Expert Review of Proteomics

Han, Yu; Wennersten, Sara A.; Lam, Maggie P. Y.

doi: 10.1080/14789450.2019.1703678pmid: 31822126

Franjou, Sebastian L.; Milazzo, Mario; Yu, Chi-Hua; Buehler, Markus J.

doi: 10.1080/14789450.2019.1697236pmid: 31756126

Introduction: The practice of turning scientific data into music, a practice known as sonification, is a growing field. Driven by analogies between the hierarchical structures of proteins and many forms of music, multiple attempts of mapping proteins to music have been made. Previous works have either worked at a low level, mapping amino acid to notes, or at a higher level, using the overall structure as a basis for composition.Areas covered: We report a comprehensive mapping strategy that encompasses the encoding of the geometry of proteins, in addition to the amino acid sequence and secondary structure information. This leads to a piece of music that is both more complete and closely linked to the original protein. By using this mapping, we can invert the process and map music to proteins, retrieving not only the amino acid sequence but also the secondary structure and folding from musical data.Expert opinion: We can train a machine learning model on ‘protein music’ to generate new music that can be translated to new proteins. By selecting proper datasets and conditioning parameters on the generative model, we could tune de novo proteins with high level parameters to achieve certain protein design features.

Thomas, Brian; Taylor, Stephen

doi: 10.1080/14789450.2019.1700114pmid: 31830833

Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.

Conlon, J. Michael; Mechkarska, Milena; Leprince, Jérôme

doi: 10.1080/14789450.2019.1693894pmid: 31729236

Introduction: The emergence of multidrug-resistant microorganisms has necessitated a search for new antimicrobial agents. Skin secretions of many frog species contain peptides that possess potent, broad-spectrum antibacterial and antifungal activities and so show promise for development into anti-infective agents. Several such peptides also possess cytokine-mediated anti-inflammatory properties and a range of anti-diabetic activities.Areas covered: A peptidomic approach, involving reversed-phase HPLC and MALDI mass spectrometry, to the comprehensive identification of peptides of potential therapeutic importance in frog skin secretions is described and its advantages over analyses involving bioassays discussed. Peptidomic studies relating to the characterization of peptides with demonstrated antimicrobial, anti-inflammatory and anti-diabetic properties in skin secretions of frogs belonging to the extensive Pipidae and Ranidae families are reviewed.Expert commentary: The initial promise of frog skin peptides as agents to treat infections produced by drug-resistant microorganisms has not been fulfilled although topical applications to treat skin diseases and a role in promoting wound healing remains a possibility. Future directions are more likely to involve the application of such peptides in the treatment of patients with sepsis and related inflammatory conditions and as a component of a therapeutic regime for Type 2 diabetes.

Bardanzellu, Flaminia; Peila, Chiara; Fanos, Vassilios; Coscia, Alessandra

doi: 10.1080/14789450.2019.1703679pmid: 31825672

Introduction: Among the OMICS technologies, that have emerged in recent years, metabolomics has allowed relevant step forwards in clinical research. Several improvements in disease diagnosis and clinical management have been permitted, even in neonatology. Among potentially evaluable biofluids, breast milk (BM) results are highly interesting, representing a fluid of conjunction between mothers newborns, describing their interaction.Areas covered: in this review, updating a previous review article, we discuss research articles and reviews on BM metabolomics and found in MEDLINE using metabolomics, breast milk, neonatal nutrition, breastfeeding, human milk composition, and preterm neonates as keywords.Expert opinion: Our research group has a profound interest in metabolomics research. In 2012, we published the first metabolomic analysis on BM samples, reporting interesting data on its composition and relevant differences with formula milk (FM), useful to improve FM composition. As confirmed by successive studies, such technology can detect the specific BM composition and its dependence on several variables, including lactation stage, gestational age, maternal or environmental conditions. Moreover, since BM contaminants or drug levels can be detected, metabolomics also results useful to determine BM safety. These are only a few practical applications of BM analysis, which will be reviewed in this paper.

DeLeon-Pennell, Kristine Y.; Lindsey, Merry L.

doi: 10.1080/14789450.2019.1664293pmid: 31483157

Introduction: Cardiovascular disease is a major cause of death in both men and women. While women are protected until the onset of menopause, after menopause women have increased risk of adverse cardiovascular disease events. Animal models of myocardial infarction recapitulate many of the sex differences observed in humans, and proteomics evaluations offer mechanistic insights to explain sex differences.Areas covered: In this review, we will discuss how proteomics has helped us understand the hormonal, chromosomal, and immune mechanisms behind sex differences in response to ischemic injury and the development of heart failure.Expert opinion: There are a number of ways in which proteomics has and will continue to facilitate our understanding of sex differences in cardiac remodeling after myocardial infarction.

Maciel, Valter Luiz; Tamashiro, Letícia Kaory; Bertolla, Ricardo Pimenta

doi: 10.1080/14789450.2019.1693895pmid: 31726898

Introduction: The seminal proteome has been shown to directly influence the male fertile potential. Post-translational modifications (PTMs) are significant changes that play a role in the biological regulation of proteins. Sperm cells are transcriptionally and translationally inactive and these modifications are essential to control protein function.Areas covered: Here we reviewed seven PTMs which importance for male reproductive function investigated in the past decade, namely S-nitrosylation and tyrosine nitration (both occurring by the action of NO), glycosylation, ubiquitination, acetylation, methylation, and SUMOylation. Since they were previously identified in human semen, we focus on their role in sperm function, as well as in physiological and pathophysiological processes which could contribute to the fertility potential. The following keywords were applied: ‘post-translational modification’, ‘sperm’, ‘semen’, ‘seminal plasma’, ‘male infertility’, ‘nitrosylation’, ‘nitration’, ‘histone methylation’, ‘SUMOylation’, ‘ubiquitination’, ‘ubiquitilation’, ‘glycosylation’, and ‘acetylation’.Expert opinion: Most biological processes orchestrated by proteins require PTMs for their activation or inhibition. Most of them are dynamic and occur in mature sperm, modulating protein function, thus exerting a significant role in sperm function and fertility. Finally, the study of PTMs should be also addressed in pathophysiological processes, as different clinical conditions are known to alter the proteome.

Di Domenico, Fabio; Zuliani, Ilaria; Tramutola, Antonella

doi: 10.1080/14789450.2019.1691919pmid: 31709850

Introduction: Autophagy is one of the most conserved clearance systems through which eukaryotes manage to handle dysfunctional and excess organelles and macromolecules. This catabolic process has not only a role in the maintenance of basal turnover of cellular components, but it is also essential in cells adaptation to stress conditions. In the last decades, defects in autophagic machinery have been identified as a feature in neurodegenerative diseases. In this context, mass spectrometry-based proteomics has become an important tool in the comprehensive analysis of proteins involved in the autophagic flux.Area covered: In this review, we discuss recent contributions of proteomic techniques in the study of defective autophagy related to neurodegenerative illness. Particular emphasis is given to the identification of i) shared autophagic markers between different disorders, which support common pathological mechanisms; ii) unique autophagic signature, which could aid to discriminate among diseases.Expert opinion: Proteomic approaches are valuable in the identification of alterations of components to the autophagic process at different steps of the process. The investigation of autophagic defects associated with neurological disorders is crucial in order to unravel all the potential mechanism leading to neurodegeneration and propose effective therapeutic strategies targeting autophagy.