Journal of Biomolecular Structure & Dynamics最新文献

Phospholipase A₂ (PLA₂) enzyme found in snakes, bees, and wasps' venoms is responsible for toxicity and pathophysiology of envenomation. Varespladib (VP, LY-315920) is among the extensively researched small molecule inhibitors targeting snake venom (SV) PLA₂ and PLA₂-like proteins. Interestingly, it could not neutralize bee venom (BV) PLA₂. To reveal this puzzle, we compared VP's in silico binding mechanisms with PLA₂s from India's 'Big Four' snake venoms (BFSVs, Naja naja, Daboia russelii, Echis carinatus, and Bungarus caeruleus), nine viper venoms from four continents, and BV. VP binds SV-PLA₂s in the same position but in a different position in the BV-PLA2s due to a clash between its phenyl ring and residues Tyr89 and Ile91, which might be the reason behind its universal activity against SV-PLA₂s but negligible activity against BV-PLA₂. Molecular docking and dynamics simulations identified optimal VP binding conformations with BFSV and BV-PLA₂ proteins. In silico analysis results showed that the BFSV-PLA₂-VP complex exhibited significantly greater binding affinity and stability than other PLA₂-VP complexes, suggesting enhanced molecular interactions. The spectrofluorometric binding data showed a significantly higher binding affinity of VP with BFSV-PLA₂s than BV-PLA₂s, corroborated by differential inhibition of catalytic activity and anticoagulant activity of PLA₂ enzymes from BV and SVs. VP showed significant neutralization of in vivo toxicity, generating reactive oxygen species and altering mitochondrial transmembrane potential induced by PLA₂s from BFSV in the Caenorhabditis elegans model. However, such activities were not shown against BV-PLA₂, indicating the limitations of broad-spectrum inhibitors like VP in neutralizing BV-PLA₂.

Upon binding to cytosolic DNA, the cyclic GMP-AMP synthase (cGAS) is activated to catalyze the synthesis of cGAMP, which then activates downstream effectors and induces innate immune responses. The activation of cGAS relies on the formation of cGAS-DNA oligomers and liquid phase condensation, which are sensitive to the length and concentration of DNA. Although significant progresses have been made for the understanding of such a length- and concentration-dependent activation, some structural and energetic details of the cGAS-DNA oligomerization remains elusive. Here, with molecular dynamics simulations, we report the structure of the cGAS-DNA monomer (the cGAS₁-DNA₁ complex), in which the DNA binds simultaneously to the major parts of two DNA-binding sites as observed in the cGAS-DNA dimer (the cGAS₂-DNA₂ complex) and its active site is largely immature. Energetic analysis indicates that two cGAS₁-DNA₁ complexes are just slightly less stable than the cGAS₂-DNA₂ complex and there exists a significant energy barrier for the formation of the cGAS₂-DNA₂ complex from two cGAS₁-DNA₁ complexes, which provides thermodynamic and kinetic explanations for an experimental observation that cGAS-DNA oligomerization is unfavored in low concentration of cGAS and DNA.

Maturity-Onset Diabetes of the Young type 14 (MODY14) is a rare monogenic diabetes linked to APPL1 variants that impair insulin signaling. This study evaluated how missense substitutions in the APPL1 PTB domain affect its interaction with the AKT2 catalytic domain, a key step in glucose regulation. Among 475 APPL1 missense SNPs, four conserved variants (R526C, H535R, S543W, G585R) were prioritized using predictive algorithms and conservation scoring. Protein-protein docking and 300-ns molecular dynamics simulations were performed. Structural stability and interaction dynamics were assessed through RMSD, RMSF, radius of gyration, hydrogen bonding, and center-of-mass distance, complemented by principal component analysis and Gibbs free energy landscapes. Docking identified the HADDOCK-derived model as the most reliable complex. Simulations showed that H535R, S543W, and G585R induced only mild deviations from the wild type, with limited effects on stability and flexibility. In contrast, R526C produced pronounced destabilization, including elevated backbone fluctuations, increased flexibility, reduced compactness, irregular hydrogen bonding, and greater inter-domain separation. PCA confirmed broader conformational sampling for R526C, and its free-energy landscape lacked the well-defined minima observed in the wild type and the other variants. R526C consistently emerged as the most destabilizing substitution, likely impairing AKT2 activation and glucose uptake, supporting its pathogenic role in MODY14. This integrative computational approach demonstrates the diagnostic value of structural modeling for prioritizing rare variants in monogenic diabetes. Importantly, disruption of the APPL1-AKT2 complex may compromise insulin-stimulated glucose uptake and represents a potential molecular target for therapeutic intervention.

