scholarly journals Heterogeneity in Proline Hydroxylation of Fibrillar Collagens Observed by Mass Spectrometry

2021 ◽  
Author(s):  
Michele Kirchner ◽  
Haiteng Deng ◽  
Yujia Xu
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Type I Collagen ◽  
Single Letter ◽  
Major Protein ◽  
Type I ◽  
Post Translational Modification ◽  
Functional Roles ◽  
Commercial Sources ◽  
And Function

AbstractCollagen is the major protein in the extracellular matrix and plays vital roles in tissue development and function. Collagen is also one of the most processed proteins in its biosynthesis. The most prominent post-translational modification (PTM) of collagen is the hydroxylation of Pro residues in the Y-position of the characteristic (Gly-Xaa-Yaa) repeating amino acid sequence of a collagen triple helix. Recent studies using mass-spectrometry (MS) and tandem MS sequencing (MS/MS) have revealed unexpected hydroxylation of Pro residues in the X-positions (X-Hyp). The newly identified X-Hyp residues appear to be highly heterogeneous in location and percent occupancy. In order to understand the dynamic nature of the new X-Hyps and their potential impact on applications of MS and MS/MS for collagen research, we sampled four different collagen samples using standard MS and MS/MS techniques. We found considerable variations in the degree of PTMs of the same collagen from different organisms and/or tissues. The rat tail tendon type I collagen is particularly variable in terms of both over-hydroxylation of Pro in the X-position and under-hydroxylation of Pro in the Y-position. In contrast, only a few unexpected PTMs in collagens type I and type III from human placenta were observed. The reproducibility of the different sequencing efforts of the same sample is also limited especially when the modified species are present at a low population, presumably due to the unpredictable nature of the ionization process. Additionally, despite the heterogeneous preparation and sourcing, collagen samples from commercial sources do not show elevated variations in PTMs compared to samples prepared from a single tissue and/or organism. These findings will contribute to the growing body of information regarding the PTMs of collagen by MS technology, and culminate to a more comprehensive understanding of the extent and the functional roles of the PTMs of collagen.Abbreviations pageBoth the single letter and the three letter abbreviations of an amino acid will be used with the following additions: Hyp or O stands for 4R-hydroxylated proline and 3Hyp stands for 3- hydroxylated proline. When needed for clarity, the lower case single letter abbreviation will be used to represent the genomic DNA sequence, and upper case ones the sequence seen in the peptides.

scholarly journals Heterogeneity in proline hydroxylation of fibrillar collagens observed by mass spectrometry

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0250544
Author(s):  
Michele Kirchner ◽  
Haiteng Deng ◽  
Yujia Xu
Keyword(s):  
Mass Spectrometry ◽  
Type I Collagen ◽  
Major Protein ◽  
Type I ◽  
Post Translational Modification ◽  
Functional Roles ◽  
Collagen Triple Helix ◽  
Commercial Sources ◽  
Tail Tendon ◽  
And Function

Collagen is the major protein in the extracellular matrix and plays vital roles in tissue development and function. Collagen is also one of the most processed proteins in its biosynthesis. The most prominent post-translational modification (PTM) of collagen is the hydroxylation of Pro residues in the Y-position of the characteristic (Gly-Xaa-Yaa) repeating amino acid sequence of a collagen triple helix. Recent studies using mass spectrometry (MS) and tandem MS sequencing (MS/MS) have revealed unexpected hydroxylation of Pro residues in the X-positions (X-Hyp). The newly identified X-Hyp residues appear to be highly heterogeneous in location and percent occupancy. In order to understand the dynamic nature of the new X-Hyps and their potential impact on applications of MS and MS/MS for collagen research, we sampled four different collagen samples using standard MS and MS/MS techniques. We found considerable variations in the degree of PTMs of the same collagen from different organisms and/or tissues. The rat tail tendon type I collagen is particularly variable in terms of both over-hydroxylation of Pro in the X-position and under-hydroxylation of Pro in the Y-position. In contrast, only a few unexpected PTMs in collagens type I and type III from human placenta were observed. Some observations are not reproducible between different sequencing efforts of the same sample, presumably due to a low population and/or the unpredictable nature of the ionization process. Additionally, despite the heterogeneous preparation and sourcing, collagen samples from commercial sources do not show elevated variations in PTMs compared to samples prepared from a single tissue and/or organism. These findings will contribute to the growing body of information regarding the PTMs of collagen by MS technology, and culminate to a more comprehensive understanding of the extent and the functional roles of the PTMs of collagen.

