Protein and Peptide Letters - Online First

Peak-shouldering elution behavior was a common and unexpected result in bind-and-elute mode Cation Exchange Chromatography (CEX), which may be due to the pH transition during the elution step and the aggregation tendency of target proteins.

Improving the concentration of acid-base pairs in the wash buffers or elution buffers without changing pH or conductivity effectively resolved the peak-shouldering issue in CEX.

In the case of molecule A, the shoulder peak was eliminated in the CEX run by increasing the NaAc-HAc concentration from 50 mM to 100 mM in the elution buffer or from 50 mM to 75 mM in the wash buffer. Higher NaAc-HAc concentrations affect the pH transition in the early stages of the elution step, which may explain the elimination of the shoulder peak. A similar result was observed for molecule B, where increasing the Tris-HCl concentration in the elution buffer from 50 mM to 80 mM also removed the shoulder peak during elution.

The successful elimination of peak-shouldering behavior by increasing acid-base pair concentrations highlights the critical role of buffer capacity in modulating pH transitions during CEX. While this strategy offers a simple and effective solution, further investigation is needed to assess its applicability across diverse protein types and buffer systems.

These results demonstrate that increasing the concentration of acid-base pairs in the elution buffer or wash buffer of CEX using NaAc-HAc or Tris-HCl buffers is an effective strategy for eliminating the shoulder-peak.

Superoxide Dismutases (SODs) are enzymes that catalyzes the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.

Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector, followed by its subcloning in an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.

The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40°C and pH 8, respectively. The enzyme remains completely stable at 40°C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50°C and 60°C for 3 h. The biophysical investigation revealed stable conformation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi-Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.

The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn²⁺ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.

The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, including therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.

Diabetic hyperglycemia is often associated with elevated levels of trimethylamine-N-oxide (TMAO), a gut microbiota-derived metabolite that was recently identified as a risk factor for cardiovascular diseases. The combined presence of hyperglycemia and TMAO can aggravate cardiac dysfunction in diabetic patients. This study aimed to evaluate the protective effects of the methanolic extract of Syzygium aromaticum against the toxic effects induced by TMAO and hyperglycemia in cultured rat cardiomyocytes.

Rat cardiomyocytes, H9C2 were exposed to high glucose and TMAO, individually and in combination to simulate diabetic and dysbiotic stress conditions. Cells were treated with optimized doses of Syzygium aromaticum extract under dual-stress conditions. Cellular and nuclear morphology were assessed microscopically. Oxidative stress markers were evaluated. Proteomic profiling using liquid chromatography-mass spectrometry (LC-MS) was conducted to identify differentially expressed proteins. Crucial targets were identified and functionally annotated using integrated bioinformatics tools and databases. Expression of the critical transcription factor Yin-Yang-1 (YY1) was analysed using quantitative PCR (qPCR).

Dual exposure to TMAO and hyperglycemia resulted in greater morphological and oxidative damage compared to exposure to either individual stressor alone. Treatment with Syzygium aromaticum extract significantly reduced cellular and nuclear damage as well as oxidative stress under dual-stress conditions. Proteomic analysis revealed several differentially expressed proteins, with YY1 identified as a key regulatory factor. qPCR confirmed the suppression of YY1 expression by Syzygium aromaticum treatment.

Our findings suggest that Syzygium aromaticum mitigates cardiomyocyte injury caused by metabolic and microbial stress. Its protective effect may be mediated through antioxidant activity and transcriptional regulation, particularly via the downregulation of YY1, a key player in cardiac stress responses.

Syzygium aromaticum exhibits multifaceted cardioprotective and prebiotic potential by mitigating TMAO and hyperglycemia-induced toxicity, highlighting its therapeutic promise in managing gut dysbiosis linked to diabetic cardiomyopathy.

Bacillus thuringiensis Cry toxins are well known for their insecticidal properties, primarily through the formation of ion-leakage pores via α4-α5 hairpins. His¹⁷⁸ in helix 4 of the Cry4Aa mosquito-active toxin has been suggested to play a crucial role in its biotoxicity.

This study aimed to investigate the functional importance of Cry4Aa-His¹⁷⁸ through experimental and computational analyses.

Ten His¹⁷⁸-substituted Cry4Aa mutants (H178D, H178E, H178K, H178R, H178G, H178F, H178Y, H178S, H178C, and H178Q) were generated via site-directed mutagenesis and expressed in Escherichia coli. Toxin solubility was assessed in carbonate buffer (pH 10.0), and biotoxicity was tested against Aedes aegypti larvae. Trypsin-treated toxins were evaluated using fluorescent dye-release assays. Ion channel formation was studied in planar lipid bilayers (PLBs), and structural analysis was performed via MD simulations and sequence alignments with known Cry toxins.

