Protein and Peptide Letters - Online First
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Structural Insights into Ligand-Induced Conformational Changes in Adenine Phosphoribosyl Transferase from Fusobacterium nucleatum
Authors: Bogeun Kim, Jisub Hwang, Hackwon Do, Youn-Soo Shim and Jun Hyuck LeeAvailable online: 22 January 2026More LessBackgroundAdenine phosphoribosyltransferase (APRT) is an enzyme that facilitates adenosine monophosphate (AMP) biosynthesis by transferring a phosphoribosyl group to adenine using phosphoribosyl pyrophosphate as a donor. While the human enzyme is well characterized, structural insights into bacterial APRTs remain limited. Fusobacterium nucleatum is associated with periodontal disease, yet its APRT enzyme (FnAPRT) has not been structurally investigated.
ObjectiveThis study aimed to examine the crystal structure of FnAPRT and ligand-induced conformational changes to understand its enzymatic and substrate recognition mechanisms.
MethodsThe FnAPRT protein was heterologously expressed in Escherichia coli, followed by initial purification using nickel-charged affinity resin chromatography and further purification through size-exclusion chromatography. The FnAPRT structure was resolved using X-ray crystallography and compared with that of E. coli APRT (EcAPRT), exhibiting the highest amino acid sequence similarity among bacterial APRT structures.
ResultsAMP and phosphate (PO4) were observed in the active site of FnAPRT. Significant differences in ligand positioning were observed between the AMP-PO4-bound structures of FnAPRT and EcAPRT. Structural shifts induced by AMP-PO4 binding were detected. The Arg78 and Lys82 residues from the alternate subunit occupied the PO4 site in the absence of ligands, but they interacted with PO4 upon AMP-PO4 binding. Structural comparison of the AMP-PO4-bound FnAPRT with that of the adenine-bound EcAPRT highlighted variations in the adenine-binding site and associated structural changes.
DiscussionStructural comparison of the AMP-PO4-bound FnAPRT with that of the adenine-bound EcAPRT highlighted variations in the adenine-binding site and the associated structural changes.
ConclusionThe AMP-PO4-bound FnAPRT exhibited distinct ligand-binding modes despite sharing a high sequence similarity with EcAPRT. The structures demonstrated ligand movement during bacterial APRT reactions.
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Prolyl 4-Hydroxylase Beta Peptide Promotes Invasion, Migration, and Epithelial-Mesenchymal Transition through Activation of the Claudin-1/ AMPK/TGF-β1 Pathway in Bladder Cancer Cells
Authors: Mingning Qiu, Shuai Zhang, Jinglan Liang, Genyin Chen and Jie LiuAvailable online: 22 January 2026More LessIntroductionProlyl 4-hydroxylase beta peptide (P4HB) is a novel diagnostic and prognostic marker associated with cancer progression and clinical outcomes, and it is upregulated in multiple types of cancer cells. However, the influence and potential mechanisms of P4HB on the migration, invasion, and epithelial-mesenchymal transition (EMT) of bladder cancer cells remain unclear. This study aims to clarify the role of P4HB in the migration, invasion, and EMT of bladder cancer cells and to explore its potential mechanism related to the Claudin-1/AMPK/TGF-β1 pathway.
MethodsThe mRNA and protein expression levels of P4HB were examined in human ureteral epithelial cells (SV-HUC-1) and five bladder cancer cell lines (J82, T24, 5637, UM-UC-3, and RT4). Stable cell lines with P4HB overexpression and knockdown were constructed, and the effects of P4HB on migration, invasion, EMT, and the expression of EMT-related genes in bladder cancer cells were analyzed using wound healing assays, Transwell invasion assays, cellular morphology observations, real-time quantitative PCR, in-cell western blotting, western blotting, and enzyme-linked immunosorbent assays. Furthermore, Claudin-1 siRNA was transfected into P4HB-overexpressing cells to investigate its potential role in P4HB-induced invasion and EMT in bladder cancer cells.
ResultsP4HB mRNA and protein expressions were significantly upregulated in human bladder cancer cell lines compared to those in ureteral epithelial cells. Cell migration, invasion, and EMT were significantly promoted in P4HB-overexpressing stable bladder cancer cells and suppressed in P4HB-knockdown cells. Furthermore, interference with P4HB downregulated EMT-related Claudin-1 mRNA and protein expressions and regulated the expression of downstream genes and proteins of Claudin-1. Moreover, interference of Claudin-1 with its siRNA significantly reversed the invasion and EMT induced by P4HB-overexpression, however, the effect of Claudin-1 siRNA was revised by TGF-β1 agonist and AMPK inhibitor.
