Effect of pH on the structure and stability of irisin, a multifunctional protein: Multispectroscopic and molecular dynamics simulation approach

Unraveling the catalase dynamics: Biophysical and computational insights into co-solutes driven stabilization under extreme pH conditions

Catalase plays a vital role in eliminating toxic peroxides from the human body and the environment. The versatile applications of this enzyme extend across biotechnological industries and innovative bioremediation approaches. Nonetheless, ensuring enzyme stability is a challenging task. This study investigated the efficacy of co-solutes (glucose and dextran 70) as stabilizing agents for catalase under denaturing pH conditions by employing a combination of spectroscopic techniques (UV-visible, circular dichroism, and Trp fluorescence), calorimetric measurements (DSC and ITC), enzymatic assay, and in silico studies. The results of spectroscopic and thermal stability studies indicated that the co-solutes tend to stabilize catalase, even under extreme pH conditions. Molecular docking and ITC findings showed that glucose has a higher binding tendency to catalase than dextran 70. MD simulations further underscore reduced structural deviations (RMSF and RMSD), compact structure (Rg and SASA), and formation of H-bonds between catalase and co-solutes, complementing the in vitro observations. This study contributes to the understanding of enzyme stability under suboptimal pH conditions and paves the way for the development of more robust enzyme formulations suitable for a range of applications.

Pharmacoinformatics-based prediction of Checkpoint kinase-1 inhibitors from Momordica charantia Linn. for cancer

Checkpoint kinase 1 (Chk-1), a serine/threonine kinase family protein, is an emerging target in cancer research owing to its crucial role in cell cycle arrest. Therefore, we aimed to predict potential Chk-1 inhibitors from Momordica charantia Linn., using high-throughput molecular docking. We used a graph theoretical network approach to determine the target protein, Chk-1. Among 86 compounds identified from M. charantia L., five molecules such as α-spinasterol (-9.7 kcal × mol-1), stigmasterol (-9.6 kcal × mol-1), stigmasta-7,22,25-trienol (-9.5 kcal × mol-1), campesterol (-9.5 kcal × mol-1), and stigmasta-7,25-dien-3beta-ol (-9.5 kcal × mol-1) and standard drug CCT245737 (-8.3 kcal × mol-1) displayed highest binding affinity with Chk-1. Besides, pharmacokinetic studies have demonstrated the non-toxic and drug-like properties of these compounds. Furthermore, molecular dynamics (MD) simulation studies confirmed the strong intermolecular interactions and stability of the compounds with Chk-1. The estimation of binding free-energy derived from molecular docking was fully recognized by the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) produced from the MD simulation paths. Altogether, these five compounds may serve as effective inhibitors of Chk-1, thereby could be used to develop new medications for cancer treatment.

Design and Characterization of pH-Responsive DGEA-Derived Peptide Scaffolds: A Comprehensive Molecular Dynamics Simulation Study

Peptide-based, functionally active, stimuli-responsive biomaterials hold immense potential for diverse biomedical applications. Functionally active motifs of extracellular matrix (ECM) proteins, when conjugated with self-assembling peptides (SAP) or polymers, demonstrate significant promise in the development of such bioactive scaffolds. However, synthesis complexity, high associated costs, limited functionality, and potential immune responses present significant challenges. This study explores collagen-I-derived DGEA motif-based SAPs, incorporating modifications such as salt bridge pairing, charged and polar residues, hydrophobic residues, amyloidogenic sequences, and non-ECM motifs, to develop stimuli-responsive, functionally active scaffolds. Extensive molecular dynamics (MD) simulations, totaling 16.7 μs, were conducted on 20 systematically designed peptide systems. These simulations also characterized the stimuli-responsive properties of the peptides, focusing on pH and temperature responsiveness. Among the 20 designs, three peptide systems─DGEA-SBD, DGEA-SBE (salt-bridge modifications), and DGEA-F4 (with hydrophobic residue addition at the C-terminus)─successfully formed large, stable, and bioactive scaffolds. These systems exhibited enhanced aggregation (greater than 90%) and improved interpeptide hydrogen bonding (more than 30 bonds) while maintaining the accessibility of functional motifs (60-70% availability) compared to the unmodified DGEA motif. Notably, the DGEA-SBD and DGEA-SBE peptides showed a transition from small, unstable, uneven gel-like structures to large, stable, uniform, and functionally active scaffolds as the pH shifted from 3.0 to physiological pH. Comprehensive MD simulation studies demonstrated that these designed peptides exhibit increased aggregation and enhanced interpeptide hydrogen bonding while retaining their functional activity under various physiological conditions, highlighting their promising potential for biomedical applications.

