Current Protein and Peptide Science - Volume 23, Issue 11, 2022

Hop Japanese (Hop J) pollen has been considered one of the major causative pollen allergens in Far East Asia in the autumn season. The sensitization rate, pollen count, and allergenicity of Hop J pollens are increasing in this region because of increased air pollution and global warming. However, commercial skin test agents for the diagnosis and allergen extracts for the allergen immunotherapy are not available. This review summarizes recent data on clinical impact of Hop J pollinosis in order to facilitate the development of diagnostic and therapeutic agents for this region.

Oak pollen allergy is common all over the world and an important cause of pollinosis. The molecular properties of some component allergens have been clearly characterized, while some of them are still waiting for characterization. Studies on some oak component allergens are neglected, possibly because of its high cross-reactivity to birch. However, the utilization of culprit allergen molecules is expected to increase the diagnostic sensitivity and efficacy of immunotherapy. Sensitization to oak pollen along with birch often causes pollen food allergy syndrome to fruits and vegetables. Acorn and wood dust from oak can cause allergic disease. We summarize the distribution and taxonomic classification of oak trees of allergenic importance. Molecular characteristics of the identified component allergens, cross-reactivity, and clinical aspects for diagnosis and immunotherapy are also described with an emphasis on Korean situations.

Birch belongs to the order Fagales and the family Betulaceae. Birch pollen is one of the most important airborne inhaled allergens in the north temperate zone, leading to allergic rhinitis, asthma and pollen-related food allergy. The sensitization rate to birch pollen is about 8-16% in the general population and 7-57% in patients seen at various allergy centers. Seven birch pollen allergens have been recognized by the International Allergen Nomenclature Sub-committee, with Bet v 1 as the sole major allergen. Component-resolved diagnostics can help to discriminate broad cross-reactivity and false-positive diagnoses of pollen allergy caused by specific IgE to pan-allergens such as Bet v 2, 4 or Bet v 7 from true birch allergy represented by the major allergen Bet v 1-specific IgE. Patients with allergic symptoms to birch pollen showed significantly higher serum anti-Bet v 1 IgE concentrations than asymptomatic individuals with birch sensitization. A higher level of IgE to Bet v 1 also predicted oral allergy syndrome after the ingestion of Rosaceae fruits, nuts, or Apiaceae vegetables, which have cross-reactive homologous allergens with birch allergens. Bet v 1 is one of the first allergens developed using recombinant technology. Many forms of genetically modified Bet v 1 hypo-allergens have been developed and have shown benefit in animal models or even clinical trials of allergen immunotherapy.

Lysine succinylation is a post-translational modification (PTM) of protein in which a succinyl group (-CO-CH2-CH2-CO2H) is added to a lysine residue of protein that reverses lysine's positive charge to a negative charge and leads to the significant changes in protein structure and function. It occurs on a wide range of proteins and plays an important role in various cellular and biological processes in both eukaryotes and prokaryotes. Beyond experimentally identified succinylation sites, there have been a lot of studies for developing sequence-based prediction using machine learning approaches, because it has the promise of being extremely time-saving, accurate, robust, and cost-effective. Despite these benefits for computational prediction of lysine succinylation sites for different species, there are a number of issues that need to be addressed in the design and development of succinylation site predictors. In spite of the fact that many studies used different statistical and machine learning computational tools, only a few studies have focused on these bioinformatics issues in depth. Therefore, in this comprehensive comparative review, an attempt is made to present the latest advances in the prediction models, datasets, and online resources, as well as the obstacles and limits, to provide an advantageous guideline for developing more suitable and effective succinylation site prediction tools.

Apolipoprotein-mimetic peptides, mimicking the biological properties of apolipoproteins, have shown beneficial properties against various diseases (central and peripheral diseases) and have emerged as potential candidates for their treatments. Progress has been made from first-generation to second-generation apolipoprotein-mimetic peptides. Understanding these peptides from the first generation to the second generation is discussed in this review. First, we discussed the structural and therapeutic potentials of first-generation apolipoprotein-mimetic peptides. Further, we discussed the development of second-generation apolipoprotein-mimetic peptides, like dual-domain and bihelical peptides the emergence of second-generation apolipoprotein-mimetic peptides as potential candidates in different preclinical and clinical studies has also been emphasized.

