{"title":"Comparative analysis of backbone atom cross-correlation matrices and folding dynamics of amyloid fibril and its complexes with novel biosurfactants isolated from Bacillus strain: a binding free energy calculation (mM-PBSA) and MD simulation approach.","authors":"Rohit Pritam Das, Santosh Kumar Behera, Banishree Sahoo, Manoranjan Arakha, Arun Kumar Pradhan","doi":"10.1080/07391102.2024.2446677","DOIUrl":"https://doi.org/10.1080/07391102.2024.2446677","url":null,"abstract":"<p><p>In the relentless pursuit of unraveling the intricate pathophysiology of Alzheimer's disease (AD), amyloid β (Aβ) proteins emerge as focal points due to their pivotal role in disease progression. The pathological hallmark of AD involves the aberrant aggregation of Aβ peptides into amyloid fibrils, precipitating a cascade of neurodegenerative events culminating in cognitive decline and neuronal loss. This study adopts a computational framework to investigate the potential therapeutic efficacy of novel biosurfactants (BS) in mitigating Aβ fibril formation. Initial analyses encompassing sequence alignment, structural elucidation, and functional characterization reveal distinctive attributes of the Aβ peptide and the identified BS candidates. Quantum chemical calculations, using the ORCA Program (v4.0) employed Density Functional Theory (DFT), specifically the Becke 3-parameter Lee-Yang-Parr (B3LYP) method, to investigate the electronic structure and energetics of novel isolates. Molecular docking through AutoDock Vina (version 1.1.2) employing advanced algorithms elucidates the binding affinities and interaction energies between Aβ fibrils and BS molecules. The observed binding energy of -7.0 kcal/mol for BG2A and -6.6 kcal/mol for BG2B, underscoring the robustness and stability of the formed complexes. The binding mechanism of docked complexes was predicted through molecular dynamics (MD) simulations using GROMACS 2021.3 and Charmm36 force field, capture complex dynamics over 100 nanoseconds. Analysis <i>via</i> RMSD, RMSF, Rg, PCA, and SASA offers insights into Aβ-BS complex stability and dynamics. These promising results highlight the potential of BG2A and BG2B as therapeutic candidates against AD. However, rigorous preclinical and clinical validation is crucial to ascertain their safety, efficacy, and translational relevance.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Modeling and interaction study of alcohol oxidase and ProteaseA in methylotrophic yeast <i>C. boidinii</i>: insights from In-silico analysis.","authors":"Mohammad Wahab Khan, Ayaluru Murali","doi":"10.1080/07391102.2024.2446679","DOIUrl":"https://doi.org/10.1080/07391102.2024.2446679","url":null,"abstract":"<p><p>Flavin adenine nucleotide (FAD)-dependent oxidoreductase enzyme Alcohol oxidase (AOX) facilitates the growth of methylotrophic yeast C. boidinii by catabolizing methanol, producing formaldehyde and hydrogen peroxide. Vacuolar Protease-A (PrA) from C. boidinii is responsible for the proteolytic activity of AOX. However, no experimental structures for these enzymes have been reported. This in-silico study involves modeling and interaction analysis of AOX and PrA. A protein-protein interaction study shows that Thr75, Gly74, Arg72, Tyr73, and Met289 amino acids of PrA have shown interaction with AOX. These residues may be crucial for AOX proteolysis. An in-silico study predicts that serine protease inhibitors bind to specific amino acids, potentially obstructing PrA's degradable activity on AOX. PrA does not interact with the FAD binding sites in AOX. Instead, it interacts with AOX at sites (Ser337, Ala34, and Tyr343) where AOX monomers interact, hindering octamer formation the active form of AOX. During simulation, strong dynamics in PrA were found in the loop regions of the structure, as observed in the complexes. This in-silico work aims to corroborate the experimental research, which lacks structural studies on the proteolysis process.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-17"},"PeriodicalIF":2.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ravikant R Karale, Savita Kamble, Suad Alwaleedy, Komal B Kabara, Pallavi Narwade, Saeed Mohammed Al-Hamdani, Ashok C Kumbharkhane, Arvind V Sarode