ConclusionP4HB promoted migration, invasion, and EMT of bladder cancer cells by activating the Claudin-1/AMPK/TGF-β1-related pathway.
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Optimized Strategy for Expression, On-Column Refolding, and Purification of NEDD8 Protein
Authors: Shalu Yadav, Neeraj Kumar Fauzdar, Yashwant Kumar Yadav and Gajendra SinghAvailable online: 22 January 2026More LessIntroductionUbiquitin and the Ubls family are known for their high solubility and excellent expression profiles in recombinant systems. In contrast, Neural Precursor Cell Expressed, Developmentally Down-Regulated 8 (NEDD8) is a ubiquitin-like modifier that shares more than 60% sequence identity with ubiquitin and exhibits a similar structural fold. NEDD8 primarily functions by modifying the cullin subunits of cullin-RING E3 ligases, thereby playing a critical role in regulating the cell cycle, embryonic development, and DNA repair processes, particularly by localizing to sites of DNA damage. Despite its structural and functional similarity to highly soluble ubiquitin family proteins, recombinant NEDD8 is predominantly expressed in inclusion bodies, making its purification challenging.
MethodsTraditional refolding and purification strategies using 6M urea have proven inefficient in recovering properly folded and functional protein. In this study, we present a streamlined, high-yield method for purifying NEDD8 based on on-column refolding using a 6xHis tag in combination with nickel-affinity chromatography, followed by size exclusion chromatography for further purification.
ResultsThe structural integrity and correct folding of the purified NEDD8 were confirmed through both nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy, validating the effectiveness of the method for producing biologically relevant, properly folded protein.
Limitation of the StudyWe applied an on-column refolding method for NEDD8, eliminating dialysis-associated losses and yielding well-folded protein. The approach is effective for small proteins but limited by size, hydrophobicity, and charge-related aggregation risks. Broader applicability requires case-specific optimization to ensure correct folding and structural fidelity across diverse proteins.
ConclusionOur results demonstrate that this on-column refolding approach significantly improves the yield and refolding efficiency of NEDD8 compared to previous urea-based methods.
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mRNA-Based Cancer Vaccines: A Review of the Current Scenario and Future Prospects
Authors: Sanchari Bhattacharya, Nilufa Easmin, Atanu Panja, Aditi Nayak and Debjeet SurAvailable online: 08 January 2026More LessMessenger RNA (mRNA) has gained increasing attention as a valuable tool to cure various human diseases, particularly malignant tumors. Such growing interest has been triggered largely by the phenomenal clinical success of mRNA vaccines developed using lipid nanoparticle (LNP) technology against COVID-19. mRNA may be used to produce cancer immunotherapies in numerous different ways, including cancer vaccines to induce or enhance immunity to tumor-specific antigens (TSAs) or tumor-associated antigens (TAAs). mRNA can also be used to adoptively transfer T-cells for the expression of antigen receptors, such as chimeric antigen receptors (CARs), therapeutic antibodies, and immunomodulatory proteins to re-engineer the tumor microenvironment. However, the therapeutic potential of mRNA-based cancer immunotherapy is not fully utilized due to a few limitations, such as mRNA instability, production of immunogenicity, and a lack of efficient in-vivo delivery methods. This review provides an overview of the current advancements and future directions of mRNA-based cancer therapies, including various delivery routes and therapeutic platforms. It addresses the mechanistic basis of mRNA cancer vaccines, non-replicating and self-amplifying mRNA, as well as their clinical development, personalized vaccines, and applications of mRNA for encoding antigen receptors, antibodies, and immunomodulatory proteins. Moreover, the review addresses nanoparticle-based platforms, such as lipid nanoparticles (LNPs), polymeric nanoparticles, and peptide-based nanoparticles, all used to improve the therapeutic effectiveness of mRNA-based drugs by improving their targeted delivery to tissues. This review aims to provide insights into the use of state-of-the-art mRNA-based cancer immunotherapy.
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Deprotection Bases as an Alternative to the Traditional Bases Used in Solid-Phase Peptide Synthesis
Available online: 04 November 2025More LessBackgroundThe use of peptides in the pharmaceutical and cosmetic industries is attracting increasing attention. Most of the peptides currently marketed are obtained by chemical processes, most frequently solid-phase peptide synthesis (SPPS).
