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International Journal of Biological Macromolecules

Elsevier BV

All preprints, ranked by how well they match International Journal of Biological Macromolecules's content profile, based on 65 papers previously published here. The average preprint has a 0.11% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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Effect of SNEDDS Loading Pentagamavunon-0 on Memory Impairment and Neurogenesis in Mice with Monosodium Glutamate-Induced Alzheimers Disease-Like Symptoms

Anas, Y.; Susidarti, R. A.; Martien, R.; Yuniarti, N.

2024-05-19 animal behavior and cognition 10.1101/2024.05.17.594779 medRxiv
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Pentagamavunon-0 (PGV-0), a curcumin analog, has antioxidant and HDAC2 inhibitory properties. It affects neurogenesis and cognitive function in Alzheimers disease (AD). Targeting neurogenesis is a strategy currently being developed for AD treatment. This study investigates the therapeutic potential of self-nanoemulsifying drug delivery systems loaded with PGV-0 (SNEDDS PGV-0) on spatial learning, memory impairment, and gene expression-related neurogenesis in mice with monosodium glutamate (MSG) induced AD-like symptoms. MSG 4 g/kg was injected (sc.) into 4-week-old Balb/C mice seven times every alternate day, followed by treatment for 60 days with CMC-Na 0.5%, PGV-0 suspension, SNEDDS PGV-0, and donepezil-HCl. The open-field test, novel object recognition, and 8-radial arm maze test were employed to assess the neurobehavioral performance of mice. Neurogenesis-related gene expression (dcx, nestin, Hes5, and NFIA) was quantified through qPCR analysis. Spatial learning and memory in mice declined with MSG treatment. SNEDDS PGV-0 effectively alleviates mices cognitive and memory deficits, as shown in improvements in behavioral parameters, including the Discrimination Index, Recognition Index, and Memory Score. It also restores mRNA expression of several essential neurogenesis-related genes, including dcx, Hes5, and NFIA. SNEDDS PGV-0 demonstrates promising potential as a neurogenesis promoter, making it a viable drug candidate for AD or other neurodegenerative pathologies.

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Development of Nature-Based Insect-Repellent Surface Coating Using ZnO Nanoparticles and Plant Extracts for Mosquito Control

Iftikhar, T.; Majeed, H.; Abid, R.; Khan, F. A.

2023-04-03 animal behavior and cognition 10.1101/2023.04.03.535318 medRxiv
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Mosquitos have been a malice and source of many diseases in humans. Later on, humans understood they learned that plants also possess mosquito-repellent properties. Different insectrepellent coatings are present in the market which are chemically prepared and can be harmful to humans and the environment. Different plants have insect-repellent properties which have been utilized in this research to make a nature-based insect-repellent surface coating. Moringa oleifera L. and Mentha piperita L. are naturally insect-repellent plants. Nanoparticles increase the surface area and efficiency of extracts of plants. Thus, ZnONP of Moringa oliefera L. and Mentha piperita L. plants were made characterization was done through UV-vis spectroscopy, FTIR, and PSA. The UV-visible spectrum showed absorption peaks for ZnO nanoparticles at 350nm for Mentha piperita L. and 356nm for Moringa oleifera L. The particle size analysis indicated the variable sizes of ZnONPs for both plants. FTIR showed vibration peaks from 3341 to 650cm-1 for Moringa oleifera L. and 3393 to 700 cm-1 for Mentha piperita L. ZnONPs were used in paint along with water extracts of plants to make the paint insect-repellent in nature. Mosquito repellent activity of paint formulations was also tested against Aedes aegypti.

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The essential role of disulfide bonds for the hierarchical self-assembly and wet-adhesion of CP20-derived peptides

Baoshan Li, B. L.; Song, J.; Zeng, L.; Mao, T.; Ye, Z.; Hu, B.

