The degradation of intracrystalline mollusc shell proteins: A proteomics study of Spondylus gaederopus

Sakalauskaite, Jorune; Mackie, Meaghan; Taurozzi, Alberto J.; Collins, Matthew J.; Marin, Frédéric; Demarchi, Beatrice

doi:10.1016/j.bbapap.2021.140718

Cited by 5 publications

(5 citation statements)

References 96 publications

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“…Evaluating the tools on human and mouse antibody data, the authors concluded that Casanovo and PointNovo show improved peptide recall across different enzymes and datasets compared with competing methods. Second, Tran et al [76] have evaluated PEAKS, PointNovo, Casanovo, and GraphNovo on five datasets: human tryptic data, Method Year Application Ind DeepNovo 2020 Detection of neoantigens [77] 2021 De novo sequencing in metaproteomics [78] ✓ 2021 Detection of neoantigens [79] ✓ 2021 Detection of junction peptides [80] ✓ 2021 Detection of shell proteins [81] ✓ 2023 Detection of neuropeptides [82] ✓ 2023 Detection of proteasome-generated spliced and non-spliced peptides [83] ✓ 2023 Antibody sequencing [84] ✓ 2023 Detection of short peptides [85] ✓ 2023 Noncanonical antigen detection [86] ✓ 2023 Detection of neoantigens [87] 2024 Antibody sequencing [88] ✓ 2024 Detection of neoantigens [89] 2024 Detection of venom proteins [ ✓ 2022 Detection of neoantigens [103] ✓ Table 3: Applications of deep learning de novo sequencing methods. The final column ("Ind") indicates whether the application was published independently of the original authors of the work.…”

Section: Performance Comparisonsmentioning

confidence: 99%

Deep learning methods for de novo peptide sequencing

Bittremieux,

Ananth,

Fondrie

et al. 2024

Preprint

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Protein tandem mass spectrometry data is most often interpreted by matching observed mass spectra to a protein database derived from the reference genome of the sample being analyzed. In many application domains, however, a relevant protein database is unavailable or incomplete, and in such settings de novo sequencing is required. Since the introduction of the DeepNovo algorithm in 2017, the field of de novo sequencing has been dominated by deep learning methods, which use large amounts of labeled mass spectrometry data to train multi-layer neural networks to translate from observed mass spectra to corresponding peptide sequences. Here, we describe these deep learning methods, outline procedures for evaluating their performance, and discuss the challenges in the field, both in terms of methods development and evaluation protocols.

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Section: Performance Comparisonsmentioning

confidence: 99%

Deep learning methods for de novo peptide sequencing

Bittremieux,

Ananth,

Fondrie

et al. 2024

Preprint

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Section: Organic Compositionmentioning

confidence: 99%

“…The content of Si also exceeds 0.1% in all the samples under study and can be explained by the impact of silicon oxide on the shell in the process of friction on the sea sand bottom or the sand in the area of coastal discharges. In fact, clam shells also contain organic matters that serve reinforcement, protection, and cover functions [64]. The basic organic elements in the composition of clam shells are conchiolin protein [65], carbohydrates, lipids, free peptides, pigments, and other metabolites [66].…”

Section: Organic Compositionmentioning

confidence: 99%

“…According to the data introduced, the common motive of all spectra corresponds to the IR spectrum of calcium carbonate, which speaks for the fact that inorganic components dominate in the clam shells from coastal discharges. Nevertheless, according to the data [64], the protein component in clam shells may be preserved for a longer time and serves as a time marker in geological investigations. The peak of bands' vibrations presented in the FTIR spectra (Figure 4) can be divided into three groups: 1-peaks corresponding to bands vibrations in calcium carbonate (2980, 2878, 2510, 1800, 1440, 872, 847, 712, and 700 cm −1 ); 2-peaks corresponding to bands' vibrations in organic structures and water (3600-3000, 2925, 1440, 1082, and 830 cm −1 ); 3-hard-to-identify peaks or peaks corresponding to vibrations of various bands between various elements (2980, 2878, 2510, 1800, 1440, 1160, 1082, and 1020 cm −1 ).…”

