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oai:figshare.com:article/34021821 2026-09-29T09:27:23Z category_25270 category_24829 category_24748 portal_549 item_type_3 month_year_09_2026

Collagen-alpha-2(VIII)-chain Degradome Foundation Atlas Axel Petzold (7076261) Theoretical and computational chemistry not elsewhere classified Ophthalmology and optometry not elsewhere classified Neurosciences not elsewhere classified Fuchs endothelial corneal dystrophy 1 FECD1 posterior polymorphous corneal dystrophy 2 PPCD2 arterial wall remodeling pial membrane This Figshare repository hosts the Collagen Alpha-2(VIII) Chain Degradome Foundation Atlas (Version 1). It is a comprehensive in silico reconstruction of the theoretical peptides that could be generated by proteolytic cleavage of the human collagen alpha-2(VIII) chain (COL8A2).The atlas is an open-access computational reference for researchers in proteomics, degradomics, mass spectrometry, extracellular matrix biology, ophthalmology, vascular biology and biomarker discovery. It systematically maps the peptide fragments that could arise from COL8A2 turnover and enzymatic processing. This gives a degradome-centred view of the peptides that may be generated during basement membrane and extracellular matrix remodeling.<h2 dir="ltr">Biological Context</h2>Collagen alpha-2(VIII) is encoded by COL8A2 and is one of the two alpha chains of type VIII collagen. Type VIII collagen is a short-chain, network-forming collagen. Its chains have a short central triple-helical region flanked by non-collagenous domains, and they assemble as homotrimers or as heterotrimers with collagen alpha-1(VIII) (COL8A1).Type VIII collagen is a major component of Descemet's membrane, the specialized basement membrane secreted by the corneal endothelium, where it forms a distinctive hexagonal lattice. It is also produced by vascular endothelial cells and smooth muscle cells. There it contributes to the extracellular matrix of blood vessel walls and has been linked to vascular remodeling.The synthesis, deposition, remodeling and proteolytic turnover of type VIII collagen can release fragments and peptides that carry information about matrix dynamics beyond what measurements of the intact protein provide. Mapping the theoretical COL8A2 fragment landscape therefore lays a foundation for studying collagen-derived peptides associated with corneal and vascular matrix turnover, tissue remodeling and disease.Variants in COL8A2 are associated with inherited corneal endothelial disorders, including early-onset Fuchs endothelial corneal dystrophy and posterior polymorphous corneal dystrophy. These conditions highlight the importance of type VIII collagen in corneal structure and endothelial function. A systematic COL8A2 degradome reference can therefore support work on peptide signatures in ocular, vascular and connective-tissue biology.<h3 dir="ltr">Key Features of the Proteomics Dataset</h3>The atlas provides a systematic computational representation of the theoretical peptide space of COL8A2. It includes:<ul><li>Predicted enzymatic and chemical cleavage sites across the collagen alpha-2(VIII) sequence</li><li>Possible contiguous peptide fragments generated by proteolytic cleavage, spanning both the triple-helical and non-collagenous regions</li><li>Physicochemical and biochemical characteristics for each fragment</li><li>Sequence-derived properties relevant to peptide characterization and detection by mass spectrometry</li></ul>Mass Spectrometry and Peptide Metrics:<ul><li>Molecular weight</li><li>Mass-to-charge ratio (m/z)</li><li>Net charge</li><li>Isoelectric point (pI)</li></ul>Biochemical and Biophysical Features:<ul><li>Hydrophobicity</li><li>Boman index</li><li>Instability index</li><li>Aliphatic index</li></ul>Together, these parameters form a feature-rich reference for evaluating COL8A2-derived peptides. They can also help prioritize candidate fragments for downstream proteomic and mass-spectrometric work.<h3 dir="ltr">Applications in Biomarker Discovery and Biomedical Research</h3>The dataset can support a broad range of research applications:<ul><li>Targeted Proteomics: Identifying and prioritizing COL8A2-derived peptides for targeted mass-spectrometry assays.</li><li>Biomarker Discovery: Exploring collagen alpha-2(VIII)-derived peptide signatures associated with extracellular matrix turnover and tissue remodeling.</li><li>Discovery Proteomics: Generating candidate peptide lists for untargeted and discovery-based proteomic studies.</li><li>Degradomics: Investigating proteolytic processing and type VIII collagen turnover within a COL8A2-focused degradome framework.</li><li>Clinical Proteomics: Identifying candidate peptide biomarkers associated with changes in corneal, vascular and connective-tissue matrix.</li><li>Corneal and Ocular Research: Supporting studies of Descemet's membrane composition, corneal endothelial biology and matrix turnover in the eye.</li><li>Corneal Dystrophy Research: Providing a computational resource for studying COL8A2-derived peptides in Fuchs endothelial corneal dystrophy and posterior polymorphous corneal dystrophy.</li><li>Vascular Biology: Exploring type VIII collagen fragments associated with vessel wall remodeling, angiogenesis and vascular disease.</li><li>Basement Membrane Research: Characterizing potential fragments from network-forming collagens in specialized basement membranes.</li><li>Fibrosis and Tissue Remodeling: Exploring COL8A2-derived peptide signatures associated with pathological extracellular matrix changes.</li><li>Computational Biology: Enabling sequence-based degradome profiling, peptide prioritization and comparative analysis across collagen types.</li><li>Assay Development: Supporting the selection and characterization of candidate COL8A2 peptides for experimental validation.</li></ul><h3 dir="ltr">Data Inclusion and Reproducibility</h3>Version 1 covers the wild-type human collagen alpha-2(VIII) chain reference sequence (UniProt accession number P25067). It provides a systematic theoretical representation of its potential degradome, including contiguous peptide fragments and their calculated physicochemical properties.The dataset represents a theoretical fragment space, not a catalogue of experimentally confirmed peptides. A predicted fragment's presence in the atlas does not establish that the peptide is generated in vivo, that it remains stable in biological samples, or that a given mass-spectrometric platform can detect it. Experimental proteomics, degradomics and mass-spectrometry studies are needed to establish the generation, stability, abundance and detectability of individual COL8A2-derived peptides.Future releases may add disease-associated sequence variants, post-translational modifications, experimentally validated cleavage products, tissue-specific degradome profiles and complementary experimental proteomics data. These additions will progressively connect the theoretical COL8A2 peptide landscape with experimentally informed models of type VIII collagen turnover, corneal and vascular biology, basement membrane remodeling and disease-associated matrix changes. 2026-09-29T09:27:23Z Dataset Dataset 10.5522/04/34021821.v1 https://figshare.com/articles/dataset/Collagen-alpha-2_VIII_-chain_Degradome_Foundation_Atlas/34021821 CC0