2022-06-15 molecular biology 10.1101/2022.06.15.496244 medRxiv
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Barnacles are typical fouling organisms which strongly adhere to immersed solid substrates by secreting proteinaceous adhesives called cement proteins (CPs). The self-assembly of the cement proteins forms a permanently bounded layer that binds barnacle to foreign surfaces. However, due to the abundance of cysteines in whole-length CP20, it is difficult to determine its natural structure and to properly describe its self-assembly properties. In this study, a putative functional motif of Balanus albicostatus CP20 (BalCP20) is identified and found to present distinctive self-assembly and wet-adhesion characteristics. The atomic force microscopy (AFM) and transmission electron microscope (TEM) investigations show that wildtype BalCP20-P3 forms grain-like spindles, which further assembly into fractal-like structures looks like ears of wheat. SDS-PAGE, AFM and LSCM show that DTT treatment opens up disulfide bonds between cysteines and disrupts the fractal-like structures (eras of wheat). Additionally, these morphologies are abolished when one of the BalCP20-P3 four cysteines is mutated by alanine. Circular dichroism (CD) results further suggest that the morphological diversity among BalCP20-P3 and its mutations lays on the proportion of -helix. The above results demonstrate that cysteines and disulfide bonds play a crucial role in the self-assembly of BalCP20-P3. This study provides new insights into BalCP20 underwater adhesion, and brings in new inspirations for the development of novel bionic underwater adhesive.

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In silico Study of the Uncertainly Significant VCP Variants reveal major Structural, Functional fluctuations leading to potential Disease-Based Associations

DAS, T.; ROYCHOWDHURY, S.; DAS, P.

2024-02-27 genomics 10.1101/2023.11.04.565542 medRxiv
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Valosin containing protein is involved in a plethora of crucial functions from proteostasis, stress granule clearance to genome maintenance and ubiquitination. Hence, mutations in VCP can lead to a plethora of fatal diseases like Amyotrophic Lateral Sclerosis, Inclusion body myopathy with Paget disease of bone and frontotemporal dementia type 1, Spastic paraplegia, Charcot-Marie-Tooth disease type 2Y, Dementia, and Osteitis Deformans to name a few. Studies on VCPs disease phenotype relationship, structural, and functional modifications of the proteins stability, conservation, molecular dynamics, and post-translational modifications havent been performed. This in silico study investigated the variants of VCP (R95C, R95G, A160P, R191P, R191Q) which have conflicting interpretations of pathogenicity which are often depreciated and lack data. Additionally, this study screens the study cohort and the fatal diseases linked to all these variants. Interestingly through various computational tools and disease-based population studies, it was found that these variants are often found in patients linked with fatal diseases. The protein-protein interaction showed UFD1 has a direct association with VCP. The physicochemical parameters showed that A160P had the highest fluctuations of all the variants. VCPs protein secondary structure, molecular dynamics simulations of RMSD, RMSF, RoG, hydrogen bonds, and solvent accessibility were all comparatively impacted due to the changes caused by the variants. Box-plot and Principal component analysis of the MD simulations visualized the changes in the wild type of the protein. Research in wet labs and screening of patient cohorts is necessary to further characterize the diseases linked with these variants. This can potentially lead to the identification of biomarkers for fatal rare diseases.

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Tardigrade secretory proteins protect biological structures from desiccation

Lim, S.; Reilly, C. B.; Barghouti, Z.; Marelli, B.; Way, J. C.; Silver, P. A.

2023-12-05 molecular biology 10.1101/2023.12.04.570007 medRxiv
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Tardigrades, microscopic animals that survive a broad range of environmental stresses, express a unique set of proteins termed tardigrade-specific intrinsically disordered proteins (TDPs). TDPs are often expressed at high levels in tardigrades upon desiccation, and appear to mediate stress adaptation. Here, we focused on the proteins belonging to the secretory family of tardigrade proteins termed secreted-abundant heat soluble ("SAHS") proteins, and investigated their ability to protect diverse biological structures. Recombinantly expressed SAHS proteins prevented desiccated liposomes from fusion, and enhanced desiccation tolerance of E. coli and Rhizobium tropici upon extracellular application. Molecular dynamics simulation and comparative structural analysis suggest a model by which SAHS proteins may undergo a structural transition upon desiccation, in which removal of water and solutes from a large internal cavity in SAHS proteins destabilizes the beta-sheet structure. These results highlight the potential application of SAHS proteins as stabilizing molecules for preservation of cells.