Mutations in the HFE gene, especially non-synonymous single-nucleotide polymorphisms (nsSNPs), are strongly associated with hemochromatosis, an autosomal recessive disorder characterized by intracellular iron overload, a key feature of tumor development. This study examined the structural and functional effects of deleterious nsSNPs in the HFE gene using bioinformatics tools, gene interaction analyses, molecular docking, molecular dynamics (MD) simulations, and assessments of clinical relevance. Functional analyses identified nine deleterious nsSNPs, including C282Y, L183P, and Q283P, which disrupted disulfide bonds, hydrogen bonds, and hydrophobic interactions, destabilizing the protein. Conservation analysis revealed these mutations occur in highly conserved regions, emphasizing their structural and functional importance. Notably, five nsSNPs (R224Q, R224W, I235T, C282Y, Q283P) within the Ig-like C1-type domain were associated with cancer. Gene interaction analyses showed HFE-related genes are linked to immunity and iron balance. Variants in interacting genes, such as HJV, TFR2, TFRC, and B2M, may influence iron disorders, infection risk, and inflammation. Molecular docking showed reduced interface interactions for the C282Y mutant and altered binding to transferrin receptor 1 (TfR1), potentially destabilizing the HFE-TfR1 complex. MD simulations highlighted key differences, with the mutant showing higher RMSD, decreased compactness (Rg), increased flexibility (RMSF), and greater solvent exposure (SASA), confirming destabilization. Furthermore, HFE expression varied across cancers, with elevated levels in twelve tumor types. Higher expression correlated with better survival in breast and gastric cancers but poorer outcomes in lung cancer. These findings highlight how deleterious nsSNPs, especially C282Y, disrupt HFE structure and function, offering insights into disease mechanisms and guiding therapeutic strategies.

Phosalone (Pln) is an organophosphate pesticide that poses potential risks to human health due to its widespread use. We investigated the interaction between Pln and human serum albumin (HSA) using molecular modeling and multi-spectral methods. Molecular docking studies identified the binding site and key residues involved in the interaction with Pln. Additionally, molecular dynamics (MD) simulations revealed that the average root mean square deviation (RMSD) of the complex exceeded that of the free HSA system, consistent with thermal stability studies indicating a decrease in $T_m\text{.}$ Ultraviolet-visible (UV-vis) spectroscopic analyses confirmed the formation of a HSA-Pln complex. Extrinsic fluorescence analysis, utilizing the fluorescent dye 8-Anilinonaphthalene-1-sulfonic acid (ANS), demonstrated that the addition of Pln quenches the fluorescence of the HSA-ANS complex through static quenching. The Stern-Volmer constants ($K_{\text{sv}}$) for the interaction between Pln and HSA-ANS were determined to be 47.99, 31.67, and 27.55 ($M^{-1}$) at temperatures of 298, 308, and 318 K, respectively. The thermodynamic parameters were calculated as ${\Delta S}^0$ = -39.88 (J. ${\text{mol}}^{-1}{K}^{-1})$ and ${\Delta H}^0$= -22.25 (kJ ${\text{mol}}^{-1}$). These thermodynamic investigations revealed that hydrogen bonds and van der Waals forces are the primary interactions responsible for the formation of the (ANS-HSA)-Pln complex. Furthermore, FT-IR spectroscopy indicated that Pln induces a conformational change in HSA, suggesting its potential to cause structural damage. These findings provide valuable insights into the interaction mechanism between Pln and HSA, enhancing our understanding of the impact of pesticides on proteins and overall health.

A new Pd(II)-phen-salicylate complex i.e. [Pd(phen)(SA)] was synthesized and characterized to evaluate its biological potential. This salicylate based complex is structurally and electronically distinct from previously reported Pd(II)-bpy or Pd(II)-phendione analogues, introducing salicylate in conjugation with 1,10-phenanthroline (phen) for the first time. Spectroscopic studies, supported by computational modeling, revealed that the complex interacts with DNA mainly through stable hydrogen bonds, while also forming hydrogen bonding and van der Waals forces with bovine serum albumin (BSA). MD simulations confirmed the stability of the Pd(II) complex-DNA/BSA adducts over time and provided insight into their dynamic conformational behavior. Binding constants (K_b,DNA = 5.30 × 10⁴ and K_b,BSA = 2.22 × 10⁵) and molecular docking provided insight into the spontaneity and orientation of these interactions. Cytotoxicity assays against human cancer cell lines (K562) demonstrated that the Pd(II) complex exhibits measurable antiproliferative activity (IC₅₀ = 37 µM), with results compared to cisplatin as the reference drug. Overall, these findings highlight the potential of new [Pd(phen)(SA)] complex and suggest its potential as a promising scaffold for the development of new Pd-based therapeutic agents.