Formation of bovine serum albumin-galangin nanoparticles and their potential to inhibit reactive oxygen species-induced inflammation: Ethanol desolvation versus pH-shifting method

The pH-shifting method, as an ecofriendly approach, is a promising alternative to the desolvation method, yet systematic comparison of their properties is still lacking. In this study, BSA-galangin nanoparticles (BSA-GA NP) were designed for alleviating reactive oxygen species (ROS)-mediated macrophage inflammation by the 2 separate methods. Compared with the desolvation method, BSA exhibited a higher loading capacity for GA under the pH-shifting method, which was attributed to the exposure of the binding site leading to enhanced affinity for GA and a more compact particle structure. Further analyses evidenced that the electron arrangement and crystal structure of GA changed with different methods. The content of the random coil of BSA was elevated after the pH-shifting method. Additionally, the smaller size rendered the pH-shifting treated BSA-GA NP easier to be taken up by macrophages, and the enhanced specific surface area conferred excellent ROS scavenging and anti-inflammatory performances. This study may provide new insights into the choice of loading methods.

Chemical composition alterations in rat brain hypothalamus induced by irisin administration using spectroscopic and machine learning techniques

This study employed Fourier transform infrared (FTIR) spectroscopy to determine the chemical composition of brain tissues and the changes induced by irisin at doses of 50 mg and 100 mg. Brain tissues were collected from control rats and those administered with irisin, and key vibrational peaks were analyzed. In the 50 mg irisin group, all described vibrations decreased compared to control tissues, while the 100 mg group showed a decrease only in lipid vibrations. Comparatively, the 50 mg group had lower absorbance of phospholipids, amides, and lipid functional groups than the 100 mg group. Lower amounts of these compounds were found in treated tissues compared to controls, with higher levels in the 100 mg group. Ratios between amide peaks revealed significant differences between groups. Principal component analysis (PCA) differentiated control and irisin-treated tissues, primarily using PC1 and PC3. The decision tree model exhibited high classification accuracy, especially in the 800-1800 cm⁻1 range, with high sensitivity and specificity. FTIR spectroscopy effectively highlighted chemical changes in brain tissues due to irisin, demonstrating dose-dependent variations. The combination of PCA, ROC analysis, and decision tree modeling underscored the potential of FTIR spectroscopy for studying the biochemical effects of compounds like irisin.

pH induced structural and conformational changes in nucleocapsid protein leads to intermediate like conformation: a biophysical and computational approach

Nucleocapsid protein (N) of SARS-CoV-2 is a multivalent protein, which is responsible for viral replication, assembly, packaging and modulates host immune response. In this study, we report conformational measurements of N protein at different pH by observing transition in secondary and tertiary structural contents by biophysical and computational approaches. Spectroscopic measurements revealed that N protein loses its secondary and tertiary structure at extreme acidic pH while maintaining its native conformation at mild acidic and alkaline pH. Molecular dynamics simulation studies validated spectroscopic findings. Secondary structure estimation confirmed circular dichroism (CD) findings that participation of total number of average residues in formation of native structure is higher at physiological pH, and coil percentage is higher at acidic pH. In molten globule (MG) state, secondary structure is conserved but here, CD data reveal more random structure at low pH. In pre-MG, ANS (8-anilino-1-napthalene sulfonate) binds weakly to protein as compared to MG but here, ANS binds strongly to protein. All the above-mentioned findings suggested formation of intermediary like state at low pH, which can be attributed to an off-pathway species. Unravelling structural characteristics of N protein will help understand phase-separation, protein-protein interaction and host-immune response modulation behaviour, which will eventually help in designing novel therapeutic target against COVID-19.

Investigating pH-induced conformational switch in PIM-1: An integrated multi spectroscopic and MD simulation study

PIM-1 is a Ser/Thr kinase, which has been extensively studied as a potential target for cancer therapy due to its significant roles in various cancers, including prostate and breast cancers. Given its importance in cancer, researchers are investigating the structure of PIM-1 for pharmacological inhibition to discover therapeutic intervention. This study examines structural and conformational changes in PIM-1 across different pH using various spectroscopic and computational techniques. Spectroscopic results indicate that PIM-1 maintains its secondary and tertiary structure within the pH range of 7.0-9.0. However, protein aggregation occurs in the acidic pH range of 5.0-6.0. Additionally, kinase assays suggested that PIM-1 activity is optimal within the pH range of 7.0-9.0. Subsequently, we performed a 100 ns all-atom molecular dynamics (MD) simulation to see the effect of pH on PIM-1 structural stability at the molecular level. MD simulation analysis revealed that PIM-1 retains its native conformation in alkaline conditions, with some residual fluctuations in acidic conditions as well. A strong correlation was observed between our MD simulation, spectroscopic, and enzymatic activity studies. Understanding the pH-dependent structural changes of PIM-1 can provide insights into its role in disease conditions and cellular homeostasis, particularly regarding protein function under varying pH conditions.

Family 3 CBM improves the biochemical properties, substrate hydrolysis and coconut oil extraction by hemicellulolytic and holocellulolytic chimeras

To understand the influence of family 3 Carbohydrate Binding Module (hereafter CBM3), single (GH5 cellulase; CelB, CelBΔCBM), bi-chimeric [GH26 endo-mannanase (ManB-1601) and GH11 endo-xylanase (XynB); ManB-XynB [1], ManB-XynB-CBM] and tri-chimeric [ManB-XynB-CelB [1], ManB-XynB-CelBΔCBM] enzyme variants (fused or deleted of CBM) were produced and purified to homogeneity. CBM3 did not alter the pH and temperature optima of bi- and tri-chimeric enzymes but improved the pH and temperature stability of ManB in CBM variants of bi-/tri-chimeric enzymes. Truncation of CBM in CelB shifted the pH optimum and increased the melting temperature (Tm 65 ℃). CBM3 improved both substrate affinity (Km) and catalytic efficiency (kcat/Km) of fused enzymes in tri-chimera and CelB but only Km for bi-chimera. Far-UV CD of CelB and bi- and tri-chimeric enzymes suggested that CBM3 improved the α-helical content and compactness in the native state but did not prevent disintegration of secondary structural contents at acidic pH. Steady-state fluorescence studies suggested that under acidic conditions CBM3 prevented the exposure of hydrophobic patches in bi-chimeric protein but could not avert the opening up of chimeric enzyme structure. Aqueous enzyme assisted treatment of mature coconut kernel using single, bi- and tri-chimeric enzymes led to cracks, peeling and fracturing of the matrix and improved the oil yield by up to 22%.

Flavor Characteristics of Umami Peptides from Wuding Chicken Revealed by Molecular Dynamics Simulation

Wuding chicken is famous for its delicious meat, and HLEEEIK, LDDALR, and ELY were jointly extracted from different processing stages of Wuding chicken. However, whether these peptides can be used as umami supplements is unclear. The sensory evaluation tests were used to study the taste characteristics. The secondary structure of the peptides and their interaction with T1R1/T1R3 were predicted by the circular dichroism spectrum and molecular dynamics simulation. The umami threshold was 0.03125 to 0.06250 mg/mL, all of which could increase umami, saltiness, sweetness, and mask bitterness. Compared with HLEEEIK, the frequency of umami active fragments and the improvement rate of the umami score of EEE increased by 133.35% and 40.09%, respectively. Peptides were dominated by umami taste according to sensory analysis, among which EE-3 (3.18) has the highest umami intensity followed by LR-4 (2.58), HK-7 (2.13), and EY-3 (1.82). The main secondary structure of umami peptides was β-folding, and Tyr74, Arg323, Arg272, and Gln35 were the key amino acid residues for binding of umami peptides to the receptor. This study further elucidated that the umami intensity of the peptides could be altered by changing the sequence composition of the peptides, which enhanced our understanding of the complex flavor properties of umami peptides.

Inhibitory potential of N-acetylaspartate against protein glycation, AGEs formation and aggregation: Implication of brain osmolyte in glycation-related complications

Protein glycation and aggregation have a pivotal role in many diseases including diabetes and neurodegenerative disorders. N-acetyl aspartate (NAA), an osmolyte derived from L-aspartic acid, is one of the most abundant metabolites in the mammalian brain. Although NAA is supposed to be a substitute for a neuronal marker, its function is not fully elucidated. Herein, we have investigated the effect of NAA on glycation, AGEs formation and aggregation of irisin. AGE-specific fluorescence showed the strong inhibition of AGEs formation in the presence of NAA, demonstrating its anti-glycating property. The aggregates present in MG-modified irisin were also reduced by NAA, which was confirmed by Thioflavin T fluorescence and fluorescence microscopy. Further, for the explanation of the strong anti-glycating potential of NAA, the interaction between irisin and NAA was also examined. Interaction studies involving steady-state fluorescence and molecular docking demonstrated that hydrogen bonding and salt bridges by NAA stabilize the irisin. It was found that glycation-prone residues i.e., lysine and arginine are specifically involved in the interaction which might prevent them from getting modified during the process of glycation. This study for the first time reported the antiglycating potential of NAA which can be implicated in the therapeutic management of various glycation-related complications.

Characterization of advanced glycation end products and aggregates of irisin: Multispectroscopic and microscopic approaches

Glycation of proteins leading to the formation of advanced glycation end products (AGEs) has been demonstrated to contribute to the pathogenesis of several diseases. Irisin is a clinically significant protein, putatively involved in obesity, diabetes, and neurological disorders. This study aimed to monitor the methyl-glyoxal (MG) induced AGEs and aggregate formation of irisin, as a function of time, employing multispectroscopic and microscopic approaches. ANS fluorescence suggested a molten globule-like state on Day 6, followed by the formation of irisin AGEs adducts, as confirmed by AGE-specific fluorescence. Glycation of irisin led to aggregate formation, which was characterized by Thioflavin T fluorescence, CD spectroscopy, and microscopic studies. These aggregates were confirmed by exploiting fluorescence microscopy, confocal, and transmission electron microscopy. Molecular docking was performed to determine the crucial residues of irisin involved in irisin-MG interaction. Usually, MG is present in trace amounts as a metabolic by-product in the body, which is found to be elevated in diseased conditions viz. diabetes and Alzheimer's disease. This study characterized the AGEs and aggregates of clinically important protein, irisin; and since MG level has been found to be increased in various pathological conditions, this study provides a clinical perspective. There is a possibility that elevated MG concentrations might glycate irisin resulting in reduced irisin levels as reported in pathological conditions. However, further investigations are required to prove it.

Unraveling the Binding Mechanism of Alzheimer's Drugs with Irisin: Spectroscopic, Calorimetric, and Computational Approaches

The prevalence of Alzheimer’s disease (AD) has been a major health concern for a long time. Despite recent progress, there is still a strong need to develop effective disease-modifying therapies. Several drugs have already been approved to retard the progression of AD-related symptoms; however, there is a need to develop an effective carrier system for the delivery of drugs to combat such diseases. In recent years, various biological macromolecules, including proteins, have been used as carriers for drug delivery. Irisin is a beneficial hormone in such diseases, including AD and related pathologies. Herein, the interaction mechanism of irisin with AD drugs such as memantine, galantamine, and fluoxetine is investigated. Fluorescence studies revealed that the above drugs bind to irisin with significant affinity, with fluoxetine having the highest binding affinity. Isothermal titration calorimetry (ITC) complemented the spontaneous binding of these drugs with irisin, delineating various associated thermodynamic and binding parameters. Molecular docking further validated the fluorescence and ITC results and unfolded the mechanism that hydrogen bonding governs the binding of fluoxetine to irisin with a significant binding score, i.e., −6.3 kcal/mol. We believe that these findings provide a promising solution to fight against AD as well as a platform for further research to utilize irisin in the drug-delivery system for an effective therapeutic strategy.

FNDC5/Irisin: Physiology and Pathophysiology

A sedentary lifestyle or lack of physical activity increases the risk of different diseases, including obesity, diabetes, heart diseases, certain types of cancers, and some neurological diseases. Physical exercise helps improve quality of life and reduces the risk of many diseases. Irisin, a hormone induced by exercise, is a fragmented product of FNDC5 (a cell membrane protein) and acts as a linkage between muscles and other tissues. Over the past decade, it has become clear that irisin is a molecular mimic of exercise and shows various beneficial effects, such as browning of adipocytes, modulation of metabolic processes, regulation of bone metabolism, and functioning of the nervous system. Irisin has a role in carcinogenesis; numerous studies have shown its impact on migration, invasion, and proliferation of cancer cells. The receptor of irisin is not completely known; however, in some tissues it probably acts via a specific class of integrin receptors. Here, we review research from the past decade that has identified irisin as a potential therapeutic agent in the prevention or treatment of various metabolic-related and other diseases. This article delineates structural and biochemical aspects of irisin and provides an insight into the role of irisin in different pathological conditions.