Journal of Biomolecular Structure & Dynamics最新文献

l-Tyrosine (l-Tyr) is not only a proteinogenic amino acid, but is also a high value natural aromatic compound that serves as a precursor for the biosynthesis of valuable biologically active compounds of pharmaceutical and food industries. In organisms that use the arogenate route for l-Tyr synthesis, a prephenate aminotransferase (PAT) is essential. Studies have demonstrated that this activity is not found independently, but is housed by other aminotransferases. The dapC encoding N-succinyldiaminopimelate aminotransferase (S-DAPAT) of Corynebacterium glutamicum has previously been shown to function as a bifunctional PAT-competent enzyme, as it displays both S-DAPAT and PLP-dependent PAT activities, and its deletion leads to l-Tyr bradytrophy. In this context, a comprehensive biochemical, structural, and phylogenetic characterization of DapC_Cg has been carried out to get clues in the acquisition of PAT activity. Similar to many PAT-competent enzymes, the purified enzyme displayed a strong preference for l-glutamate (l-Glu) as the amino donor to a lesser extent, for l-aspartate (l-Asp) as amino group donors. High prephenate concentrations resulted in substrate inhibition of the enzyme. Sequence and structural alignments with enzymes known to possess PAT activity have shown that key residues that may be critical for activity were conserved. Furthermore, phylogenetic analysis, supported by structural and sequence alignments shed light on the evolutionary trajectory of PAT activity. Based on their evolutionary distance and similarity to S-DAPAT of C. glutamicum in the conserved residues for PAT activity, aminotransferases encoded by pat and hisC of C. glutamicum have been suggested to be involved in l-tyrosine biosynthesis in C. glutamicum.HighlightsDapC bifunctionality in C. glutamicum was characterizedKey residues for prephenate aminotransferase activity were proposedEnzymes with potential to exhibit PAT activity in C. glutamicum were proposed.

Studying aqueous amino acids at low temperatures is crucial for gaining insights into protein behavior, their interactions with water, and their potential applications across various fields. Temperature variations can influence amino acid interactions and conformations, thereby affecting protein stability and functionality. In this study, we aim to investigate the thermoacoustic and thermophysical properties of aqueous alanine by measuring acoustic and related parameters over the temperature range of 303.15 to 278.15 K at atmospheric pressure. The study focuses mainly on the molecular interactions between alanine and water molecules below room temperatures. Using the pulse-echo technique, ultrasonic velocity (u) was measured at a fixed frequency of 5 MHz. The measured ultrasonic velocity (u) of an aqueous alanine towards higher concentrations suggests an increased induced intermolecular interaction between alanine-water molecules. The study also concludes the intermolecular interaction between alanine-alanine molecules towards low temperature via isolated hydrated monomers of alanine. Adiabatic compressibility (β), intermolecular free length (L_f), absorption coefficient (α/f²) and relaxation time (τ) and thermodynamical parameters i.e. the free energy of activation (ΔF), entropy of activation (ΔS) and enthalpy of activation (ΔH) of aqueous alanine solution also supported for the dynamics of aqueous alanine in the icy environment. The significant achievement of the study is that there found a formation of water network (higher values of hydration number) or hydration shell around alanine molecules and induced interaction between nearby alanine molecules in the low temperature region.

In recent years, the development of novel therapeutic strategies to inhibit emerging viruses has become a major challenge in pharmaceutical research. This study aimed to design innovative nanostructures to prevent the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from interacting with host cells. DNA origami and heparin molecules were incorporated into various nanocomplexes, consisting of a U-shaped DNA origami cage, heparins of different lengths (tetrasaccharide, hexasaccharide, decasaccharide), and a spermidine-functionalized linker positioned near the viral RBD. Molecular dynamics (MD) simulations, complemented by steered MD (SMD) simulations, were performed to evaluate stability and quantify the forces required to detach the RBD. The SMD results reveal strong electrostatic and van der Waals interactions that effectively prevent RBD dissociation. Furthermore, MM/GBSA calculations show negative binding free energies (${\text{ΔG}}_{\text{bind}}$ ranging from - 36.9 ± 7.9 kJ/mol for tetrasaccharide to - 170.9 ± 14.0 kJ/mol for decasaccharide), confirming that longer heparin chains enhance binding affinity and complex stability. These findings underscore the computationally promising potential of these nanostructures for inhibiting viral attachment to the ACE2 receptor. The calculated binding affinity and pulling work further confirm the computationally observed affinity of these nanocomplexes for the RBD. While these computational findings indicate high binding affinity and inhibitory potential, further studies are required to evaluate biocompatibility, stability in biological fluids, immunogenicity, and suitable delivery methods for these nanostructures. This study provides a structural modeling framework integrating DNA origami, heparin, and SMD-MM/GBSA analyses, highlighting the potential of these nanostructures for SARS-CoV-2 inhibition and antiviral therapeutic development.