Section: Organic Compositionmentioning

confidence: 99%

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Study of the Composition and Properties of Bivalve Mollusk Shells as Promising Bio-Indifferent Materials for Photocatalytic Applications (Example of Practical Use)

Zaitsev,

Astapov

2023

Catalysts

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This paper studies the composition and properties of shells of bivalve mollusks (Crenomytilus grayanus, Callista brevisiphonata, and Mizuhopecten yessoensis) from coastal discharges with a view to the possibility of their use in photocatalytic water treatment systems. The clam shells are considered in terms of application in the form of a powder material as a precursor for creating photocatalysts, and also as a carrier of photocatalytic coatings. It was shown that the main phase composing the shell material was calcium carbonate in two crystallographic modifications—calcite and aragonite. The presence of inorganic impurities in all studied clam shells did not exceed one mass percent. The main share was made up of elements included in the composition of calcium carbonate, which confirmed the high bio-indifference of the materials under study. Depending on the physiological and environmental features of the structure of clam shells, different contents of the organic component in their composition were observed. The granulometric characteristics of crushed clam shells (average diameter, specific surface area, and distribution modality) were studied. It was shown that the maximum values of bending strength of 5 MPa and compressive strength of 2 MPa are characterized by Mizuhopecten yessoensis shells with the lowest porosity of 2.91%. The features of sorption and photosorption processes of both whole and crushed shells in relation to four organic dyes at different temperatures and degrees of illumination were studied. Based on crushed shells of Mizuhopecten Yessoensis and titanium dioxide, functional materials (CaxTiyOz) were obtained, and their morphology and photocatalytic properties were studied. An example of the practical use of clam shells as a carrier of a photocatalytic coating is given.

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“…Despite that it is known that biominerals can preserve proteins at room temperature for a long time, it is unclear that the extent of protein degradation under high temperature. A recent study found that the shell proteins of the thorny oyster, Spondylus gaederopus can still be identified after heating the shell at 140 • C (Sakalauskaite et al, 2021). In this study, to find out if proteins can be extracted and identified from seashells heated at even higher temperatures, we extracted proteins from toasted abalone shells (200, 300 • C) and used liquid chromatography tandem-mass spectrometry (LC-MS/MS) to analyze their proteome.…”

Section: Introductionmentioning

confidence: 99%

Proteins Are Well-Preserved in Shells Toasted at 300°C Revealed by Proteomics

Huang

et al. 2022

Front. Mar. Sci.

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The development of protein anti-degradation strategies is important for storage at ambient conditions, for example in vaccine storage. Despite that it is known that biominerals, typical inorganic-organic composites, can preserve proteins at room temperature for a long time, it is unclear the extent of protein degradation under high temperatures. In this study, we examined remaining proteins in the toasted abalone shell under high temperatures (200 and 300°C) by biomineral proteomics method. Surprisingly, 21 proteins including carbonic anhydrase, hemocyanin, actin can still be identified from shells even after toasting under 300°C, not much decreased compared to that in the 200°C-treated and the native shell. However, the microstructure and composition (both mineral and organic matrix) of shells were altered significantly revealed by scanning electron microscopy, infrared spectroscopy, and X-ray diffraction. The well-preserved proteins may be partially due to the sacrifice of mineral/organic interfaces and the formation of nanopores in the shell at high temperatures. Moreover, the extracted proteins from both groups were able to affect calcium carbonate in vitro, indicating certain remaining bioactivities of proteins. This study has potential implications in various fields such as protein storage at high temperatures and palaeoproteomics.

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The degradation of intracrystalline mollusc shell proteins: A proteomics study of Spondylus gaederopus

Cited by 5 publications

References 96 publications

Deep learning methods for de novo peptide sequencing

Deep learning methods for de novo peptide sequencing

Study of the Composition and Properties of Bivalve Mollusk Shells as Promising Bio-Indifferent Materials for Photocatalytic Applications (Example of Practical Use)

Proteins Are Well-Preserved in Shells Toasted at 300°C Revealed by Proteomics

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