ObjectiveAlthough SPPS is efficient, it requires hazardous solvents, such as N,N-dimethylformamide, dichloromethane, and N-methylpyrrolidone, as well as the bases piperidine and 4-methylpiperidine in the deprotection step. This study presents two alternative reagents, 2-aminoethanol and 2-amino-2-methyl-1-propanol, for the removal of the fluorenyl-methyloxycarbonyl protecting group used in SPPS.
MethodsThe traditional and alternative green SPPS using Fmoc protocol were employed.
ResultsThe synthesis of two peptides showed that the 2-aminoethanol and 2-amino-2-methyl-1-propanol are viable replacements for piperidine-derived reagents in peptide synthesis.
DiscussionThe use of these reagents in SPPS afforded two peptides in high yield in an environmentally sustainable solvent.
ConclusionThe reagents are thus promising alternatives to piperidine derivatives, particularly 2-amino-2-methyl-1-propanol, in SPPS.
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Customizing Proteins: Reassigning Functionality of Proteins via Incorporation of Unnatural Amino Acids
Available online: 21 October 2025More LessThe natural horizon of the genetic code has expanded to incorporate amino acids, such as selenocysteine and pyrrolysine. Researchers have incorporated unnatural amino acids (UAAs) into target proteins, demonstrating increased protein functionality depending on their choice and target. The primary challenge in protein engineering is identifying novel antimicrobial short peptides effective against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which are categorized as multidrug-resistant (MDR). UAAs can be preferentially incorporated into short peptides to display therapeutic activity, potentially leading to next-generation targeted therapeutics. In purview of this, we have curated and summarized the applicability of genetic incorporations of UAAs in antimicrobial short peptides with a special emphasis on the importance of green synthesis. The approach affirmed a reduction in the toxicity of peptide drugs, making it biocompatible. This is an efficient protocol to develop novel antimicrobial short peptides catering to precision medications, particularly against MDR pathogens, as a sustainable pharmaceutical approach.
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Effective Plant-Derived Proteins and Peptides in Leukemia Treatment
Authors: Zahra Moghaddasi, Azam Bolhassani and Elnaz AgiAvailable online: 10 September 2025More LessLeukemia is one of the most prevalent malignancies worldwide that causes the unusual evolution of hematopoietic stem cells. The type of leukemia determines the optimal treatment plan and the patient's survival. However, finding safer and more effective medications and developing novel therapeutic strategies are still the most challenging research topics. Nowadays, over half of the medications used to treat cancer are derived from natural ingredients. Medicinal plants are a reliable natural source of anti-leukemic medications. Plant-derived biologically active compounds, including secondary metabolites, have long been considered extremely valuable for treating various human illnesses. However, the limitations of secondary metabolites have led scientists to seek alternative biologically active compounds. Plant-derived proteins and peptides have recently been explored as potential treatments for various human ailments, showing anti-microbial, anti-oxidant, anti-HIV, anti-cancer, ribosome-inactivating, and neuromodulatory properties. Until now, no review article has documented the biologically active proteins and peptides against leukemia. This review article explores the therapeutic properties of plant-derived proteins and peptides against leukemia.
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Antimicrobial Activity of a Defensin-Rich Fraction from Capsicum chinense Fruits: Insights for Biotechnological Applications against Fungal Infections
Available online: 16 July 2025More LessBackgroundThe increasing resistance of fungal pathogens to conventional antifungal treatments has led to a global rise in fungal infections, affecting human health (Candida spp.) and agricultural productivity (Colletotrichum and Fusarium spp.). Antimicrobial peptides (AMPs), such as defensins, have gained attention for their potential in controlling these infections due to their broad-spectrum activity.
ObjectivesThe aim of this study was to partially purify and characterize the antifungal activity of a defensin-enriched fraction (F3) from Capsicum chinense fruits. Specifically, we sought to evaluate its efficacy against pathogenic fungi and yeasts, and to assess the relative abundance of defensins in the fraction.
MethodsThe F3 fraction was obtained using ion exchange and molecular exclusion chromatography. Reverse-phase chromatography (HPLC) was then employed for further purification. The antifungal activity of F3 was tested against Colletotrichum, Fusarium, and Candida species. Mass spectrometry was used to identify and characterize the defensin (CcDef3) within the fraction. The presence of the defensin relative to other components was inferred from electrophoretic profiles and peptide analysis.