All His¹⁷⁸-substituted mutants were overexpressed as 130-kDa protoxin inclusions at levels comparable to the wild-type (WT). Replacing His¹⁷⁸ with nonpolar or bulky polar residues reduced Cry4Aa biotoxicity to less than 10%, while substitutions with small, moderately polar, or negatively charged residues retained 50-85% activity, consistent with their in vitro solubility. Selected bioactive mutants, H178C and H178D, retained membrane-perturbing ability, like trypsin-activated WT, while the bioinactive H178Y mutant exhibited decreased membrane permeability. All tested mutants, including WT, induced cation-selective channels in PLBs with ~130-pS conductance. Sequence-structure analysis indicated that Cry4Aa-His¹⁷⁸ likely forms a hydrogen bond with His²¹⁷, a conserved His residue in helix 5.

Specific physicochemical properties of residue 178 are critical for optimal larvicidal activity, making it a promising target for engineering more potent mosquito-control toxins.

His¹⁷⁸ in Cry4Aa-α4 potentially forms a stabilizing hydrogen bond with α5-His²¹⁷, which maintains the structural integrity of the α4-α5 hairpin. This structural stability is essential for efficient membrane insertion and optimal larvicidal activity.

Neurodegenerative disorders such as Alzheimer's, Parkinson's, and ALS are characterized by progressive neuronal dysfunction with limited therapeutic options. Recent advances in molecular biology and drug development have highlighted the therapeutic promise of precision enzyme targeting, offering novel strategies for disease modulation and symptom management.

A comprehensive literature review spanning recent/current was conducted using PubMed, Scopus, and ScienceDirect. Studies focusing on enzyme-based targets, high-throughput screening, and molecular docking in neurodegeneration were included. Thematic synthesis was employed to categorize findings based on enzyme class, disease relevance, and therapeutic outcomes.

Key enzyme families such as kinases, proteases, and oxidoreductases were identified as pivotal modulators in disease progression. Emerging enzyme-targeted compounds demonstrated enhanced bioavailability, blood-brain barrier permeability, and disease-specific efficacy. Novel screening platforms and computational modeling enabled the precise selection of inhibitors, significantly improving the therapeutic index and reducing off-target effects.

Targeting enzymes implicated in neuroinflammation, oxidative stress, and protein misfolding has shown disease-modifying potential. Integrating precision drug discovery tools, such as AI-assisted modeling and enzyme kinetics, supports rational drug design. However, translational challenges persist due to variability in enzyme expression and disease heterogeneity.

Future research should focus on refining enzyme inhibitors and integrating biomarkers to facilitate personalized treatment strategies for neurodegenerative disorders. As the understanding of enzymatic roles in neurodegeneration deepens, precision enzyme-targeted drug discovery holds significant promise in transforming neurotherapeutic approaches.

italic>Mycobacterium tuberculosis (Mtb) is a Gram-positive bacterium that causes tuberculosis (TB). It remains viable for extended periods within host macrophages by entering a dormant state. Alpha crystallin 1 (Acr1) is a 16 kDa protein of Mtb and is reported to be highly upregulated in latent TB. Acr1 suppresses the host’s immune system by impairing the differentiation and maturation of dendritic cells and macrophages. We hypothesize that Mtb judiciously utilizes its Acr1 protein to paralyse the immune system of the host by inducing the release of IL-10 and generating an immunosuppressive environment.

We employed in silico tools to identify highly promiscuous, IL-10-inducing and IL-6-non-inducing epitopes of Mtb. Moreover, the selected epitope was synthesized and tested for its suppressive activity and generation of Tregs.

We identified the presence of a specific epitope in Acr1 (F18) that is responsible for bolstering the release of IL-10 and Tregs through in silico tools and verified the activity by in vitro assays. In hPBMCs, the F18 epitope could suppress the proliferation of CD4 T cells stimulated with PHA and expand the pool of Tregs in a dose-dependent manner.

The F18 epitope from Mtb’s Acr1 protein promotes IL-10 and Treg responses without triggering pro-inflammatory IL-6, suggesting its probable immunoregulatory role. While it holds potential for treating autoimmune diseases, its impact on infection in tuberculosis should be further investigated.

Our findings suggest that the F18 epitope induces IL-10 production and Treg differentiation while inhibiting CD4⁺ T cell proliferation and IL-6 secretion, thereby promoting an immunosuppressive environment. Furthermore, this study highlights the possible role of Acr1 and its immunosuppressive epitope F18 as therapeutic agents for inducing suppressive Tregs, which may help in the management of autoimmune diseases.

The 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.

The 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.

The 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.

The 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.

The 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.

These 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.