The Protein Journal最新文献

The anaphase promoting complex (APC or cyclosome) is a major ubiquitin ligase that coordinates mitotic and G1 progression, acting as a major regulator of chromosome segregation. While the human APC contains fourteen subunits, it is yet to be explored in the pathogen Entamoeba histolytica. Our study reveals the existence of a single functional Apc10 homolog in E. histolytica, which acts as a processivity factor of ubiquitin ligase activity in human. A cDNA library generated from HM1:IMSS strain of E. histolytica was screened for interaction partners of EhApc10 in yeast two hybrid study. The novel interactor, a glycolytic enzyme, pyruvate phosphate dikinase (Ppdk) was found to interact with EhApc10 and further validated by in vitro assay. A comprehensive in silico study has emphasized the structural and functional aspects, encompassing physicochemical traits, predictive 3D structure modelling, validation of EhApc10-EhPpdk interaction through molecular docking and simulation. The interplay between a cell cycle protein and a glycolytic enzyme highlights the connection between cellular metabolism and the cell cycle regulatory mechanism. The study serves as the groundwork for future research on the non-mitotic role of APC beyond cell cycle.

Seeds are essential for plant reproduction, ensuring species survival and dispersal while adapting to diverse environments throughout a plant’s life. Proteomics has emerged as a powerful tool for deciphering the complexities of seed growth, germination, and stress responses. Advanced proteomic technologies enable the analysis of protein changes during germination, dormancy, and ageing, enhancing our understanding of seed lifespan and vitality. Recent studies have revealed detailed insights into metabolic processes and storage protein profiles across various plant species. This knowledge is crucial for improving seed storage, conserving quality, and maintaining viability. Additionally, it contributes to sustainable agriculture by identifying stress-responsive proteins and signalling pathways that can mitigate stress and enhance farming practices. This review highlights significant advancements in seed proteomics over the past decade, discussing critical discoveries related to storage proteins, protein interactions, and proteome modifications due to stress. It illustrates how these insights transform seed biology, boosting productivity, food security, and environmentally friendly practices. The review also identifies existing knowledge gaps and provides direction for future research, underscoring the need for continued interdisciplinary collaboration in this dynamic field.

The αA-crystallin protein plays a vital role in maintaining the refractive index and transparency of the eye lens. Significant clinical studies have emerged as the αA-crystallin is prone to aggregation, resulting in the formation of cataracts with varied etiologies due to mutations. This work aims to comprehend the structural and functional role of cataract-causing mutations in αA-crystallin, particularly at N-Terminal and α-Crystallin Domains, using in-silico approaches including molecular dynamics simulation. About 19 mutants of αA-crystallin along with native structure were simulated for 100 ns and the post-simulations analyses reveal pronounced dynamics of αA-crystallin due to the enhanced structure flexibility as its native compactness was lost and is witnessed mainly by the mutants R12L, R21L, R21Q, R54L, R65Q, R116C and R116H. It is observed that αA-crystallin discloses the NTD motions as the dominant one and the same was endorsed by the linear variation between Rg and the center-of-mass of αA-crystallin. Interestingly, such enhanced dynamics of αA-crystallin mutants associated with the structure flexibility is internally modulated by the dynamic exchange of secondary structure elements β-sheets and coils (R² = 0.619) during simulation. Besides, the observed pronounced dynamics of dimer interface region (β3-L6-β4 segment) of ACD along with CTD dynamics also gains importance. Particularly, the highly dynamic mutants are also characterized by enhanced non-covalent and hydrophobic interactions which renders detrimental effects towards its stability, and favours possible protein unfolding mechanisms. Overall, this study highlights the mutation-mediated structural distortions in αA-crystallin and demands the need for further potential development of inhibitors against cataract formation.

Salt-tolerant proteins, also known as halophilic proteins, have unique adaptations to function in high-salinity environments. These proteins have naturally evolved in extremophilic organisms, and more recently, are being increasingly applied as enzymes in industrial processes. Due to an abundance of salt-tolerant sequences and a simultaneous lack of experimental structures, most computational methods to predict stability are sequence-based only. These approaches, however, are hindered by a lack of structural understanding of these proteins. Here, we present HaloClass, an SVM classifier that leverages ESM-2 protein language model embeddings to accurately identify salt-tolerant proteins. On a newer and larger test dataset, HaloClass outperforms existing approaches when predicting the stability of never-before-seen proteins that are distal to its training set. Finally, on a mutation study that evaluated changes in salt tolerance based on single- and multiple-point mutants, HaloClass outperforms existing approaches, suggesting applications in the guided design of salt-tolerant enzymes.