ResultsThe F3 fraction exhibited significant antifungal activity, with growth inhibition of Colletotrichum lindemuthianum of 51% and 60.9% at concentrations of 100 and 200 μg mL-1, respectively. The fraction also inhibited the growth of several Candida species, notably C. nivariensis (93.8%) and C. bracarensis (79.6%) at 100 μg mL-1. Cell viability analysis indicated a fungistatic effect. Fluorescence microscopy assays showed that F3 induced membrane permeabilization in C. parapsilosis and C. lindemuthianum, and increased ROS production in C. pelliculosa and F. solani. The defensin-rich H8 fraction, containing a 6.5 kDa protein (CcDef3), was identified as a major component via mass spectrometry.
DiscussionThe ongoing development of resistance in fungal strains, particularly Candida species, against traditional antibiotics and antifungals has turned into a significant medical concern and has increased the need for new treatment options.
ConclusionThese results suggest that the F3 fraction, particularly the defensin CcDef3, has potential as an antifungal agent for biotechnological and therapeutic applications. However, further studies are needed to quantify the contribution of CcDef3 relative to other components in the fraction and to fully isolate the defensin for in-depth analysis.
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Use of Plant Peptidases for the Production of Therapeutic Peptides
Available online: 11 April 2025More LessPeptidases play crucial roles in numerous physiological processes within living organisms. Therefore, they have been employed in various pharmaceutical applications. Plant peptidases have attracted considerable attention in various areas due to their specificity, stability across a diverse range of pH and temperatures, and safety profile. Here, we have focused on the use of plant peptidases, mostly papain and bromelain, to produce biologically active peptides, which confer various health advantages, including antioxidant, antimicrobial, antihypertensive, analgesic, antidiabetic, and anti-inflammatory effects. We have also discussed the importance of the action mechanism of peptidases for generating bioactive peptides with specific sequences and functions, the ecological and sustainability benefits of plant-derived peptidases compared to animal alternatives, digestive stability and bioavailability of peptides, as well as some obstacles to the commercialization of bioactive peptides and key challenges in peptidase-based industrial applications. Finally, we have examined enzyme immobilization as a viable method to enhance the production of bioactive peptides, offering numerous advantages in both research and industry contexts.
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Plant-derived Cyclotides in Immunomodulation and their Therapeutic Potential
Authors: Reema Mishra, Preeti Agarwal, Anshita Sharma, Meenal Mittal, Pooja Gulati and Aparajita MohantyAvailable online: 18 March 2025More LessThe incidences of immune-related disorders have drastically increased in recent years across the world population. Treatment and management of these diseases, especially autoimmune disorders, are complex and challenging. Available synthetic drugs are not completely effective and also pose serious side effects for the patients. Cyclotides are a class of plant-derived cyclic peptides (28-37 amino acids) with three conserved disulfide linkages establishing a cyclic cystine knot (CCK) motif that makes them very stable biomolecules. Their inherent stability, bioavailability and membrane-penetrating capabilities render them attractive potential pharmacological agents. Studies have demonstrated that cyclotides can either enhance or suppress immune responses, making them versatile candidates for treating various immune-related disorders. Of more than 1000 cyclotides discovered to date, only up to 15 native cyclotides (e.g. kalata B1, pase and caripe cyclotides) have been screened to demonstrate their immunomodulatory activity. Of special significance is the chemically synthesised lysine mutant of kalata B1 viz. [T20K], where preclinical studies have shown promise in the treatment of the autoimmune disorder, multiple sclerosis. In vivo studies in mice models have demonstrated that daily administration of 1mg/day of [T20K] led to a significant decrease in the level of cytokine secretion, lesser demyelination (<1%) and very low inflammatory index (<0.5), in the immunized mice. Moreover, when compared with other immunosuppressive drugs (azathioprine, prednisolone, and cyclosporine A) there was a notable drop in mortality and morbidity in mice administered with [T20K]. The cyclotides, kalata B1 and MCoTI-I have also been used as scaffolds to graft bioactive peptides with immunomodulatory activity. Subsequent in vitro and in vivo studies of these grafted cyclotides have demonstrated their therapeutic ability. Keeping in view the therapeutic potential of cyclotides as immunomodulatory peptides, the present review discusses its current research scenario and implications for the future in tackling immune-related disorders.
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