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Structural analysis of Sub16 sedolisin of Trichophyton rubrum reveals a flexible nature of its pro domain

Latka, C.; Bikshapathi, J.; Aggarwal, P.; Bhavesh, N. S.; Chakraborty, R.; Khan, S. H.; Taneja, B.

2020-01-29 biophysics 10.1101/2020.01.28.922815 medRxiv
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Trichophyton rubrum is one of the leading causes of superficial skin infections worldwide. It is a keratinolytic fungus specialized in colonization of keratinized tissue of skin, hair and nails for long periods of time. The fungus encodes a wide repertoire of secreted proteases in its genome that not only aid in nutrient acquisition but also establishment of infection on the host. The proteases are synthesized in prepro form that requires removal of the prosegment for activation. In order to gain insights into the structural association of the pro domain with the catalytic domain, we investigate the structural features of the pro domain of the secreted sedolisin member Sub16 of T. rubrum. Our results show that the pro domain of Sub16 may have inherent flexibility in the absence of the associated catalytic domain which is stabilized in complex with catalytic domain. This is the first report of structural investigation on a stand-alone pro domain of sedolisin family of subtilases that will help in design of further structural studies of this protein.

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Iota-carrageenan protects the ocular surface from desiccation-induced cell death and tissue damage in vitro and ex vivo

Roch-Nakowitsch, S.; Russo, A.; Koller, C.; Dolischka, A.; Koenig-Schuster, M.; Dellago, H.; Prieschl-Grassauer, E.

2026-03-12 physiology 10.64898/2026.03.10.709798 medRxiv
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1.Iota-carrageenan is a natural polymer with moisturizing, mucoadhesive and shear-thinning properties. In this study, we aimed to evaluate the protective effects of iota-carrageenan on ocular surface against dehydration, to demonstrate its suitability for the use in lubricant eye drops. We utilized a human epithelial corneal cell culture model to test if pre-incubation with iota-carrageenan solution could protect cells from desiccation-induced cell death, to compare its effect with other natural polymers commonly used in artificial tear products, and to determine the optimal iota-carrageenan concentration. An ex vivo porcine eye model was established to confirm the protective effect of iota-carrageenan against dehydration on ocular tissue. Pre-incubation with 1.2 mg/ml iota-carrageenan increased the survival half-life of human corneal epithelial cells upon dehydration by three-fold; the effect was in the same range as observed for large molecular weight hyaluronic acid, and superior to all other tested natural polymers. The highest tested concentration of iota-carrageenan, 1.6 mg/ml, extended the cellular survival half-life by eight-fold while maintaining healthy cellular morphology. Repeated ex vivo instillation of an iota-carrageenan-based ophthalmic formulation into porcine eyes significantly protected the ocular surface from desiccation-induced corneal damage, as shown by corneal fluorescein staining These data suggest that Iota-carrageenan effectively moisturizes and protects the ocular surface, supporting its potential as a promising novel ingredient for eye drops in the management of dry eye disease.

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A novel lethal cuticular structural protein, AaCPR100A and its upstream interaction protein, G12-like, function in cuticle and egg shell formation in the yellow fever mosquito, Aedes aegypti

Chen, J.; Wu, Y.; Lu, H.; Cheng, G.; Tu, Z.; Liao, C.; Han, Q.

2023-02-05 molecular biology 10.1101/2023.02.05.527159 medRxiv
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AaCPR100A is a structural protein, found in the soft cuticle of Ae. Aegypti. RNAi of AaCPR100A resulted in high mortality in Ae. Aegypti and abnormal egg development in the surviving mosquitoes. Over thirty proteins that could interact with AaCPR100A were screened out by yeast two-hybrid assay, and subsequently, further verification by hybrid and GST pull-down assays identified that G12-like had the strongest interaction with AaCPR100A. RNAi of G12-like suggested it may be related to larva development. Interestingly, the adults in which the G12-like gene was knocked down were sensitive to low temperature, and their egg shell formation, production, and hatching were affected. G12-like has the opposite effect in the upstream expression of AaCPR100A, promoting AaCPR100A function in the larval stage and inhibiting AaCPR100A in the adult stage. In all, functional studies of AaCPR100A and its interaction protein G12-like provide insight into its involvement in cuticle development and formation and egg shell formation.

