lens fibre cell metabolism and results in mature lens fibre cells having no mechanism for protein expression and a complete absence of protein recycling or turnover. As a result, the crystallins are some of the oldest proteins in the human body. Lack of protein repair or recycling means the lens tends to accumulate damage with age in the form of protein post-translational modifications. The crystallins can be subject to a wide range of age-related changes, including isomerisation, deamidation and racemisation. Many of these modification are highly correlated with cataract formation and represent a biochemical mechanism for age-related blindness.

Immunohistochemical localization of D-β-aspartic acid-containing proteins in pterygium

Biologically uncommon D-β-aspartic acid (D-β-Asp) residues have been reported to accumulate in organs affected by age-related disorders. In the present study, we investigated the localization of D-β-Asp-containing proteins in cases of pterygium, one of the most prominent age-related ocular conditions. Immunohistochemical localization of D-β-Asp-containing proteins was investigated in surgical specimens of pterygium from 20 patients and control specimens from 10 patients. Strong immunoreactivity to D-β-Asp-containing proteins was observed in subepithelial elastotic lesions and surrounding collagenous lesions from all surgical specimens with pterygia. In contrast, no immunoreactivity to D-β-Asp-containing proteins was seen in pterygium-free specimens. D-β-Asp-containing proteins are produced in organs as they are affected by the aging process. In addition, conversion of L- to D-aspartyl residues is accelerated by ultraviolet (UV) irradiation. Since pterygia can form due to aging or UV exposure, it is reasonable to find D-β-Asp-containing proteins in specimens with pterygia. Furthermore, since D-β-Asp is a non-native amino acid, D-β-Asp-containing proteins may be recognized as allogeneic antigens. Therefore, D-β-Asp-containing proteins in pterygia may responsible for the fibrovascular changes seen in the disorder.

Molecular ageing: free radical initiated epimerization of thymopentin--a case study

The epimerization of amino acid residues increases with age in living organisms. In the present study, the structural consequences and thermodynamic functions of the epimerization of thymopentin (TP-5), the active site of the thymic hormone thymopoietin, were studied using molecular dynamics and density functional theory methods. The results show that free radical-initiated D-amino acid formation is energetically favoured (-130 kJmol(-1)) for each residue and induces significant changes to the peptide structure. In comparison to the wild-type (each residue in the L-configuration), the radius of gyration of the D-Asp(3) epimer of the peptide decreased by 0.5 Å, and disrupted the intramolecular hydrogen bonding of the native peptide. Beyond establishing important structural, energetic and thermodynamic benchmarks and reference data for the structure of TP-5, these results disseminate the understanding of molecular ageing, the epimerization of amino acid residues.

Kinetics of isomerization and inversion of aspartate 58 of αA-crystallin peptide mimics under physiological conditions

Although proteins consist exclusively of L-amino acids, we have reported that aspartyl (Asp) 58 and Asp 151 residues of αA-crystallin of eye lenses from elderly cataract donors are highly inverted and isomerized to D-β, D-α and L-β-Asp residues through succinimide intermediates. Of these Asp isomers, large amounts of D-β- and L-β-isomers are present but the amount of D-α-isomer is not significant. The difference in abundance of the Asp isomers in the protein may be due to the rate constants for the formation of the isomers. However, the kinetics have not been well defined. Therefore, in this study, we synthesized a peptide corresponding to human αA-crystallin residues 55 to 65 (T(55)VLD(58)SGISEVR(65)) and its isomers in which L-α-Asp at position 58 was replaced with L-β-, D-β- and D-α-Asp and determined the rate of isomerization and inversion of Asp residues under physiological conditions (37°C, pH7.4). The rate constant for dehydration from L-α-Asp peptide to L-succinimidyl peptide was 3 times higher than the rate constant for dehydration from L-β-Asp peptide to L-succinimidyl peptide. The rate constant for hydrolysis from L-succinimidyl peptide to L-β-Asp peptide was about 5 times higher than the rate constant for hydrolysis from L-succinimidyl peptide to L-α-Asp peptide. The rate constant for dehydration from L-α-Asp peptide to L-succinimidyl peptide was 2 times higher than the rate constant for dehydration from D-α-Asp peptide to D-succinimidyl peptide. The rate constants for hydrolysis from L-succinimidyl peptide to L-β-Asp peptide and for hydrolysis from D-succinimidyl peptide to D-β-Asp peptide were almost equal. Using these rate constants, we calculated the change in the abundance ratios of the 4 Asp isomers during a human lifespan. This result is consistent with the fact that isomerized Asp residues accumulate in proteins during the ageing process.