{"title":"Hydration behavior of asparagine: an approach using time domain reflectometry at low temperatures.","authors":"Ravikant R Karale, Savita Kamble, Suad Alwaleedy, Komal B Kabara, Pallavi Narwade, Saeed Mohammed Al-Hamdani, Ashok C Kumbharkhane, Arvind V Sarode","doi":"10.1080/07391102.2024.2445153","DOIUrl":"https://doi.org/10.1080/07391102.2024.2445153","url":null,"abstract":"<p><p>The dielectric behavior of Asparagine (C<sub>4</sub>H<sub>8</sub>N<sub>2</sub>O<sub>3</sub>) in water over the frequency range of 10 MHz to 30 GHz in the temperature region of 278.15-303.15 K in a step of 5 K has been carried out using time domain reflectometry (TDR) at various concentrations of asparagine. The obtained dielectric spectra reveal two relaxation peaks. The low frequency relaxation is attributed to the interaction between solute-solute molecules, while the high frequency relaxation is due to the reorientation of solvent molecules. The various dielectric and thermodynamic parameters were calculated such as the dielectric constant (ε<sub>j</sub>), relaxation time (τ<sub>j</sub>), effective dipole moment (μ<sub>eff</sub>), Kirkwood correlation factor (g<sub>1</sub>), hydration number or the number of solvent molecules effectively bounded to solute molecule (Z<sub>ib</sub>), effective volume of rotation (V<sub>eff</sub>), free energy of activation (ΔF<sub>j</sub>), entropy of activation (ΔS<sub>j</sub>) and enthalpy of activation (ΔH<sub>j</sub>). The static dielectric constant (ε<sub>1</sub>) shows increasing trend towards the higher concentration of asparagine, where as the high frequency dielectric constant (ε<sub>2</sub>) decreases with the concentration of asparagine. The relaxation time of low frequency (τ<sub>1</sub>) and high frequency (τ<sub>2</sub>) processes increases towards higher concentration of solute molecule and also towards lower temperature. As the concentration of asparagine increases, the value of effective dipole moment (μ<sub>eff</sub>) decreases. With increasing amino acid concentrations hydration dynamics get affected and indicated by decreasing the hydration number (Z<sub>ib</sub>) but the hydration dynamics of aqueous asparagine was found least temperature dependent.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-14"},"PeriodicalIF":2.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dilay Kahvecioglu, Serap Yilmaz Ozguven, Yusuf Sicak, Fatih Tok, Mehmet Öztürk, Bedia Kocyigit-Kaymakcioglu
{"title":"Synthesis and molecular docking analysis of novel hydrazone and thiosemicarbazide derivatives incorporating a pyrimidine ring: exploring neuroprotective activity.","authors":"Dilay Kahvecioglu, Serap Yilmaz Ozguven, Yusuf Sicak, Fatih Tok, Mehmet Öztürk, Bedia Kocyigit-Kaymakcioglu","doi":"10.1080/07391102.2024.2442758","DOIUrl":"https://doi.org/10.1080/07391102.2024.2442758","url":null,"abstract":"<p><p>The increasing global prevalence of Alzheimer's disease necessitates the development of novel therapeutic approaches. Neurodegenerative diseases are associated with increased oxidative stress and levels of cholinesterase enzymes. Hence, the development of cholinesterase inhibitors and antioxidants may provide neuroprotective effects. Our study focused on the synthesis of a new series of hydrazone and thiosemicarbazide derivatives bearing a pyrimidine ring. The compounds of structures were characterized by FT-IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, and HR-MS spectroscopic methods. Compounds <b>3a</b> and <b>4f</b> were determined using COSY and HSQC spectra. Compared to the standard drug galantamine (IC<sub>50</sub> = 4.82 ± 0.75 µM), compound <b>3d</b> exhibited remarkable inhibitory activity against AChE (IC<sub>50</sub> values of 20.15 ± 0.44 µM). This compound was more effective against BChE (IC<sub>50</sub> = 36.42 ± 0.73 µM) than galantamine (IC<sub>50</sub> = 45.54 ± 0.18 µM). Antioxidant assays revealed the robust antioxidant activity of compound <b>3d</b>. Furthermore, docking studies have shown that the active site of enzymes interacts strongly with electron donors through hydrogen bonds, while the aromatic ring structure plays an active role in π interactions.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-15"},"PeriodicalIF":2.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Antidiabetic potency of glimepiride and naringin: an <i>in silico</i> and <i>in vitro</i> investigation.","authors":"Deepankar Rath, Gurudutta Pattnaik, Biswakanth Kar, Gopal Krishna Padhy, Chandra Sekhar Patro, Pallishree Bhukta","doi":"10.1080/07391102.2024.2442759","DOIUrl":"https://doi.org/10.1080/07391102.2024.2442759","url":null,"abstract":"<p><p>Glimepiride (GLM) is one of the potential antidiabetic drugs used in clinics for a long time. It is currently used in combination with metformin along with other drugs, but has shown various complications in patients from long-term use. Thus, the hypothesis is to use a lower dose of GLM with a non-toxic class of flavonoid, naringin (NARN), for better therapy with minimal side-effects. Initially, we assessed the binding efficacy of GLM and NARN against nine putative target enzymes using AutoDock 4.2 software. We also analysed the drug chemistry, drug-ability, and cytotoxicity, as well as performed molecular dynamic (MD) simulation at 100 ns with individual and combination states using GROMACS-2022 software. Both candidates showed higher binding efficacy, especially against the AKT-serine/threonine kinase-1 (AKT1) target enzyme (-11.85 kcal/mol), and demonstrated higher stability and compatibility with AKT1 from MD-simulation (based on RMSD, Rg, RMSF, and H-bond plots) in combination than individual form. The <i>in vitro</i> cytotoxicity with human embryonic kidney (HEK-293) cells suggested 100 µg/mL (observed 80% of the cell viability) as a non-toxic dose for further study. Alpha-amylase, alpha-glucosidase, and DPP-IV inhibition assays revealed that both GLM and NARN inhibited up to 60% at 100 µg/mL in a concentration-dependent manner. At the end, selecting a lower dose of GLM and a higher dose of NARN (2:8 v/v ratio) showed up to 87% inhibition at 100 µg/mL. Both <i>in silico</i> and <i>in vitro</i> studies suggest that the investigated formulation could be a potential and non-toxic dose for diabetics.