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Hidden potential of the supporting scaffold as a structural module for plant cystatin design

Tremblay, J.; Goulet, M.-C.; Goulet, C.; Michaud, D.

2022-03-01 plant biology 10.1101/2022.02.26.482125 medRxiv
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Protein engineering approaches have been proposed to improve the inhibitory properties of plant cystatins towards herbivorous pest digestive Cys proteases, typically involving sequence alterations in the inhibitory loops and/or N-terminal trunk of the protein interacting with specific amino acid residues of the target protease. In this study, we assessed whether the loops-supporting frame, or scaffold, would represent a valuable structural module for cystatin function improvement. Twenty hybrid cystatins were designed in silico, consisting of the N-terminal trunk and two inhibitory loops of a given donor cystatin grafted onto the scaffold of an alternative, recipient cystatin. Synthetic genes for the hybrids were expressed in E. coli, and the resulting proteins assessed for their potency to inhibit model Cys protease papain and the digestive Cys proteases of Colorado potato beetle (Leptinotarsa decemlineata) used as an insect pest model. In line with the occurrence of positively selected amino acids presumably influencing inhibitory activity in the scaffold region of plant cystatins, grafting the N-terminal trunk and inhibitory loops of a given cystatin onto the scaffold of an alternative cystatin generally had an effect on the inhibitory potency of these function-related elements against Cys proteases. For instance, hybrid cystatins including the three structural elements of model tomato cystatin SlCYS8 grafted on the scaffold of cystatins from other plant families showed Ki values altered by up to 3-fold for papain, and inhibitory efficiencies increased by up to 8-fold against L. decemlineata cathepsin L-like proteases, compared to wild-type SlCYS8 bearing the original scaffold. Our data point to a significant influence of the cystatin scaffold on the inhibitory activity of the N-terminal trunk and protease inhibitory loops. They also suggest the potential of this structural element as a module for plant cystatin design to generate functional variability against Cys proteases, including the digestive proteases of herbivorous pests.

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Conformational stability of a peroxidase from Artocarpus lakoocha: Effect of pH, chaotrophs and temperature.

Sonkar, K. S.; Pachauri, M.; Kumar, A.; Medicherla, J.

2023-01-28 biophysics 10.1101/2023.01.27.525866 medRxiv
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A novel heme-peroxidase has been extracted from the latex of the medicinal plant Artocarpus lakoocha (A. lakoocha), known for its potential anti-inflammatory and wound healing properties. To study its stability, structure, and dynamics, this protein was analyzed using far-UV circular dichroism, fluorescence spectroscopy, and activity measurements. The results demonstrated the presence of three folding states: the native state (N) at neutral pH, intermediate states including molten globule (MG) at pH 2 and acid-unfolded (UA) at pH 1.5 or lower, and acid-refolded (A) at pH 0.5, along with alkaline denatured (UB) at pH 8-12 and the third denatured state (D) at GuHCl concentrations exceeding 5 M. Absorbance studies indicated the presence of free heme in the pH range of 1-2. The protein showed stability and structural integrity across a wide pH range (3-10), temperature (70 {degrees}C), and high concentrations of GuHCl (5 M) and urea (8 M). This study is the first to report multiple partially folded intermediate states of A. lakoocha peroxidase, with varying amounts of secondary structure, stability, and compactness. These results demonstrate the high stability of A. lakoocha peroxidase and its potential for biotechnological and industrial applications, making it a valuable model system for further studies on its structure-function relationship.

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In Silico-Driven Engineering of Halomonas elongata L-Asparaginase: Towards Enhanced Proteolytic Resistance in Lymphoblastic Leukemia

Samadaei Ghadikolaei, M.; Asad, S.; Hassan-Zadeh, V.