Collagen-the Ultrastructural Element of the Bone Matrix

2018 ◽  
Vol 69 (7) ◽  
pp. 1706-1709
Author(s):  
Nicoleta Dumitru ◽  
Andra Cocolos ◽  
Andra Caragheorgheopol ◽  
Constantin Dumitrache ◽  
Ovidiu Gabriel Bratu ◽  
...  
Keyword(s):  
Type I Collagen ◽  
Bone Microarchitecture ◽  
Complex Structure ◽  
Bone Matrix ◽  
Organic Matrix ◽  
Bone Diseases ◽  
Bone Collagen ◽  
Type I ◽  
New Therapeutic Approaches ◽  
And Function

There is an increased interest and more studies highlight the fact that bone strength depends not only on bone tissue quantity, but also on its quality, which is characterized by the geometry and shape of bones, trabecular bone microarchitecture, mineral content, organic matrix and bone turnover. Fibrillar type I collagen is the major organic component of bone matrix, providing form and a stable template for mineralization. The biomedical importance of collagen as a biomaterial for medical and cosmetic purposes and the improvement of the molecular, cellular biology and analytical technologies, led to increasing interest in establishing the structure of this protein and in setting of the relationships between sequence, structure, and function. Bone collagen crosslinking chemistry and its molecular packing structure are considered to be distinct features. This unique post-translational modifications provide to the fibrillar collagen matrices properties such as tensile strength and viscoelasticity. Understanding the complex structure of bone type I collagen as well as the dynamic nature of bone tissues will help to manage new therapeutic approaches to bone diseases.

scholarly journals Structural and Functional Consequences of Age-Related Isomerization in α-Crystallins

2018 ◽  
Author(s):  
Yana A. Lyon ◽  
Dylan L. Riggs ◽  
Miranda P. Collier ◽  
Matteo T. Degiacomi ◽  
Justin L.P. Benesch ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Amino Acid ◽  
Native Mass Spectrometry ◽  
Salt Bridges ◽  
Loss Of Function ◽  
Post Translational Modification ◽  
Age Related ◽  
Αb Crystallin ◽  
Functional Consequences

AbstractLong-lived proteins are subject to spontaneous degradation and may accumulate a range of modifications over time, including subtle alterations such as isomerization. Recently, tandem-mass spectrometry approaches have enabled the identification and detailed characterization of such peptide isomers, including those differing only in chirality. However, the structural and functional consequences of these perturbations remain largely unexplored. Here we examine the site-specific impact of isomerization of aspartic acid and epimerization of serine in human αA- and αB-crystallin. From a total of 81 sites of modification identified in aged eye lenses, four (αBSer59, αASer162, αBAsp62, αBAsp109) map to crucial oligomeric interfaces. To characterize the effect of isomerization on quaternary assembly, molecular dynamics calculations and native mass spectrometry experiments were performed on recombinant forms of αA- and αB-crystallin that incorporate, or mimic, isomerized residues. In all cases, oligomerization is significantly affected, with epimerization of a single serine residue (αASer162) sufficing to weaken inter-subunit binding dramatically. Furthermore, phosphorylation of αBSer59, known to play an important regulatory role in oligomerization, is severely inhibited by serine epimerization and altered by isomerization of nearby αBAsp62. Similarly, isomerization of αBAsp109 disrupts a vital salt-bridge with αBArg120, a loss previously shown to yield aberrant oligomerization and aggregation in several disease variants. Our results illustrate how isomerization of amino-acid residues, which may seem like a minor structural perturbation, can have profound consequences on protein assembly and activity by disrupting specific hydrogen bonds and salt bridges.Significance StatementProteins play numerous critical roles in our bodies but suffer damage with increasing age. For example, isomerization is a spontaneous post-translational modification that alters the three-dimensional connectivity of an amino acid, yet remains invisible to traditional proteomic experiments. Herein, radical-based fragmentation was used for isomer identification while molecular dynamics and native mass spectrometry were utilized to assess structural consequences. The results demonstrate that isomerization disrupts both oligomeric assembly and phosphorylation in the α-crystallins, which are long-lived proteins in the lens of the eye. The loss of function associated with these modifications is likely connected to age-related diseases such as cataract and neurodegenerative disorders, while the methodologies we present represent a framework for structure-function studies on other isomerized proteins.

scholarly journals EFFECT OF COLLAGEN I GEL ON APOPTOSIS OF RAT HEPATIC STELLATE CELLS

2013 ◽  
Vol 56 (2) ◽  
pp. 73-79
Author(s):  
Lenka Bittnerová ◽  
Alena Jiroutová ◽  
Emil Rudolf ◽  
Martina Řezáčová ◽  
Jiří Kanta
Keyword(s):  
Hepatic Stellate Cells ◽  
Type I Collagen ◽  
Collagen Gel ◽  
Stellate Cells ◽  
Type I ◽  
Function Type ◽  
Fibrotic Liver ◽  
Normal Rat ◽  
And Function