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-12"},"PeriodicalIF":2.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maryam Zulfat, Hind A Alkhatabi, Roaa M Alreemi, Mubarak A Alamri, Asaad Khalid, Ashraf N Abdalla, Abdul Wadood
{"title":"<i>In-silico</i> identification of potential peptide inhibitors to disrupt NLRP3 inflammasome complex formation by blocking NLRP3-ASC pyrin-pyrin interactions.","authors":"Maryam Zulfat, Hind A Alkhatabi, Roaa M Alreemi, Mubarak A Alamri, Asaad Khalid, Ashraf N Abdalla, Abdul Wadood","doi":"10.1080/07391102.2024.2444417","DOIUrl":"https://doi.org/10.1080/07391102.2024.2444417","url":null,"abstract":"<p><p>The NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome is a well-known and frequently cited regulator of caspase-1 activation. It plays a significant role in several pathophysiological processes and is a major regulator of the innate immune response. A growing amount of scientific evidences for its aberrant activation in various chronic inflammatory diseases attracts a growing interest in the development of new NLRP3 inhibitors. One of the successful strategies used to identify new inhibitors is peptide inhibitors. Compared to small molecule inhibitors, peptide inhibitors show greater selectivity and less toxicity. In this study, we used an <i>in-silico</i> mutagenesis approach to design new peptide inhibitors from reported peptide inhibitor of NLRP3. The sequence of the peptide inhibitor against NLRP3 was searched from the literature and modeled using the online server PEP-FOLD3. The <i>in-silico</i> alanine scanning mutagenesis of the reference peptide revealed that residues, Y23, R28, E6, I26, R20, L19, Q33, K11, L14, and K13 have positive affinity values and are therefore better candidates for substitution to increase binding affinity. By replacing these residues, the affinity of the newly designed peptide inhibitors for the NLRP3 PYD protein was significantly increased. Further, molecular dynamics simulations and binding energy calculations validated the stability and higher binding affinities of the newly designed peptide inhibitors compared to the wild-type peptide inhibitor. Our research revealed that all the suggested peptide inhibitors have higher binding affinities for the NLRP3 protein as compared to the native wild-type peptide inhibitor and could block NLRP3-ASC pyrin-pyrin interaction.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-12"},"PeriodicalIF":2.7,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muhammad Faisal, Potchanapond Graidist, Varomyalin Tipmanee
{"title":"Identification of promising cancer target proteins of major sesquiterpene lactones from <i>Vernonia</i> spp.","authors":"Muhammad Faisal, Potchanapond Graidist, Varomyalin Tipmanee","doi":"10.1080/07391102.2024.2446662","DOIUrl":"https://doi.org/10.1080/07391102.2024.2446662","url":null,"abstract":"<p><p>The potential sesquiterpene lactone groups from the Vernonia genus; namely vernolide-A, vernolide-B, and vernodalin, have been reported for anticancer effects by downregulating cancer promoter proteins. Nevertheless, prior investigations have failed to identify the target proteins that are associated with the compounds' actions. Subsequently, the present investigation attempts to identify the target proteins associated with cancer. The number of candidate target proteins predicted by our molecular docking study for vernolide-A, vernolide-B, and vernodalin were one, five, and seven, respectively. Vernolide-A, vernolide-B, and vernodalin were predicted to have the most selective and attractive interactions with candidate target proteins; such as p38α, PGEP2R, and HSP90α, respectively. In addition, our MD simulation study revealed that the compounds' effects on the residual flexibility were not substantial. This suggested that their relative binding-free energy was similar to that of well-established ligands; including PD169316, dinoprostone, and Pu-H54. We also addressed the potential molecular mechanisms that may be associated with compounds in this report. Vernolide-A, vernolide-B, and vernodalin may potentially inhibit the proliferation, survival, angiogenesis, and migration of cancer cells through their strong affinity for a variety of cancer-related molecules. Additional laboratory experimental designs; including <i>in vitro</i> and <i>in vivo</i> studies, are suggested to further our computational findings.