2024-06-08 molecular biology 10.1101/2024.06.07.597648 medRxiv
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The shortened L-asparaginases half-life in leukemia patients due to elevated serum proteases, poses a challenge. This study aimed to enhance the stability of Halomonas elongata L-asparaginase against trypsin. Employing the trRosetta server, we modeled the enzymes 3D structure with a quality score of 96.5, revealing predominant secondary structure of random coils (42%), alpha helices (33%), and extended strands (20%) organized in two domains. Molecular docking unveiled a triad alignment among residues Thr16, Ser65, and Asp97 with L-asparagine. Site selection for mutation considered secondary structure prediction, dimerization analysis, trypsin cleavage site determination and epitope mapping. A library of enzyme variants was constructed through site saturation mutagenesis which led to the identification of the Arg206 to Thr, resulting in a 1.7-fold increased enzyme-specific activity (2400 U/mg) and heightened trypsin resistance. The mutant displayed a half-life of 3.47 hin human serum, approximately 50% longer than the wild type. In silico analyses confirmed structural stability, reduced flexibility, and enhanced substrate binding, contributing to increased proteolysis resistance and enzymatic activity. The Arg206Thr mutant exhibited anti-proliferative activity (IC50 of 1.45 U/ml) on leukemia cell line K562, suggesting potential therapeutic implications.

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An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2

Kumar, S.; Azad, G. K.

2021-04-02 molecular biology 10.1101/2021.04.02.438155 medRxiv
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The on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has infected hundreds of millions of people and killed more than two million people worldwide. Currently, there are no effective drugs available for treating SARS-CoV-2 infections; however, vaccines are now being administered worldwide to control this virus. In this study, we have studied SARS-CoV-2 helicase, Nsp13, which is critical for viral replication. We compared the Nsp13 sequences reported from India with the first reported sequence from Wuhan province, China to identify and characterize the mutations occurring in this protein. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited high antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were also analysed. Furthermore, several of these Nsp13 epitopes harbour mutations, which were further characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. Altogether, we report the candidate epitopes of Nsp13 that may help the scientific community to understand the evolution of SARS-CoV-2 variants and their probable implications.

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A novel LysinB from an F2 sub-cluster mycobacteriophage RitSun

Arora, R.; Nadar, K.; Bajpai, U.

2024-02-29 molecular biology 10.1101/2024.02.29.582697 medRxiv
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With the growing antibiotic resistance in mycobacterial species posing a significant threat globally, there is an urgent need to find alternative solutions. Bacteriophage-derived endolysins aid in releasing phage progeny from the host bacteria by attacking the cell wall at the end of their life cycle. Endolysins are attractive antibacterial candidates due to their rapid lytic action, specificity and low risk of resistance development. In mycobacteria, owing to the complex, hydrophobic cell wall, mycobacteriophages usually synthesize two endolysins: LysinA, which hydrolyzes peptidoglycan; LysinB, which delinks mycolylarabinogalactan from peptidoglycan and releases mycolic acid. In this study, we conducted domain analysis and functional characterization of a recombinant LysinB from RitSun, an F2 sub-cluster mycobacteriophage. Several properties of RitSun LysinB are important as an antimycobacterial agent: its ability to lyse Mycobacterium smegmatis from without, a specific activity of 1.36 U/mg, higher than the reported ones and its inhibitory effect on biofilm formation. Given the impervious nature of the mycobacterial cell envelope, native endolysins ability to damage cells on exogenous applications warrants further investigation. A molecular dissection of RitSun LysinB to identify its cell wall destabilizing sequence could be utilized to engineer other native lysins as fusion proteins and expand their activity profile.

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Purification, crystallization, and preliminary structural analysis of multivalent immunogenic effector protein-anchored SARS-CoV-2 RBD

Kwon, T. H.; Kim, T. G.

