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Functional Proteomics in Cell Biology and Beyond

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

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 14553

Special Issue Editor


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Guest Editor
Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
Interests: mass spectrometry; proteomics; phosphoproteomics; cellular senescence; aging; type 2 diabetes; plant proteomics; protein complexes; protein–protein interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in proteomics, including post-translational modifications, protein–protein and protein–ligand interactions, and structural elucidation, have been driven by the development of new and advanced mass spectrometers as well as better algorithms and bioinformatics software. The complementary coupling of mass spectrometry with different chromatographic separation techniques has improved the analysis of complex biological mixtures as well as the enhanced molecular characterization of proteins at the proteome or sub-proteome levels, and this information is being applied in the context of cell biology and diseases. Researchers investigating complex cell biology and diseases such as Alzheimer’s disease, neurodegenerative disease, diabetes, and cancer are taking advantage of these advanced proteomics technologies. Therefore, MS-based proteomics is now routinely and increasingly applied in many labs to address a large range of biological questions, mainly because of its unparalleled ability to acquire high-content quantitative information about biological samples of enormous complexity. MS technologies, including the instrumentation and the methods for data acquisition and analysis, continue to advance in the quest for further improvements in sensitivity, throughput, and proteome coverage.

In this Special Issue, we invite original research and review articles that focus on the development and application of new and emerging proteomics technologies to study basic cell biology and diseases including biomarker discovery, molecular signaling, disease mechanisms, drug resistance, the roles and regulation of post-translational modifications, protein complexes, and interactions in cell biology and diseases. 

Dr. Uma K. Aryal
Guest Editor

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Keywords

  • quantitative proteomics
  • mass spectrometry
  • post-translational modifications
  • phosphorylation
  • protein–protein interactions
  • protein–ligand interactions
  • systems biology
  • bioinformatics
  • multi-omics analysis

Published Papers (7 papers)