A rapid, comprehensive liquid chromatography-mass spectrometry (LC-MS)-based survey of the Asp isomers in crystallins from human cataract lenses

Cataracts are caused by clouding of the eye lens and may lead to partial or total loss of vision. The mechanism of cataract development, however, is not well understood. It is thought that abnormal aggregates of lens proteins form with age, causing loss of lens clarity and development of the cataract. Lens proteins are composed of soluble α-, β-, and γ-crystallins, and as long lived proteins, they undergo post-translational modifications including isomerization, deamidation, and oxidation, which induce insolubilization, aggregation, and loss of function that may lead to cataracts. Therefore, analysis of post-translational modifications of individual amino acid residues in proteins is important. However, detection of the optical isomers of amino acids formed in these proteins is difficult because optical resolution is only achieved using complex methodology. In this study, we describe a new method for the analysis of isomerization of individual Asp residues in proteins using LC-MS and the corresponding synthetic peptides containing the Asp isomers. This makes it possible to analyze isomers of Asp residues in proteins precisely and quickly. We demonstrate that Asp-58, -76, -84, and -151 of αA-crystallin and Asp-62 and -96 of αB-crystallin are highly converted to lβ-, dβ-, and dα-isomers. The amount of isomerization of Asp is greater in the insoluble fraction at all Asp sites in lens proteins, therefore indicating that isomerization of these Asp residues affects the higher order structure of the proteins and contributes to the increase in aggregation, insolubilization, and disruption of function of proteins in the lens, leading to the cataract.

Co-localisation of advanced glycation end products and D-β-aspartic acid-containing proteins in gelatinous drop-like corneal dystrophy

PURPOSE

Gelatinous drop-like corneal dystrophy (GDLD), also known as familial subepithelial corneal amyloidosis, is an autosomal recessive disorder that causes progressive corneal opacity due to accumulation of amyloid fibrils in the corneal stroma. Genetic analyses have revealed that a mutation in membrane component chromosome 1 surface marker 1 gene is responsible for GDLD. However, the mechanism of amyloid formation in the corneal stroma remains unclear. The present study attempted to reveal the role of advanced glycation end products (AGE) and d-amino acids in amyloid formation in GDLD.

METHODS

Informed consent was obtained from five patients with GDLD, three patients with bullous keratopathy and three patients with interstitial keratitis and all the specimens were analysed. Localisation of amyloid fibrils was analysed using Congo-red and thioflavin T staining. In addition, the localisation of AGE (N(ε)-carboxy(methyl)-L-lysine, pyrraline and pentosidine) and D-β-aspartic acid-containing proteins, a major form of d-amino acid-containing proteins, was analysed immunohistochemically.

RESULTS

In all GDLD specimens, strong immunoreactivity to AGE and D-β-aspartic acid-containing proteins was detected in the subepithelial amyloid-rich region. In contrast, amyloid fibrils, AGE, or D-amino acid-containing proteins were slightly detected in the corneal stroma of patients with bullous keratopathy and interstitial keratitis.

CONCLUSIONS

Abnormally accumulated proteins rich in AGE and D-β-aspartic acid co-localise in the amyloid lesions in GDLD. These results indicate that non-enzymatic post-translational modifications of proteins, including AGE formation and isomerisation of aspartyl residues, will be the cause as well as the result of amyloid fibril formations in GDLD.

Analysis of D-β-aspartyl isomers at specific sites in proteins

Recent studies have shown that biologically uncommon D-β-aspartic acid residues accumulate in specific proteins during the aging process. However, aspartyl residues are not racemized uniformly because D-Asp appears to be confined to particular sites in these proteins. We here describe the method to identify the specific sites of D-β-aspartic acids inversion in proteins.

Age estimation of bloodstains: a preliminary report based on aspartic acid racemization rate

This study describes an innovative application of a well-established method of age determination. The conventional method of aspartic acid racemization (AAR) is based on estimation of the d-l-aspartic acid ratio in slow turnover tissues, such as tooth tissue, to reflect the age of an individual. This method has been recently applied to age estimation in forensic investigations, and is also widely used for archeological dating of fossils. We suggest that the aspartic acid racemization method could be applied to a significant, although unresolved, forensic issue: that of bloodstain dating. Standard kinetic experiments were used to describe the characteristics of the racemization reaction in bloodstains, which were then employed to estimate the age of various samples. The soluble protein fraction of a bloodstain produced a stronger correlation between elapsed time and d-aspartic acid content than total amino acid fractions. According to our preliminary results, the time lapse after the creation of a bloodstain can be determined ex vivo by measuring the extent of aspartic acid racemization. Our analysis highlights the need for further study into the preservation and composition of bloodstains to assist in further development of this pioneering application.