2023-08-18 biophysics 10.1101/2023.08.17.553661 medRxiv
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The continuous spread of highly transmissible variants of concern and the potential diminished effectiveness of existing vaccines necessitate ongoing research and development of new vaccines. Immunogenic molecule-anchored antigen has demonstrated superior efficacy in subunit vaccination, primarily due to enhanced cellular uptake facilitated by the affinity between the surface of Immunogenic molecule and the cell membrane. Based on the Immunogenic recombinase B. malayi RecA (BmRecA), we have overexpressed the construct of BmRecA with SARS-CoV-2 RBD (BmRecA-RBD) that exists as a stable helical filament formation; it was purified and crystallized to obtain X-ray diffraction data at 2.7 [A], belonged to the hexagonal symmetry group P65 in the unit-cell parameters of a=b=122.12, c=75.55 and ={beta}=90{degrees}, {gamma}=120{degrees}. The Matthews coefficient was estimated to be 3.12 [A]3 Da-1, corresponding to solvent contents of 52.65.

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Unveiling the effect of phosphorylation on the structural and aggregation properties of the amyloidogenic intrinsically disordered protein DPF3a

Leyder, T.; Mignon, J.; Bongiovanni, E.; Machiels, Q.; Waeytens, J.; Raussens, V.; Monari, A.; Mottet, D.; Michaux, C.

2025-08-22 biophysics 10.1101/2025.08.17.670156 medRxiv
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The double plant homeodomain fingers 3a (DPF3 isoform a) is a human epigenetic regulator involved in chromatin remodelling, cell division, and ciliogenesis. Most notably, this protein is deregulated in various cancer types and neurodegenerative diseases. In our previous work, the disorder nature of DPF3a, as well as its propensity to aggregate into amyloid fibrils, have been highlighted, making it an amyloidogenic intrinsically disordered protein (IDP). Due to their high chain accessibility, IDPs structure and function are modulated by phosphorylation. It has been reported that phosphorylation of DPF3a at S348 (pS348) by the casein kinase 2 (CK2) is implicated in cardiac hypertrophy. CK2 can also phosphorylate DPF3a at S138 (pS138), which is also located in an intrinsically disordered region (IDR). However, no structural information is available on phosphorylated DPF3a. In the present study, we investigated the effect of phosphorylation on DPF3a structural and aggregation properties. Two single-mutated phosphomimetics (S138E and S348E) were characterised in vitro and compared to DPF3a WT, while in silico analyses were performed on pS138 and pS348 to assess structural changes at the molecular level. Circular dichroism and fluorescence spectroscopy revealed that both phosphomimetics are hybrid IDPs, with increased turn and antiparallel {beta}-sheet content as well as more buried aromatic residues compared to DPF3a WT, suggesting conformational rearrangements and a more folded N-terminal region. In silico characterisation supported these results, showing that phosphorylation of S138 and S348 induce extended conformation, especially the C-terminal extremity, due to electrostatic repulsion, while local folding occurs due to a proximity with arginine and lysine residues. Furthermore, spectroscopic and microscopic analyses unveiled that S138E and S348E exhibit slower fibrillation kinetics compared to DPF3a WT involving distinct aggregation mechanisms.

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Spike protein E2 of chikungunya virus: a plant-based vaccine exhibited potent immunogenicity in BALB/c mice

Qamar, S.; Dalal, M.; Amna, S.; Abdin, M. Z.; Qamar, F.; Ahmad, A.; Beg, M. A.; Quadri, S. N.; Ahmad, J.; Parvez, S.; Qureshi, M. I.

2025-08-22 molecular biology 10.1101/2025.08.21.671458 medRxiv
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Over the last two decades, chikungunya virus (CHIKV) infections have surged worldwide, causing significant suffering. CHIKV E2 gene codes for spike protein E2, essential for virus-host interactions and thus serves as a potential vaccine candidate. We expressed a full-length E2 (S27 African prototype) in both E. coli and Nicotiana tabacum, which triggered an immune response in BALB/c mice. First, E2 was computationally analyzed for PTM patterns and prediction of B-cell and T-cell epitopes. Next, molecular docking of epitopes with MHCs (Class I and II) revealed high affinity, confirmed by Molecular Dynamics Simulation. Then, the chemically synthesized E2-6xHis tag was cloned and expressed in both E. coli and N. tabacum under T7 and CaMV promoters, respectively. E2 was cloned into the pUC57 vector (E. coli) and expressed using the pET28a(+) vector in BL21(DE3)pLysS cells, followed by cloning into the pCAMBIA1302 vector and transformation into Agrobacterium tumefaciens. RT-PCR and confocal visualization confirmed the formation of E2 transcripts. Recombinant E2 was purified on Ni-NTA columns and visualized as a protein of [~]49 kDa on SDS PAGE. Finally, E2 was injected into BALB/c mice; neutralizing antibodies, including IgG, were detected as positive in the indirect ELISA, with the highest levels observed at 3 days post-infiltration (3 dpi). Western blot also confirmed E2 expression in E coli and tobacco, and induction of E2-specific antibodies in BALB/c mice. This study presents a promising approach to developing a safe and effective vaccine against chikungunya fever in plants.