Activated hepatic stellate cells (HSC) are a major source of fibrous proteins in cirrhotic liver. Inducing or accelerating their apoptosis is a potential way of liver fibrosis treatment. Extracellular matrix (ECM) surrounding cells in tissue affects their differentiation, migration, proliferation and function. Type I collagen is the main ECM component in fibrotic liver. We have examined how this protein modifies apoptosis of normal rat HSC induced by gliotoxin, cycloheximide and cytochalasin D in vitro and spontaneous apoptosis of HSC isolated from CCl4-damaged liver. We have found that type I collagen gel enhances HSC apoptosis regardless of the agent triggering this process.

scholarly journals Chitin-binding proteins in potato (Solanum tuberosum L.) tuber. Characterization, immunolocalization and effects of wounding

1992 ◽  
Vol 283 (3) ◽  
pp. 813-821 ◽  
Author(s):  
D J Millar ◽  
A K Allen ◽  
C G Smith ◽  
C Sidebottom ◽  
A R Slabas ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Proteins ◽  
Solanum Tuberosum L ◽  
Major Protein ◽  
Post Translational Modification ◽  
Terminal Amino Acid ◽  
Terminal Amino ◽  
Terminal Amino Acid Sequence

Tubers of potato (Solanum tuberosum L.) contain a number of chitin-binding proteins which have possible functions in defence against pathogens. A major protein of the tuber is the chitin-binding lectin which has been further characterized with respect to its antigenicity and N-terminal amino acid sequence. By using an antiserum monospecific for tuber lectin in unwounded potato the protein was found in the cytoplasm and vacuole, unusually for a hydroxyproline-rich glycoprotein, but consistent with its soluble nature in subcellular extracts. Little increased synthesis of the lectin precursor or the post-translationally modified form could be demonstrated in excised potato tuber discs. However, after wounding there is increased synthesis of another hydroxyproline-containing glycoprotein of Mr 57,000, which binds to chitin and shares common epitopes with the lectin. In comparison with the tuber lectin, this novel glycoprotein contains less hydroxyproline, but from its overall composition it is clearly not an underhydroxylated form of the tuber lectin. It differed in its N-terminal amino acid sequence and was much less glycosylated, although arabinose was still present. Synthesis of the Mr-57,000 polypeptide began after the initial burst of protein synthesis and increased, reaching a peak at 24 h after wounding. The protein was produced with its enzymes of post-translational modification, prolyl hydroxylase and arabinosyltransferase, concomitantly with the marker enzymes for wounding, phenylalanine ammonia-lyase and membrane-bound phenol oxidase and peroxidase.

scholarly journals Developmentally regulated cytokeratin gene in Xenopus laevis.

1985 ◽  
Vol 5 (10) ◽  
pp. 2575-2581 ◽  
Author(s):  
J A Winkles ◽  
T D Sargent ◽  
D A Parry ◽  
E Jonas ◽  
I B Dawid
Keyword(s):  
Amino Acid ◽  
Xenopus Laevis ◽  
Intermediate Filament ◽  
Type I ◽  
Developmentally Regulated ◽  
Amino Acid Homology ◽  
Intermediate Filament Proteins ◽  
Functional Roles ◽  
Terminal Domain ◽  
Terminal Domains

We have determined the sequence of cloned cDNAs derived from a 1,665-nucleotide mRNA which transiently accumulates during Xenopus laevis embryogenesis. Computer analysis of the deduced amino acid sequence revealed that this mRNA encodes a 47-kilodalton type I intermediate filament subunit, i.e., a cytokeratin. As is common to all intermediate filament subunits so far examined, the predicted polypeptide, named XK70, contains N- and C-terminal domains flanking a central alpha-helical rod domain. The overall amino acid homology between XK70 and a human 50-kilodalton type I keratin is 47%; homology within the alpha-helical domain is 57%. The N-terminal domain, which is not completely contained in our cDNAs, is basic, contains 42% serine plus alanine, and includes five copies of a six-amino-acid repeating unit. The C-terminal domain has a high alpha-helical content and contains a region with sequence homology to the C-terminal domains of other type I and type III intermediate filament proteins. We suggest that different keratin filament subtypes may have different functional roles during amphibian oogenesis and embryogenesis.

scholarly journals Preparation and Characterization of Gelatin and Antioxidant Peptides from Gelatin Hydrolysate of Skipjack Tuna (Katsuwonus pelamis) Bone Stimulated by in vitro Gastrointestinal Digestion