Molecular pathology and age estimation

Over the course of our lifetime a stochastic process leads to gradual alterations of biomolecules on the molecular level, a process that is called ageing. Important changes are observed on the DNA-level as well as on the protein level and are the cause and/or consequence of our 'molecular clock', influenced by genetic as well as environmental parameters. These alterations on the molecular level may aid in forensic medicine to estimate the age of a living person, a dead body or even skeletal remains for identification purposes. Four such important alterations have become the focus of molecular age estimation in the forensic community over the last two decades. The age-dependent accumulation of the 4977bp deletion of mitochondrial DNA and the attrition of telomeres along with ageing are two important processes at the DNA-level. Among a variety of protein alterations, the racemisation of aspartic acid and advanced glycation endproducs have already been tested for forensic applications. At the moment the racemisation of aspartic acid represents the pinnacle of molecular age estimation for three reasons: an excellent standardization of sampling and methods, an evaluation of different variables in many published studies and highest accuracy of results. The three other mentioned alterations often lack standardized procedures, published data are sparse and often have the character of pilot studies. Nevertheless it is important to evaluate molecular methods for their suitability in forensic age estimation, because supplementary methods will help to extend and refine accuracy and reliability of such estimates.

Elastin-derived peptides: matrikines critical for glioblastoma cell aggressiveness in a 3-D system

In the most common primary brain tumors, malignant glioma cells invade the extracellular matrix (ECM) and proliferate rapidly in the cerebral tissue, which is mainly composed of hyaluronan (HA) along with the elastin present in the basement membrane of blood vessels. To determine the role of ECM components in the invasive capacity of glioma cell lines, we developed a 3-D cell-culture system, based on a hydrogel in which HA can be coreticulated with kappa-elastin (HA-kappaE). Using this system, the invasiveness of cells from four glioma cell lines was dramatically increased by the presence of kappaE and a related, specific peptide (VGVAPG)(3). In addition, MMP-2 secretion increased and MMP-12 synthesis occurred. Extracellular injections of kappaE or (VGVAPG)(3) provoked a pronounced and dose-dependent increase in [Ca(2+)](i). kappaE significantly enhanced the expression of the genes encoding elastin-receptor and tropoelastin. We propose the existence of a positive feedback loop in which degradation of elastin generates fragments that stimulate synthesis of tropoelastin followed by further degradation as well as migration and proliferation of the very cells responsible for degradation. All steps in this ECM-based loop could be blocked by the addition of either of the EBP antagonists, lactose, and V-14 peptide, suggesting that the loop itself should be considered as a new therapeutic target.

Comparison of aspartic acid racemization between mammoth and human dentinal tissues

OBJECTIVE

Comprehensive research has revealed the complexity and heterogeneity of amino acid racemization (AAR) in biological samples. Therefore, to date, inherent uncertainties in relative dating as well as in determination of age at death have highlighted the significance of further investigations to explore aspartic acid kinetics in biominerals. Here we present data on an archaeological sample obtained from a mammoth tusk, in comparison to a previously well-described biomineral, to modern human dentin.

DESIGN

Since no experimental investigations were carried out on this topic earlier, we provide the first estimates on racemization kinetics and time dependent tendencies in mammoth dentin. We analysed our samples using a protocol, which has been adopted for tooth dentin investigation. We measured different racemization rates amongst mammoth dentin layers.

RESULTS AND CONCLUSIONS

Significantly, an overall low racemization rate was detected compared to human dentin. Kinetic experiments were performed by heating the samples, and linear correlations were established between racemization rates and heating time. The results allow us to derive racemization rate constants and activation energy for both samples. Extrapolation for ambient temperature showed increased velocity in mammoth dentin, which can be explained by biodeterioration of ancient collagen and by diagenetic changes in amino acid composition influenced by environmental conditions.

Age estimation in children by measurement of open apices in teeth

This paper concerns a method for estimating the age of children based on their teeth. The sample consisted of 455 Italian white children (213 boys, 242 girls) aged between 5 and 15 years. The purpose of the present investigation was to present a method for assessing chronological age based on the relationship between age and measurement of the open apices in teeth. Pearson's correlation coefficients between age and these variables showed that the correlations between age and the open apices in teeth were significant and negative. Furthermore, gender and the number of teeth with the apical end of the root canals completely closed (N(0)) showed a significant correlation with chronological age. With the aid of a stepwise multiple regression model, a linear relationship between open apices, N(0), and age was shown. Statistical analysis indicated that these morphological variables explain 83.6% of the variations in estimated chronological age. The median of residual errors between the actual and estimated ages was -0.035 years [interquartile range (IQR)=1.18 years].