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Room-temperature Storage of Lyophilized Engineered Bacteria using Tardigrade Intrinsically Disordered Proteins

Yang, Y.; Jiao, Z.; Zhang, S.; Shan, M.; Duan, S.; Wang, X.; Wang, S.; Tang, Y.; Wang, S.

2021-06-26 synthetic biology 10.1101/2021.06.25.449888 medRxiv
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Tardigrades, which live in transiently wet environments such as moss, are well-known for their extreme resistance to desiccation. Tardigrade intrinsically disordered proteins (TDPs) have been reported to also protect bacteria and yeast under desiccation [4, 5, 32]. In this study, we utilized lyophilization to achieve room-temperature storage of engineered bacteria. By using TDPs, engineered bacteria are protected under lyophilization and their original functions are preserved [12, 17, 18]. This study shows that TDPs can be expressed in the Escherichia coli (E. coli) BL21 and DH5, and bacteria treated with Cytosolic-abundant heat soluble protein (CAHS) 106094 displayed the highest survival rate after lyophilization [16, 41, 44]. Moreover, this study shows that the co-expression of TDPs can improve the preservation of bacteria and maintain high survival rates after prolonged room temperature storage. Additionally, the TDPs can be expressed using different vectors, which means that they can be used in different types of engineered bacteria. This study offers a new storage method that not only improves the storage of biological material for industrial and daily usage, but also for future iGEM (International Genetically Engineered Machine Competition) teams to store and use their engineered bacteria in different applications.

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Functional diversity of Arabidopsis late embryogenesis abundant proteins in response to changes in the physicochemical environment

Palomino-Navarrete, L. D.; Perez-Villanueva, D.; Moses, D.; Gollub, E.; Nguyen, K. H.; Sanchez Martinez, S.; Yu, F.; Martinez, K.; Boothby, T. C.; Sukenik, S.; Cuevas-Velazquez, C. L.

2025-08-29 biophysics 10.1101/2025.08.26.672499 medRxiv
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Some desiccation-tolerant organisms accumulate intrinsically disordered proteins (IDPs), such as Late Embryogenesis Abundant (LEA) proteins, which help protect other proteins from inactivation and/or aggregation during desiccation. Like other IDPs, LEA proteins adopt ensembles of extended conformations that shift in response to environmental changes. Desiccation causes dramatic changes in the cellular environment, but it is unclear how the structural malleability of LEAs is related to their protective function. In this work, we measured the in vitro protective function and structural sensitivity to changes in the environment of four Arabidopsis thaliana LEA proteins from different families. We found that all LEAs showed different protection efficiencies of the labile enzyme lactate dehydrogenase under desiccation in vitro. In line with this, we identified distinct ensemble structural changes when these LEA proteins were exposed to different physicochemical environments. Specifically, AtEM1, AtLEA7, and AtLEA4-5 showed compaction when the solution was crowded with polymers, whereas AtLEA6-2.2 showed larger structural changes when salt concentrations were increased. Furthermore, the ensembles of AtEM1, AtLEA7, and AtLEA4-5 gained helicity under desiccated conditions, while that of AtLEA6-2.2 remained largely disordered. Our results highlight how ensemble properties of LEA proteins contribute to their distinct functional activities in vitro. This work advances our understanding of the molecular features that contribute to functional diversity in desiccation-related IDPs.