Lung cancer is the leading cause of cancer-related mortality worldwide and arises from a complex interplay of genetic predispositions and environmental exposures. Epidemiological studies have shown that alterations in key DNA repair genes, such as MSH2, can significantly impact an individual's susceptibility to cancer. In the present study, we focused on MSH2 polymorphisms and their potential role in increasing the risk of lung cancer. Our analysis revealed that four out of six polymorphisms showed a strong association with increased risk of lung cancer in individuals carrying heterozygous or mutant genotypes, specifically 118 T > C, 1032 G > A, T > C/-6, and Asn127Ser. Among these, the T > C/-6 polymorphism exhibited the strongest effect, conferring a 13-fold increased risk of lung cancer (Pcorr = 0.0006) in patients with the variant allele. Stratified analysis further indicated subtype-specific associations: in adenocarcinoma (ADCC) patients, the T > C/-6 variant was linked to a 12-fold higher risk (Pcorr = 0.0018), while in squamous cell carcinoma (SQCC) and small-cell lung carcinoma (SCLC) patients, the same polymorphism was associated with a 2-fold (Pcorr = 0.0006) and 16.5-fold increased risk, respectively, particularly in carriers of the combined or mutant genotypes. MDR analysis predicted the best interaction model (MSH2 118 T > C, IVS 1 + 9 G > C, T > C/-6) with a maximum CVC of 10/10 and the least prediction error of 0.355, accompanied by a significant p-value. Furthermore, MD simulations reveal that the Gly322Asp polymorphism in MSH2 induces pronounced structural destabilisation, which may compromise DNA binding and repair efficiency.

The aggregation of the tau protein into pathological assemblies is a pivotal event in Alzheimer's disease and related tauopathies. Understanding how different cofactors influence the Tau aggregation pathway is crucial for elucidating disease mechanisms. This study directly compares the aggregation pathways of human Tau (hTau441, 4 R/1 N) induced by heparin with those induced by aluminum/sodium fluoride (AlF₃/NaF). We employed time-resolved Raman spectroscopy, a technique uniquely suited for label-free, real-time secondary structure analysis of intrinsically disordered proteins in solution, to monitor structural transitions. Our results reveal two distinct trajectories: Heparin drives a classical pathway of progressive β-sheet enrichment, culminating in mature fibrils. In stark contrast, fluoride conditions suppress β-sheet formation and stabilize granular, nonfibrillar oligomers. These findings suggest that the neurotoxicity associated with fluoride may not arise from accelerating fibril formation but from diverting tau into an off-pathway oligomeric state. This work establishes Raman spectroscopy as a powerful tool for mechanistic studies of protein aggregation and identifies fluoride as a modulator of Tau misfolding with significant pathological implications.

To effectively combat and mitigate the adverse effects associated with the use of bio-based pesticides and to understand their stability in various environmental contexts, it is essential to analyze and fully understand the fundamental characteristics and properties of these complex materials. In this research, a detailed study was conducted to investigate the interaction between chlordecone (CD) and human serum albumin (HSA) under neutral pH conditions. The findings showed that increasing the CD concentration resulted in a significant quenching effect on the static fluorescence emitted by HSA, indicating a significant interaction between the pesticide and the protein. According to thermodynamic analysis and molecular docking data, the binding between CD and HSA primarily occurs within Subdomain IIIB of HSA and is influenced by van der Waals forces, as well as the formation of hydrogen bonds, which play a crucial role in stabilizing the complex. Furthermore, our findings revealed that the presence of CD increased the thermal stability of the protein, a phenomenon that can be attributed to the stabilization of the structural integrity of HSA as a direct result of CD binding. The results obtained from FTIR spectroscopy further confirmed these findings by showing that the presence of CD induces changes in the secondary structure of HSA, leading to structural damage. Furthermore, the use of computational techniques provided further validation of the results obtained through various spectroscopic methods. Taken together, the results of this comprehensive study provide significant insight into the potential health risks that CD may pose to human health.