Despite the efficacy of brain derived neurotrophic factor (BDNF) in neuro-regenerative medicine, it can’t pass the blood–brain barrier. Recently, exosomes have been harnessed for targeted delivery of therapeutics into brain. Given these facts, an engineered exosome capable of BDNF expression on the surface would be an amenable tool for drug delivery. The BDNF gene was cloned into a plex-lamp lentiviral vector and virus particles were packaged using the Torano method. HEK293T cells were transduced by the purified viruses to produce and purify recombinant exosomes displaying the fusion protein on their surfaces. Western blot, Zeta sizer, TEM, and ELISA methods were used for exosome characterization. The effect of engineered exosomes on menstrual blood-derived mesenchymal stem cells (Mens-MSCs) proliferation was evaluated by cell counting assay, MTT assay, and qPCR on the bcl2 and nestin genes. Approximately, 1.8 × 10⁸ TdU/ml of the viral particles was purified from the transfected cells and transduced into the HEK293T. Western blot and ELISA methods confirmed the surface display of the LAMP-BDNF fusion. TEM graphs and Zeta sizer results confirmed the morphology and the size of purified exosomes. Treatment of Mens-MSCs with the targeted exosomes augmented the expression level of bcl2 and nestin genes, increased the cell proliferation, and elevated the cell number. Chimeric BDNF on the exosome surface could retain its biological activity and elevate the expression of bcl2 and nestin genes. Moreover, these exosomes are capable of elevating the Mens-MSCs proliferation.

The synthesis of new agents for cancer treatment persists due to its global lethality. A series of thirteen derivatives, namely salicylic acid-5-sulfohydrazide (SA-SH) analogs, were designed and synthesized from 5-(chlorosulfonyl)-2-hydroxybenzoic acid via nucleophilic substitution reaction with different acid hydrazides, thiocarbohydrazide & thiosemicarbazide scaffolds. Confirmation of the designed derivative’s structures employed various spectroscopic techniques (FT-IR and NMR) and elemental analysis. The newly synthesized synthons were evaluated for cytotoxic activity against HepG-2 and HCT-116 cell lines in comparison to Doxorubicin. Notably, SA-SH derivatives (5, 7, 8a, 8b and 11) exhibited significantly higher efficacy against HepG-2 and HCT-116 cell lines than other analogs. Furthermore, compound (8a) demonstrated a superior activity against HepG-2 cell lines with IC₅₀ values of 3.99 ± 0.2 μM than the reference drug, Doxorubicin, (IC₅₀ HepG-2 = 4.50 ± 0.2 µM). The molecular docking simulation of the most active SA-SH derivatives and the reference drug doxorubicin into the active site of FGFR4 (fibroblast growth factor receptor, the predominant isoform expressed in human hepatocytes) (PDB ID: 6V9C) proved the usefulness of hybridizing salicylic scaffold with SO₂ and hydrazide moieties as a promising approach in designing new anticancer agents. Finally, ADME and drug-likeness features of the most active compounds compared to positive controls were investigated to increase the success possibilities in clinical trials and they were found to be promising candidates for further investigation and development as drugs.

Graphical Abstract

Cationic amino acid binding protein (CLasArgBP), one of the two amino acid binding receptor in Candidatus Liberibacter asiaticus (CLas), is predominately expressed in citrus psyllids as a part of ATP-binding cassette transport system. The present study describes characterization of CLasArgBP by various biophysical techniques and in silico study, to identify potential inhibitor molecules against CLasArgBP through virtual screening and MD simulations. Further, in planta study was carried out to assess the effect of selected inhibitors on Huanglongbing infected Mosambi plants. The results showed that CLasArgBP exhibits pronounced specificity for arginine, histidine and lysine. Surface plasmon resonance (SPR) study reports highest binding affinity for arginine (Kd, 0.14 µM), compared to histidine and lysine (Kd, 15 µΜ and 26 µΜ, respectively). Likewise, Differential Scanning Calorimetry (DSC) study showed higher stability of CLasArgBP for arginine, compared to histidine and lysine. N(omega)-nitro-L-arginine, Gamma-hydroxy-L-arginine and Gigartinine emerged as lead compounds through in silico study displaying higher binding energy and stability compared to arginine. SPR reports elevated binding affinities for N(omega)-nitro-L-arginine and Gamma-hydroxy-L-arginine (Kd, 0.038 µΜ and 0.061 µΜ, respectively) relative to arginine. DSC studies showed enhanced thermal stability for CLasArgBP in complex with selected inhibitors. Circular dichroism and fluorescence studies showed pronounced conformational changes in CLasArgBP with selected inhibitors than with arginine. In planta study demonstrated a substantial decrease in CLas titer in treated plants as compared to control plants. Overall, the study provides the first comprehensive characterization of cationic amino acid binding protein from CLas, as a potential drug target to manage HLB disease.

Protein solubility is a critical parameter that determines the stability, activity, and functionality of proteins, with broad and far-reaching implications in biotechnology and biochemistry. Accurate prediction and control of protein solubility are essential for successful protein expression and purification in research and industrial settings. This study gathered information on soluble and insoluble proteins. In characterizing the proteins, they were mapped to STRING and characterized by functional and structural features. All functional/structural features were integrated to create a 5768-dimensional binary vector to encode proteins. Seven feature-ranking algorithms were employed to analyze the functional/structural features, yielding seven feature lists. These lists were subjected to the incremental feature selection, incorporating four classification algorithms, one by one to build effective classification models and identify functional/structural features with classification-related importance. Some essential functional/structural features used to differentiate between soluble and insoluble proteins were identified, including GO:0009987 (intercellular communication) and GO:0022613 (ribonucleoprotein complex biogenesis). The best classification model using support vector machine as the classification algorithm and 295 optimized functional/structural features generated the F1 score of 0.825, which can be a powerful tool to differentiate soluble proteins from insoluble proteins.