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-12"},"PeriodicalIF":2.7,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Is it feasible to use AI-based drug design methods in the process of generating effective COVID-19 inhibitors? A validation study using molecular docking, molecular simulation, and pharmacophore methods.","authors":"Hanyang Qu, Shengpeng Wang, Mingyang He, Yuhui Wu, Fei Yan, Tiaotiao Liu, Meiling Zhang","doi":"10.1080/07391102.2024.2445169","DOIUrl":"https://doi.org/10.1080/07391102.2024.2445169","url":null,"abstract":"<p><p>Although the COVID-19 pandemic has been brought under control to some extent globally, there is still debate in the industry about the feasibility of using artificial intelligence (AI) to generate COVID small-molecule inhibitors. In this study, we explored the feasibility of using AI to design effective inhibitors of COVID-19. By combining a generative model with reinforcement learning and molecular docking, we designed small-molecule inhibitors targeting the COVID-19 3CLpro enzyme. After screening based on molecular docking scores and physicochemical properties, we obtained five candidate inhibitors. Furthermore, theoretical calculations confirmed that these candidate inhibitors have significant binding stability with COVID-19 3CLpro, comparable to or better than existing COVID-19 inhibitors. Additionally, through ligand-based pharmacophore model screening, we validated the effectiveness of the generative model, demonstrating the potential value of AI in drug design.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-14"},"PeriodicalIF":2.7,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Prajna Ritaparna, Ajit Kumar Dhal, Rajani Kanta Mahapatra
{"title":"An <i>in-silico</i> study of FIKK9.5 protein of <i>Plasmodium falciparum</i> for identification of therapeutics.","authors":"Prajna Ritaparna, Ajit Kumar Dhal, Rajani Kanta Mahapatra","doi":"10.1080/07391102.2024.2446671","DOIUrl":"10.1080/07391102.2024.2446671","url":null,"abstract":"<p><p>The FIKK protein family, encompassing 21 serine-threonine protein kinases, is a distinctive cluster exclusive to the Apicomplexa phylum. Predominantly located in <i>Plasmodium falciparum</i> which is a malarial parasite, with a solitary gene identified in a distinct apicomplexan species, this family derives its nomenclature from - phenylalanine, isoleucine, lysine, lysine (FIKK), a conserved amino acid motif. Integral to the parasite's life cycle and consequential to malaria pathogenesis, the absence of orthologous proteins in eukaryotic organisms designates it as a promising antimalarial drug target. Among the FIKKs, FIKK9.5 plays a pivotal role in the parasite's development within red blood cells (RBCs). This investigation acquired the three-dimensional structure of FIKK9.5 and its ligands through extensive database searches and literature review. Computational screening of natural phytochemicals derived from plants traditionally used in antimalarial remedies was conducted by employing the Glide docking suite. AutoDock Vina was utilized to discern the inhibitor exhibiting optimal binding affinity. Subsequently, Molecular Dynamics (MD) simulations employing GROMACS validated Rufigallol as the most potent inhibitory compound against FIKK9.5. The robustness of the protein-ligand complex was scrutinized through a 200 nanosecond molecular dynamics (MD) trajectory. Trajectory analysis and determination of binding free energies were accomplished using MM-GBSA and MM-PBSA approaches. The ligand-binding exhibited sustained stability throughout the simulation, manifesting an approximate binding free energy of -25.5986 kcal/mol. This comprehensive computational study lays the groundwork for potential experimental validation in the laboratory, paving the way for the development of novel therapeutics targeting FIKK9.5 in the pursuit of innovative antimalarial.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-14"},"PeriodicalIF":2.7,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abdus Samad, Abu Hamza, Md Ali Imam, Anis Ahmad Chaudhary, Abdullah S Alawam, Eman Abdullah Almuqri, Asimul Islam, Shama Parveen
{"title":"pH induced structural and conformational changes in nucleocapsid protein leads to intermediate like conformation: a biophysical and computational approach.","authors":"Abdus Samad, Abu Hamza, Md Ali Imam, Anis Ahmad Chaudhary, Abdullah S Alawam, Eman Abdullah Almuqri, Asimul Islam, Shama Parveen","doi":"10.1080/07391102.2024.2442791","DOIUrl":"https://doi.org/10.1080/07391102.2024.2442791","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-12"},"PeriodicalIF":2.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}