DNA gyrase B is a validated antibacterial target for combating resistance. A new series of 2-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-N-phenylacetamides was synthesized and characterized by spectroscopic techniques. Compounds 6e and 6h displayed potent antibacterial activity, with MIC values of 50 μg/mL against Escherichia coli and Pseudomonas aeruginosa, comparable to chloramphenicol and superior to other analogues. Molecular docking revealed binding affinities of -4.7 and -5.1 kcal/mol for 6e and 6h, similar to chloramphenicol (-5.0 to -5.3 kcal/mol). MM-GBSA analysis indicated stronger binding free energies for 6e (-46.76 kcal/mol) and 6h (-44.59 kcal/mol) than chloramphenicol (-28.19 to -40.03 kcal/mol). A 100 ns MD simulation confirmed stable complex formation, with 6e showing minimal RMSD fluctuations and reduced RMSF values for key binding site residues, consistent with strong hydrogen bonding, hydrophobic, and ionic interactions. ADME profiling predicted favorable oral bioavailability. Overall, compounds 6e and 6h represent promising scaffolds for further optimization as potent antibacterial agents targeting DNA gyrase B.

In this study, a comprehensive bioinformatics workflow is employed to investigate the impact of APOE gene variants on Alzheimer's disease (AD) and to explore their relevance for improving therapeutic strategies. Multiple databases were screened to identify key non-synonymous single nucleotide polymorphisms (nsSNPs) in APOE. Six variants: rs769452 (L46P), rs429358 (C130R), rs267606664 (G145D), rs121918393 (R154S), rs7412 (R176C), and rs267606661 (R269G) were selected, of which five were predicted to be deleterious. Given its high interaction score (0.789), the FDA-approved AD drug Donepezil was chosen as the ligand to assess binding with both wild-type and mutant APOE proteins. Structural modeling using AlphaFold3 generated high-quality APOE structures, and in silico mutagenesis revealed mutation-dependent destabilization. AutoDock4 molecular docking was performed to evaluate binding affinities of Donepezil with the predicted active-site residues of wild-type and mutant APOE. Furthermore, 100 ns molecular dynamics simulations using AMBER20 were conducted for all APOE-Donepezil complexes. Analyses of RMSD, RMSF, and radius of gyration indicated overall structural stability, residue-level flexibility, and protein compactness throughout the simulations. Interaction profiling revealed stable hydrophobic contacts and hydrogen bonds in both wild-type and mutant complexes. Our findings suggest that structural variations arising from APOE genotypes may modulate Donepezil binding and potentially influence therapeutic response in AD patients. However, these computational predictions require validation through biophysical assays, cellular experiments, and genotype-stratified clinical studies. Integrating molecular modeling with experimental research will be essential for advancing APOE-guided precision medicine and optimizing Donepezil therapy for Alzheimer's disease.

Dihydroorotate dehydrogenase (DHODH) is a key enzyme in de novo pyrimidine biosynthesis and has emerged as a promising target for cancer, inflammation, and autoimmune diseases. In this study, a series of computational techniques-HQSAR, 3D-QSAR (CoMSIA), molecular docking, molecular dynamics (MD) simulations, and MM/PBSA free energy calculations-were employed to investigate the structure-activity relationships (SAR) of thiazole-based DHODH inhibitors. HQSAR (R²_cv = 0.846; R²_test = 0.700) and CoMSIA (R²cv = 0.742; R²_test = 0.817) models demonstrated strong predictivity. Contour maps highlighted the significance of hydrophobic and electrostatic groups on both fused and aromatic rings for inhibitory activity. Docking studies revealed that LEU46, PRO52, ARG136, TYR356, and THR360 are key residues in ligand binding. MD simulations over 500 ns confirmed M33, P26, and P39 as the most stable complexes, while P44 and P46 showed more flexibility. