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Proteomics and Protein Biochemistry in Diseases

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Special Issue Information
Keywords
Published Papers

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Macromolecular Chemistry".

Deadline for manuscript submissions: closed (15 October 2021) | Viewed by 10044

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Special Issue Editor

Dr. Jiří Petrák

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Guest Editor

Biotechnology and Biomedical Center of the Academy of Sciences and Charles University (BIOCEV) in Vestec, Czech Republic
Interests: proteins; proteomics; molecular pathology

Special Issue Information

Dear Colleagues,

Advanced methods of protein biochemistry and proteomics enable focused and detailed studies of protein structure, expression and function, or provide holistic molecular snapshots of protein landscapes of tissues, cells or body fluids. Their application in disease-oriented research unearths key protein players, elucidates underlying pathological processes, identifies clinically useful protein biomarkers and novel drug targets or assists drug development. Buzzwords such as “bench-to-bedside research”, “personalized medicine” or “patient-tailored therapy” inevitably come to mind, reflecting the ultimate goals of our shared endeavor—early and accurate diagnoses and highly efficient but also safe therapies.

This Special Issue welcomes disease-oriented proteomics and protein biochemistry studies and reviews addressing, namely:

Molecular processes and proteins associated with human diseases;
Disease-related proteins and their structural and functional characterization;
Identification of disease markers or novel drug targets;
Molecular processes underlying the action of therapeutic drugs or principles of drug resistance.

Dr. Jiří Petrák
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

proteomics
protein biochemistry
mass spectrometry
molecular pathology
molecular pathways
protein structure
protein function
therapeutic drugs and drug resistance
biomarkers
diagnosis and treatment
druggable targets

Published Papers (4 papers)

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Research

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10 pages, 1657 KiB

Open AccessArticle

Prion Strains Differ in Susceptibility to Photodynamic Oxidation

by Marie Kostelanska and Karel Holada

Molecules 2022, 27(3), 611; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27030611 - 18 Jan 2022

Viewed by 1441

Abstract

Prion disorders, or transmissible spongiform encephalophaties (TSE), are fatal neurodegenerative diseases affecting mammals. Prion-infectious particles comprise of misfolded pathological prion proteins (PrP^TSE). Different TSEs are associated with distinct PrP^TSE folds called prion strains. The high resistance of prions to conventional sterilization increases the risk of prion transmission in medical, veterinary and food industry practices. Recently, we have demonstrated the ability of disulfonated hydroxyaluminum phthalocyanine to photodynamically inactivate mouse RML prions by generated singlet oxygen. Herein, we studied the efficiency of three phthalocyanine derivatives in photodynamic treatment of seven mouse adapted prion strains originating from sheep, human, and cow species. We report the different susceptibilities of the strains to photodynamic oxidative elimination of PrP^TSE epitopes: RML, A139, Fu-1 > mBSE, mvCJD > ME7, 22L. The efficiency of the phthalocyanine derivatives in the epitope elimination also differed (AlPcOH(SO₃)₂ > ZnPc(SO₃)_1-3 > SiPc(OH)₂(SO₃)_1-3) and was not correlated to the yields of generated singlet oxygen. Our data suggest that the structural properties of both the phthalocyanine and the PrP^TSE strain may affect the effectiveness of the photodynamic prion inactivation. Our finding provides a new option for the discrimination of prion strains and highlights the necessity of utilizing range of prion strains when validating the photodynamic prion decontamination procedures. Full article

(This article belongs to the Special Issue Proteomics and Protein Biochemistry in Diseases)

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17 pages, 5680 KiB

Open AccessArticle

Deep Membrane Proteome Profiling Reveals Overexpression of Prostate-Specific Membrane Antigen (PSMA) in High-Risk Human Paraganglioma and Pheochromocytoma, Suggesting New Theranostic Opportunity

by Ondrej Vit, Mayank Patel, Zdenek Musil, Igor Hartmann, Zdenek Frysak, Markku Miettinen, Karel Pacak and Jiri Petrak

Molecules 2021, 26(21), 6567; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26216567 - 29 Oct 2021

Cited by 5 | Viewed by 2165

Abstract

Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors arising from chromaffin cells of adrenal medulla or sympathetic or parasympathetic paraganglia, respectively. To identify new therapeutic targets, we performed a detailed membrane-focused proteomic analysis of five human paraganglioma (PGL) samples. Using the Pitchfork strategy, which combines specific enrichments of glycopeptides, hydrophobic transmembrane segments, and non-glycosylated extra-membrane peptides, we identified over 1800 integral membrane proteins (IMPs). We found 45 “tumor enriched” proteins, i.e., proteins identified in all five PGLs but not found in control chromaffin tissue. Among them, 18 IMPs were predicted to be localized on the cell surface, a preferred drug targeting site, including prostate-specific membrane antigen (PSMA), a well-established target for nuclear imaging and therapy of advanced prostate cancer. Using specific antibodies, we verified PSMA expression in 22 well-characterized human PPGL samples. Compared to control chromaffin tissue, PSMA was markedly overexpressed in high-risk PPGLs belonging to the established Cluster 1, which is characterized by worse clinical outcomes, pseudohypoxia, multiplicity, recurrence, and metastasis, specifically including SDHB, VHL, and EPAS1 mutations. Using immunohistochemistry, we localized PSMA expression to tumor vasculature. Our study provides the first direct evidence of PSMA overexpression in PPGLs which could translate to therapeutic and diagnostic applications of anti-PSMA radio-conjugates in high-risk PPGLs. Full article

(This article belongs to the Special Issue Proteomics and Protein Biochemistry in Diseases)

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19 pages, 3203 KiB

Open AccessArticle

Proteomic Signature of Extracellular Vesicles for Lung Cancer Recognition

by Svetlana E. Novikova, Natalia A. Soloveva, Tatiana E. Farafonova, Olga V. Tikhonova, Pao-Chi Liao and Victor G. Zgoda

Molecules 2021, 26(20), 6145; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26206145 - 12 Oct 2021

Cited by 13 | Viewed by 3149

Abstract

The proteins of extracellular vesicles (EVs) that originate from tumors reflect the producer cells’ proteomes and can be detected in biological fluids. Thus, EVs provide proteomic signatures that are of great interest for screening and predictive cancer diagnostics. By applying targeted mass spectrometry with stable isotope-labeled peptide standards, we assessed the levels of 28 EV-associated proteins, including the conventional exosome markers CD9, CD63, CD81, CD82, and HSPA8, in vesicles derived from the lung cancer cell lines NCI-H23 and A549. Furthermore, we evaluated the detectability of these proteins and their abundance in plasma samples from 34 lung cancer patients and 23 healthy volunteers. The abundance of TLN1, TUBA4A, HSPA8, ITGB3, TSG101, and PACSIN2 in the plasma of lung cancer patients was measured using targeted mass spectrometry and compared to that in plasma from healthy volunteers. The most diagnostically potent markers were TLN1 (AUC, 0.95), TUBA4A (AUC, 0.91), and HSPA8 (AUC, 0.88). The obtained EV proteomic signature allowed us to distinguish between the lung adenocarcinoma and squamous cell carcinoma histological types. The proteomic cargo of the extracellular vesicles represents a promising source of potential biomarkers. Full article

(This article belongs to the Special Issue Proteomics and Protein Biochemistry in Diseases)

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Review

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27 pages, 3709 KiB

Open AccessReview

The Relationship of Glutathione-S-Transferase and Multi-Drug Resistance-Related Protein 1 in Nitric Oxide (NO) Transport and Storage

by Tiffany M. Russell, Mahan Gholam Azad and Des R. Richardson

Molecules 2021, 26(19), 5784; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26195784 - 24 Sep 2021

Cited by 2 | Viewed by 2626

Abstract

Nitric oxide is a diatomic gas that has traditionally been viewed, particularly in the context of chemical fields, as a toxic, pungent gas that is the product of ammonia oxidation. However, nitric oxide has been associated with many biological roles including cell signaling, macrophage cytotoxicity, and vasodilation. More recently, a model for nitric oxide trafficking has been proposed where nitric oxide is regulated in the form of dinitrosyl-dithiol-iron-complexes, which are much less toxic and have a significantly greater half-life than free nitric oxide. Our laboratory has previously examined this hypothesis in tumor cells and has demonstrated that dinitrosyl-dithiol-iron-complexes are transported and stored by multi-drug resistance-related protein 1 and glutathione-S-transferase P1. A crystal structure of a dinitrosyl-dithiol-iron complex with glutathione-S-transferase P1 has been solved that demonstrates that a tyrosine residue in glutathione-S-transferase P1 is responsible for binding dinitrosyl-dithiol-iron-complexes. Considering the roles of nitric oxide in vasodilation and many other processes, a physiological model of nitric oxide transport and storage would be valuable in understanding nitric oxide physiology and pathophysiology. Full article

(This article belongs to the Special Issue Proteomics and Protein Biochemistry in Diseases)

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