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Research

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16 pages, 4860 KiB  
Article
Biocytin-Labeling in Whole-Cell Recording: Electrophysiological and Morphological Properties of Pyramidal Neurons in CYLD-Deficient Mice
by Shuyi Tan, Xiuping Mo, Huihui Qin, Binbin Dong, Jiankui Zhou, Cheng Long and Li Yang
Molecules 2023, 28(10), 4092; https://doi.org/10.3390/molecules28104092 - 15 May 2023
Viewed by 2810
Abstract
Biocytin, a chemical compound that is an amide formed from the vitamin biotin and the amino acid L-lysine, has been used as a histological dye to stain nerve cells. Electrophysiological activity and morphology are two key characteristics of neurons, but revealing both the [...] Read more.
Biocytin, a chemical compound that is an amide formed from the vitamin biotin and the amino acid L-lysine, has been used as a histological dye to stain nerve cells. Electrophysiological activity and morphology are two key characteristics of neurons, but revealing both the electrophysiological and morphological properties of the same neuron is challenging. This article introduces a detailed and easy-to-operate procedure for single-cell labeling in combination with whole-cell patch-clamp recording. Using a recording electrode filled with a biocytin-containing internal solution, we demonstrate the electrophysiological and morphological characteristics of pyramidal (PNs), medial spiny (MSNs) and parvalbumin neurons (PVs) in brain slices, where the electrophysiological and morphological properties of the same individual cell are elucidated. We first introduce a protocol for whole-cell patch-clamp recording in various neurons, coupled with the intracellular diffusion of biocytin delivered by the glass capillary of the recording electrode, followed by a post hoc procedure to reveal the architecture and morphology of biocytin-labeled neurons. An analysis of action potentials (APs) and neuronal morphology, including the dendritic length, number of intersections, and spine density of biocytin-labeled neurons, were performed using ClampFit and Fiji Image (ImageJ), respectively. Next, to take advantage of the techniques introduced above, we uncovered defects in the APs and the dendritic spines of PNs in the primary motor cortex (M1) of deubiquitinase cylindromatosis (CYLD) knock-out (Cyld−/−) mice. In summary, this article provides a detailed methodology for revealing the morphology as well as the electrophysiological activity of a single neuron that will have many applications in neurobiology. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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13 pages, 2408 KiB  
Article
Ribosome Biogenesis Regulator 1 Homolog (RRS1) Promotes Cisplatin Resistance by Regulating AEG-1 Abundance in Breast Cancer Cells
by Junying Song, Cuixiu Peng, Runze Wang, Yanan Hua, Qinglan Wu, Lin Deng, Yi Cao, Li Zhang and Lin Hou
Molecules 2023, 28(7), 2939; https://doi.org/10.3390/molecules28072939 - 25 Mar 2023
Cited by 2 | Viewed by 1302
Abstract
Many ribosomal proteins are highly expressed in tumors and are closely related to their diagnosis, prognosis and pathological characteristics. However, few studies are available on the correlation between ribosomal proteins and chemoresistance. RRS1 (human regulator of ribosome synthesis 1), a critical nuclear protein [...] Read more.
Many ribosomal proteins are highly expressed in tumors and are closely related to their diagnosis, prognosis and pathological characteristics. However, few studies are available on the correlation between ribosomal proteins and chemoresistance. RRS1 (human regulator of ribosome synthesis 1), a critical nuclear protein involved in ribosome biogenesis, also plays a key role in the genesis and development of breast cancer by protecting cancer cells from apoptosis. Given that apoptosis resistance is one of the causes of the cisplatin resistance of tumor cells, our aim was to determine the relationship between RRS1 and cisplatin resistance in breast cancer cells. Here, we report that RRS1 is associated with cisplatin resistance in breast cancer cells. RRS1 silencing increased the sensitivity of MCF-7/DDP cells to cisplatin and inhibited cancer cell proliferation by blocking cell cycle distribution and enhancing apoptosis. AEG-1 (astrocyte elevated gene-1) promotes drug resistance by interfering with the ubiquitination and proteasomal degradation of MDR1 (multidrug resistance gene 1), thereby enhancing drug efflux. We found that RRS1 binds to and stabilizes AEG-1 by inhibiting ubiquitination and subsequent proteasomal degradation, which then promotes drug efflux by upregulating MDR1. Furthermore, RRS1 also induces apoptosis resistance in breast cancer cells through the ERK/Bcl-2/BAX signaling pathway. Our study is the first to show that RRS1 sensitizes breast cancer cells to cisplatin by binding to AEG-1, and it provides a theoretical basis to improve the efficacy of cisplatin-based chemotherapy. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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12 pages, 2044 KiB  
Article
Prediction of Phage Virion Proteins Using Machine Learning Methods
by Ranjan Kumar Barman, Alok Kumar Chakrabarti and Shanta Dutta
Molecules 2023, 28(5), 2238; https://doi.org/10.3390/molecules28052238 - 28 Feb 2023
Cited by 2 | Viewed by 1714
Abstract
Antimicrobial resistance (AMR) is a major problem and an immediate alternative to antibiotics is the need of the hour. Research on the possible alternative products to tackle bacterial infections is ongoing worldwide. One of the most promising alternatives to antibiotics is the use [...] Read more.