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A first-in-Plasmodium study on tRNA intron splicing endonuclease PfTSEN1 and its substrate expression in clinical stage malaria

Maurya, M. K.; Behl, A.; Kahlon, A. K.; Leon, F. D.; Middha, P.; Nirban, R.; Joshi, P.; Singhal, J.; Kumari, G.; Munjal, A.; Shoaib, R.; Jha, N.; Pandey, J.; Dutta, T.; Arenz, C.; Ranganathan, A.; Singh, S.

2024-06-07 molecular biology 10.1101/2024.06.07.597859 medRxiv
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Mature tRNAs play critical role in several cellular processes including protein translation, post-translational-modifications and programmed-cell-death. Maturation of pre-tRNAs require removal of 5-leaders, 3-trailers, splicing of introns and addition of conserved 3-terminal CCA sequence. The tRNA splicing mechanism, an essential step in tRNA maturation govern by a tRNA splicing endonuclease. While the existence of functional tRNA splicing endonuclease(s) in Plasmodium falciparum has not been identified, its significance in other eukaryotes suggests a potential role in tRNA splicing event. Our study identified total tRNAs in Plasmodium and characterize a PftRNA splicing endonuclease (annotated as PfTSEN1) recognised recently as a component of ribonucleoprotein (RNP) complex, and synthesized a naphthoquinone derivative as a novel anti-malarial compound ( TSENi) targeting the functional activity of this protein. Enzyme activity assays elucidated that PfTSEN1 catalyses splicing of in vitro transcribed pre-tRNAleu, the expression of which was confirmed during the clinical stages of malaria parasite by RT-PCR. Interestingly, TSENi binds to and inhibits enzymatic activity of PfTSEN1, and showed potent anti-malarial activity against chloroquine-sensitive 3D7 and resistant strains Dd2 of P. falciparum. Overall, our study deliver key knowledge towards the functional role of PftRNA splicing endonuclease, and its inhibitor TSENi as potent anti-malarial.

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Prioritization of The Zinc finger domain within BCL11A gene by the Amelioration capability of hemoglobinopathies using CRISPR-Cas9 technology

Mumtaz, K.; Hussain, I.; Iftikhar, F.; Rehman, F. u.; Muhammad, J.; Farooq, S.; Hassan, H.; Ottmann, O. G.; Mian, A. A.

2023-11-28 molecular biology 10.1101/2023.11.28.568974 medRxiv
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BCL11A/EVI9, a zinc-finger protein primarily expressed in brain and hematopoietic cells, plays a central role in lymphocyte development, gamma-globin suppression, spinal neuron development, sensory innervation, neuronal polarity, migration, and is associated with microcephaly and dysregulated brain-related genes, offering therapeutic potential for sickle cell disease. The function of the transcriptional regulator is intricately linked to its structural organization, which determines its ability to interact with specific DNA sequences and modulate gene expression. BCL11A boasts multiple domains, including six C2H2 zinc fingers, a C2HC zinc finger, a NuRD-interacting domain, an acidic domain, and a proline-rich domain. In the present study, we delve into the intricate structure and function of the zinc finger domains located in the BCL11A gene, which plays a crucial role in regulating the expression of gamma-globin gene. Specifically, three C2H2-type zinc finger domains, Znf4, Znf5, and Znf6, within BCL11A, are known to bind to DNA. Znf4 and Znf5 demonstrate a significant interaction with the TGACCA motif in the gamma-globin -115 HPFH region sequence, contributing substantially to DNA binding specificity. Although Znf3 and Znf6 also interact with DNA, their contributions are comparatively minor. Employing CRISPR-Cas9 technology, targeted genomic deletions of Znf4 exhibit high efficiency, opening doors for further research. Edited CD34+ cells successfully differentiate into erythrocytes without impairments, underscoring CRISPR-Cas9s suitability for studying gene functions in erythropoiesis. Furthermore, BCL11A knockdown via sgRNAs results in elevated gamma-globin expression, offering a promising therapeutic avenue for beta-hemoglobinopathies. HPLC analysis reveals a substantial increase in HbF levels, particularly upon Znf4 deletion, emphasizing BCL11A gene potential as a therapeutic target. These findings also highlight the connection between the function of BCL11A and its structural organization, which can be modulated, and this insight can potentially be extended to uncover its roles in various other domains.