Marine Drugs ◽  
2019 ◽  
Vol 17 (2) ◽  
pp. 78 ◽  
Author(s):  
Xiu-Rong Yang ◽  
Yu-Qin Zhao ◽  
Yi-Ting Qiu ◽  
Chang-Feng Chi ◽  
Bin Wang
Keyword(s):  
Amino Acid ◽  
Type I Collagen ◽  
Type I ◽  
Skipjack Tuna ◽  
Antioxidant Peptides ◽  
Gastrointestinal Digestion ◽  
Katsuwonus Pelamis ◽  
In Vitro Gastrointestinal Digestion ◽  
Gelatin Hydrolysate

In China, a large amount of fish bones are produced during the processing of tuna cans production. For full use of those by-products, gelatin (STB-G) with a yield of 6.37 ± 0.64% was extracted from skipjack tuna (Katsuwonus pelamis) bone using water at 60 °C for 8 h. Amino acid analysis showed that STB-G contained Gly (340.3 residues/1000 residues) as the major amino acid and its imino acid content was 177.3 residues/1000 residues. Amino acid composition, SDS-PAGE, and Fourier transform infrared (FTIR) spectrum investigations confirmed that the physicochemical properties of STB-G were similar to those of type I collagen from skipjack tuna bone (STB-C), but partial high molecular weight components of STB-G were degraded during the extraction process, which induced that the gelatin was easier to be hydrolyzed by protease than mammalian gelatins and was suitable for preparation of hydrolysate. Therefore, STB-G was hydrolyzed under in vitro gastrointestinal digestion (pepsin-trypsin system) and five antioxidant peptides were purified from the resulted hydrolysate (STB-GH) and identified as GPDGR, GADIVA, GAPGPQMV, AGPK, and GAEGFIF, respectively. Among the gelatin hydrolysate, fractions, and isolated peptides, GADIVA and GAEGFIF exhibited the strongest scavenging activities on 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical (EC50 0.57 and 0.30 mg/mL), hydroxyl radical (EC50 0.25 and 0.32 mg/mL), superoxide anion radical (EC50 0.52 and 0.48 mg/mL), and 2,2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical (EC50 0.41 and 0.21 mg/mL). Moreover, GADIVA and GAEGFIF showed a high inhibiting ability on lipid peroxidation in a linoleic acid model system. The strong activities of five isolated peptides profited by their small molecular sizes and the antioxidant amino acid residues in their sequences. These results suggested that five isolated peptides (STP1–STP5), especially GADIVA and GAEGFIF, might serve as potential antioxidants applied in health food industries.

scholarly journals Regulation of type I collagen mRNA in lung fibroblasts by cystine availability

1998 ◽  
Vol 331 (2) ◽  
pp. 417-422 ◽  
Author(s):  
David C. RISHIKOF ◽  
Ping-Ping KUANG ◽  
Christine POLIKS ◽  
Ronald H. GOLDSTEIN
Keyword(s):  
Amino Acids ◽  
Steady State ◽  
Amino Acid ◽  
Type I Collagen ◽  
State Level ◽  
Lung Fibroblasts ◽  
Type I ◽  
Mrna Levels ◽  
Collagen Mrna ◽  
Amino Acid Availability

The steady-state level of α1(I) collagen mRNA is regulated by amino acid availability in human lung fibroblasts. Depletion of amino acids decreases α1(I) collagen mRNA levels and repletion of amino acids induces rapid re-expression of α1(I) mRNA. In these studies, we examined the requirements for individual amino acids on the regulation of α1(I) collagen mRNA. We found that re-expression of α1(I) collagen mRNA was critically dependent on cystine but not on other amino acids. However, the addition of cystine alone did not result in re-expression of α1(I) collagen mRNA. Following amino acid depletion, the addition of cystine with selective amino acids increased α1(I) collagen mRNA levels. The combination of glutamine and cystine increased α1(I) collagen mRNA levels 6.3-fold. Methionine or a branch-chain amino acid (leucine, isoleucine or valine) also acted in combination with cystine to increase α1(I) collagen mRNA expression, whereas other amino acids were not effective. The prolonged absence of cystine lowered steady-state levels of α1(I) collagen mRNA through a mechanism involving decreases in both the rate of gene transcription as assessed by nuclear run-on experiments and mRNA stability as assessed by half-life determination in the presence of actinomycin D. The effect of cystine was not mediated via alterations in the level of glutathione, the major redox buffer in cells, as determined by the addition of buthionine sulphoximine, an inhibitor of γ-glutamylcysteine synthetase. These data suggest that cystine directly affects the regulation of α1(I) collagen mRNA.

Sign in / Sign up

Export Citation Format

Share Document