Vibrio cholerae is a gram-negative bacterium known for causing severe diarrhea and disrupting the barrier function of intestinal cells. Its outer membrane proteins (OMPs), particularly TolC, are crucial for maintaining bacterial homeostasis and pathogenicity. TolC is vital for antibiotic resistance and molecular efflux, making it a key target for study. However, extracting large quantities of soluble OMPs is challenging. To address this, TolC from V. cholerae is refolded in vitro using detergents and lipids and characterized biophysically. Additionally, its antigenic potential is explored through immunoinformatics. The results show that different folding reagents vary in effectiveness, with some promoting a near-native quaternary structure, specifically a trimer held together by non-covalent interactions. Moreover, TolC has surface-exposed epitopes capable of triggering an immune response. Owing to its role in antimicrobial resistance, this study provides valuable structural insights into refolded TolC in various detergents and lipids, potentially aiding large-scale production of structurally accurate protein for drug and vaccine development.

The γ-class carbonic anhydrase EcoCAγ, reported in Escherichia coli in 2022, contains a 72-residue N-terminal extension absent in the canonical YrdA isoform. A genomic analysis confirmed that the full-length EcoCAγ is conserved (95-100% identity) across multiple E. coli and Shigella strains but is not present in the laboratory strain K-12. A full-length trimeric model was generated using AlphaFold-Multimer and subjected to molecular dynamics simulations in aqueous and membrane environments. In membrane conditions, the N-terminal segment maintained an extended α-helical conformation, whereas in aqueous solution it underwent compaction and self-association. Throughout all simulations, the trimeric assembly and the geometry of the catalytic site remained preserved. No disruption of the active-site architecture was observed under either condition. These simulations provide structurally resolved observations of the environment-dependent behavior of the N-terminal region and its effect on the conformational dynamics of the EcoCAγ trimer.

Dengue virus methyltransferase (DENV MTase) facilitates the methylation of the viral RNA cap and continues to be a confirmed target for antiviral development. This study examined papaya-derived flavonoids as potential MTase inhibitors through an extensive computational workflow that integrated molecular docking, molecular dynamics (MD) simulations, MM/GBSA binding energy, and steered molecular dynamics-umbrella sampling (SMD-US) to assess unbinding energetics. Neohesperidin, Quercetin, and Myricetin exhibited the highest binding affinities for DENV MTase among the analysed flavonoids, with binding free energies (ΔG_US) of -15.31, -14.67, and -13.69 kcal/mol, respectively from umbrella sampling. Potential mean force (PMF) profiles derived from umbrella sampling offer insights about the unbinding mechanisms and thermodynamic feasibility of these naturally occurring inhibitors. The results of MMGBSA binding energy and the identification of key amino acids at the active site, namely ASP131, LYS105, and ILE147, in the context of MTase-flavonoid binding through non-covalent interaction analysis further corroborated these conclusions. To evaluate Carica papaya-derived flavonoids as MTase inhibitors, this work is the first to combine SMD-US and MMGBSA analyses. The findings substantiate the promise of papaya-associated flavonoids as scaffolds for dengue MTase inhibition.

Colorectal cancer (CRC) is a leading global malignancy, with many stage IV cases requiring surgery and chemotherapy. However, chemoresistance limits treatment efficacy. Targeting resistance pathways such as CXCR2 with therapeutic antibodies offers a promising solution. This study harnessed deep mutational scanning guided by modified heated coarse-grained molecular dynamics (CGMD) simulations, to enhance the binding affinity of the HY29-1 antibody toward CXCR2. The structural stability and intermolecular binding of the variable heavy (vH) and light (vL) chains of the HY29-1 antibody fragment (Fv-HY29-1) alone and complexed with CXCR2 were assessed using modified heated CGMD simulations under thermal stress conditions. Using a modified heated CGMD protocol, the Fv-HY29-1 antibody fragment, modeled via ClusPro (C7) exhibited remarkable conformational stability, maintaining complete (100%) complexation with CXCR2 over a 70 ns simulation. Meanwhile, a benchmark model of the established Fv-Fab14-canine parvovirus capsid complex retained 100% stability under similar conditions. Extended deep mutational scanning over a 1000 ns trajectory pinpointed critical framework residues in the vL chain (A43, L47, and F98) as key determinants of paratope-epitope binding. Rational substitutions (A43P, L47V, F98W) significantly enhanced binding affinity, improving from -36.02 kcal/mol to -94.09 kcal/mol, approximately two-fold increase in binding strength. This marked affinity gain translated into strengthened CXCR2 engagement, highlighting the promise of structure-guided antibody engineering in optimizing therapeutic interactions. This study demonstrated that a 1 μs modified heated simulation with coarse-grained models and deep mutational scanning enables cost-effective optimization of antibody binding affinity and will guide future design of high-affinity antibodies across diverse antigen targets.