Proteomics: Concepts and applications in human medicine

Al-Amrani, Safa; Al-Jabri, Zaaima; AlZaabi, Adhari; Alshekaili, Jalila; Al-Khabori, Murtadha

doi:10.4331/wjbc.v12.i5.57

Cited by 128 publications

(92 citation statements)

References 109 publications

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“…The rapid need to understand the mechanisms and impacts of SARS-CoV-2 makes omics strategies stand out as they can offer a holistic and comprehensive view of thousands of molecules ( Colinge & Bennett, 2007 ; Haas, Muralidharan, Krogan, Kaake, & Hüttenhain, 2021 ). The ability to study alterations of a large number of proteins and transcripts in a single experiment is attractive ( Al-Amrani, Al-Jabri, Al-Zaabi, Alshekaili, & Al-Khabori, 2021 ). Furthermore, accessing the modulation of molecules based on a clinical status can answer many questions about a given disease ( Amiri-Dashatan, Koushki, Abbaszadeh, Rostami-Nejad, & Rezaei-Tavirani, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data

Macedo-da-Silva

Rosa-Fernandes²,

Marie³

et al. 2022

Advances in Protein Chemistry and Structural Biology

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Section: Discussionmentioning

confidence: 99%

Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data

Macedo-da-Silva

Rosa-Fernandes²,

Marie³

et al. 2022

Advances in Protein Chemistry and Structural Biology

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“…Mouse sera (30 μg) from different infection time points (14,28,42, and 56 days post-infection) were separated using 12% SDS-PAGE. Protein bands were stained with Coomassie Blue G. After de-staining, protein bands were cut into 12 small pieces for in-gel digestion.…”

Section: Separation Of Protein From Mouse Serummentioning

confidence: 99%

Discovery of Schistosoma mekongi circulating proteins and antigens in infected mouse sera

et al. 2022

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Schistosomiasis is a neglected tropical disease caused by an infection of the parasitic flatworms schistosomes. Schistosoma mekongi is a restricted Schistosoma species found near the Mekong River, mainly in southern Laos and northern Cambodia. Because there is no vaccine or effective early diagnosis available for S. mekongi, additional biomarkers are required. In this study, serum biomarkers associated with S. mekongi-infected mice were identified at 14-, 28-, 42-, and 56-days post-infection. Circulating proteins and antigens of S. mekongi in mouse sera were analyzed using mass spectrometry-based proteomics. Serine protease inhibitors and macrophage erythroblast attacher were down-regulated in mouse sera at all infection timepoints. In addition, 54 circulating proteins and 55 antigens of S. mekongi were identified. Notable circulating proteins included kyphoscoliosis peptidase and putative tuberin, and antigens were detected at all four infection timepoints, particularly in the early stages (12 days). The putative tuberin sequence of S. mekongi was highly similar to homologs found in other members of the genus Schistosoma and less similar to human and murine sequences. Our study provided the identity of promising diagnostic biomarkers that could be applicable in early schistosomiasis diagnosis and vaccine development.

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“…Consequently, surfactants can provide valuable information about the protein structure depending on how they affect it. This can be combined with traditional methods of investigating proteins in the field of proteomics, where the structure and function of proteins are systematically and comprehensively evaluated, providing a unique and global overview of how these vital molecules interact and cooperate in organisms. − …”

Section: Introductionmentioning

confidence: 99%

Self-Assembled Protein–Surfactant Nanoaggregates for Tunable Peptide Bond Hydrolysis by Polyoxometalate Nanoclusters

Savić

Marcano

Swinnen

et al. 2022

ACS Appl. Nano Mater.

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The development of robust artificial proteases is of crucial importance for the study of proteins since natural proteases only retain their proteolytic activity under specific conditions. The presence of surfactants, which aid in solubilizing proteins and in probing their structure, is particularly detrimental to natural proteases. Therefore, artificial proteases that can function in the presence of surfactants are needed. Here, we report the hydrolysis of horse heart myoglobin (Mb) in the presence of a Zr(IV)-substituted Keggin polyoxometalate cluster (Et2NH2)8[{α-PW11O39Zr-(μ-OH)(H2O)}2]·7H2O (Zr–K 2:2) as an artificial protease and different surfactants: sodium dodecyl sulfate (SDS), N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (Zw3-12), and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS). The formation of nanoaggregates consisting of micellar structures containing the protein, the surfactant, and Zr–K 2:2 was detected by dynamic light scattering and conductivity measurements. Hydrolytic reactions were monitored by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the hydrolytic efficiency was observed to increase in the presence of all three surfactants, but the fragmentation pattern was different depending on the nature of the surfactant used. Furthermore, a multitechnique approach combining cyclic voltammetry, 31P nuclear magnetic resonance, fluorescence, circular dichroism, and UV–vis spectroscopy was used to gain a better understanding of the protease activity of Zr–K 2:2 in the presence of surfactants. Based on this approach, a general model for the interactions typically observed in protein/surfactant/POM ternary nanoassemblies has been proposed. The hydrolytic efficiency of a POM nanocluster toward a protein in the presence of surfactants was found to depend on (i) the structure of the protein and accessibility of the cleavage sites, (ii) the structure of the surfactants, (iii) the ease of exchange between the POM and the surfactants on the surface of the protein, and (iv) the influence of surfactants on the speciation of the POM catalyst.

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Proteomics: Concepts and applications in human medicine

Cited by 128 publications

References 109 publications

Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data

Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data

Discovery of Schistosoma mekongi circulating proteins and antigens in infected mouse sera

Self-Assembled Protein–Surfactant Nanoaggregates for Tunable Peptide Bond Hydrolysis by Polyoxometalate Nanoclusters

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