Antimicrobial resistance (AMR) is a major problem and an immediate alternative to antibiotics is the need of the hour. Research on the possible alternative products to tackle bacterial infections is ongoing worldwide. One of the most promising alternatives to antibiotics is the use of bacteriophages (phage) or phage-driven antibacterial drugs to cure bacterial infections caused by AMR bacteria. Phage-driven proteins, including holins, endolysins, and exopolysaccharides, have shown great potential in the development of antibacterial drugs. Likewise, phage virion proteins (PVPs) might also play an important role in the development of antibacterial drugs. Here, we have developed a machine learning-based prediction method to predict PVPs using phage protein sequences. We have employed well-known basic and ensemble machine learning methods with protein sequence composition features for the prediction of PVPs. We found that the gradient boosting classifier (GBC) method achieved the best accuracy of 80% on the training dataset and an accuracy of 83% on the independent dataset. The performance on the independent dataset is better than other existing methods. A user-friendly web server developed by us is freely available to all users for the prediction of PVPs from phage protein sequences. The web server might facilitate the large-scale prediction of PVPs and hypothesis-driven experimental study design. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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14 pages, 873 KiB  
Article
Proteomic Analysis of the Effect of Salmonella Challenge on Broiler Chicken
by Adedeji Adetunji, Theresa Casey, Jackeline Franco, Devendra Shah and Yewande Fasina
Molecules 2022, 27(21), 7277; https://doi.org/10.3390/molecules27217277 - 26 Oct 2022
Cited by 2 | Viewed by 1319
Abstract
Salmonella enteritidis is a foodborne pathogen that causes high morbidity in poultry. Proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to study the effects of Salmonella infection on spleen proteome in broiler chickens. Day-old broilers were assigned to control (CON; [...] Read more.
Salmonella enteritidis is a foodborne pathogen that causes high morbidity in poultry. Proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to study the effects of Salmonella infection on spleen proteome in broiler chickens. Day-old broilers were assigned to control (CON; n = 60) or Salmonella challenge (CON−SE; n = 60), and gavaged with Tryptic soy agar broth or SE. A subset of chicks was euthanized on D3 and D7 (n = 4/group/day) and the spleen was removed, and rapidly frozen, subsequently proteome was measured using label-free LC-MS/MS. Protein spectra were mapped to Gallus gallus Uniprot database. Differentially abundant proteins (DAP; FDR < 0.05) between days and treatments were identified using ANOVA. Cecal content of Salmonella in CON−SE was 3.37 log10 CFU/g and CON were negative. Across the 16 samples, 2625 proteins were identified. Proteins that decreased in abundance between days mediated cell cycle progression, while those that increased in abundance function in cytoskeleton and mRNA processing. SE infection caused an increase in proteins that mediated redox homeostasis, lysosomal activities, and energy production, while proteins decreased in abundance-mediated developmental progression. Proteomic signatures of spleen suggest SE infection was metabolically costly, and energy was diverted from normal developmental processes to potentiate disease resistance mechanisms. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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20 pages, 3096 KiB  
Article
Isoquinoline Antimicrobial Agent: Activity against Intracellular Bacteria and Effect on Global Bacterial Proteome
by Caroline W. Karanja, Nimishetti Naganna, Nader S. Abutaleb, Neetu Dayal, Kenneth I. Onyedibe, Uma Aryal, Mohamed N. Seleem and Herman O. Sintim
Molecules 2022, 27(16), 5085; https://doi.org/10.3390/molecules27165085 - 10 Aug 2022
Cited by 6 | Viewed by 1958
Abstract
A new class of alkynyl isoquinoline antibacterial compounds, synthesized via Sonogashira coupling, with strong bactericidal activity against a plethora of Gram-positive bacteria including methicillin- and vancomycin-resistant Staphylococcus aureus (S. aureus) strains is presented. HSN584 and HSN739, representative compounds in this class, reduce methicillin-resistant [...] Read more.
A new class of alkynyl isoquinoline antibacterial compounds, synthesized via Sonogashira coupling, with strong bactericidal activity against a plethora of Gram-positive bacteria including methicillin- and vancomycin-resistant Staphylococcus aureus (S. aureus) strains is presented. HSN584 and HSN739, representative compounds in this class, reduce methicillin-resistant S. aureus (MRSA) load in macrophages, whilst vancomycin, a drug of choice for MRSA infections, was unable to clear intracellular MRSA. Additionally, both HSN584 and HSN739 exhibited a low propensity to develop resistance. We utilized comparative global proteomics and macromolecule biosynthesis assays to gain insight into the alkynyl isoquinoline mechanism of action. Our preliminary data show that HSN584 perturb S. aureus cell wall and nucleic acid biosynthesis. The alkynyl isoquinoline moiety is a new scaffold for the development of potent antibacterial agents against fatal multidrug-resistant Gram-positive bacteria. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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Review

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19 pages, 1814 KiB  
Review
Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates
by Andrew G. DeMarco and Mark C. Hall
Molecules 2023, 28(9), 3675; https://doi.org/10.3390/molecules28093675 - 24 Apr 2023
Cited by 1 | Viewed by 1981
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification [...] Read more.
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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23 pages, 1178 KiB  
Review
Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways
by Panshak P. Dakup, Song Feng, Tujin Shi, Jon M. Jacobs, H. Steven Wiley and Wei-Jun Qian
Molecules 2023, 28(3), 1143; https://doi.org/10.3390/molecules28031143 - 23 Jan 2023
Cited by 3 | Viewed by 2730
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial [...] Read more.
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)—also known as multiple reaction monitoring (MRM)—and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease. Full article
(This article belongs to the Special Issue Functional Proteomics in Cell Biology and Beyond)
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