Background: Glycation of immunoglobulin-G (IgG) molecules with monosaccharides may cause significant structural disability, thus resulting in their loss of function. The accumulation of AGEs formed from glycation plays an important role in the aliments associated with metabolic diseases. Therefore, excess sugar in plasma interferes with the functioning of IgG and may contribute to a wide range of diabetes-associated complications. The long-term formation of these heterogeneous AGEs may accumulate and affect plasma proteins, especially long-lived proteins. In this study, we analyze immunoglobulin-G (IgG) glycation with 2’-deoxyribose (deoxyribose) instigated modification in IgG structure and AGEs formation. Methods: This study aims to glycate IgG from varying concentrations of pentose sugar, 2’-deoxyribose (deoxyribose). Various physicochemical methods and techniques characterized post glycation of IgG, both the native and its glycated analogue. The glycated protein will be assessed for its stability and perturbations by UV-VIS., fluorescence and FT-IR spectroscopic techniques. Moreover, the early glycation product will be done by NBT assay, and other biochemical parameters like HMF, carbonyl content and thioflavin-T assays were also performed to see the biochemical changes induced in the glycated IgG macromolecule. Results: Glycation of protein macromolecules generates stable early glycation products (Amadori products). Later, these Amadori products involved a series of chemical reactions to form more stable advanced glycation end products (AGEs). Our experimental study results could validate the modification in IgG structure and AGEs formation. Conclusion: The formation of IgG-AGEs from glycation of IgG with deoxyribose could exert cellular toxicity, and might initiates secondary complications of diabetes. Therefore, this study emphasized the glycation reaction of IgG from deoxyribose, which has not been reported yet.

Background: Exosome research is a current trend in functional proteomics as it provides important data on the pathophysiology and pathogenesis of diseases. The scientific outputs regarding these topics often only approach disease-protein/peptide/exosome or mechanismprotein/ peptide/exosome association. Approaching all three aspects could be the key to a better understanding of the pathophysiology and uncovering novel biomarkers for urogenital diseases. The focus of this work is to study exosome datasets to understand the possible role of underlying proteins in disease manifestation. We also attempt to link 4 different diseases that affect renal functions and are genetically inherited. Methods: For this purpose, the existing literature is consulted to understand the importance of exosomes in disease prediction, diagnosis and therapy. Available biotechnological methods of exosome analysis and the tools of proteomic analysis, data mining and visualization are discussed. The database PRIDE is selected to query the information of several datasets related to urinary exosome analysis. Results: We have obtained a list of 19 proteins/genes involved in the mentioned diseases. On this list, we found a proteomic fingerprint consisting of Rab-7a, PDCD6, and CDC42, among others, and we are exploring their biological significance and underlying processes. Conclusion: APOA1, CD59, CD9, IGHG1, RAB7A, RAP1A, SEMG1 and SEMG2 are common in four urogenital diseases, and are involved in interactions with podosomes and endosomes, remodeling of chylomicrons, regulation of interleukin production, regulation of endopeptidase activity, and establishment of apical/basal polarity of epithelial cells.

Objective: Skin cutaneous melanoma(SKCM) is the most severe, and complex disease of all skin cancers. The molecular mechanisms of this cancer progression are not well understood. Methods: GEPIA online database was used to validate the differentially expressed genes from two GEO datasets. The prognostic value was calculated by the Kaplan-Meier method. RT-qPCR verified the expression of TUBB4A in SKCM cell line, and the immunohistochemistry of TUBB4A in SKCM and normal skin tissues were gained from Human Protein Atlas. Seven target prediction databases predicted potential microRNAs(miRNAs), and upstream long non-coding RNAs(lncRNAs) were predicted by starBase. The co-expressed gene of TUBB4A was obtained using the two online analysis sites UALCAN and starBase. These co-expressed genes were performed by enrichment analysis, and immune infiltration result was obtained by the TIMER2 online database. The receiver operating characteristic( ROC) curve was applied to evaluate the diagnostic value of TUBB4A in the SKCM and normal skin group. A new nomogram about TUBB4A was constructed to forecast the survival rate of SKCM patients at 1, 3, and 5 years. Results: Firstly, we found that DLL3 and TUBB4A were significantly higher expressed in skin cutaneous melanoma than normal skin. Subsequently, by analyzing progress-free interval(PFI), diseasespecific survival(DSS), and disease-free survival(DFS), only TUBB4A was the most potent gene for inhibiting shin cutaneous melanoma progression. In gene ontology(GO)/ kyoto encyclopedia of genes and genomes(KEGG) analysis, TUBB4A may play a key role in the progression of skin cutaneous melanoma by regulating mitochondrial function and affecting cellular metabolism, possibly related to the immune infiltration of CD4+Th1 cells and NK cells. The upstream non-coding RNA(ncRNA) acts through the SNHG16-hsa-let-7b-5p-TUBB4A axis. Conclusion: In conclusion, we elucidated the regulatory role of the SNHG16-hsa-let-7b-5p-TUBB4A axis in the progression of skin cutaneous melanoma by modulating mitochondrial function to affect cellular metabolism. TUBB4A may be a promising diagnostic biomarker and therapeutic target for cutaneous skin melanoma.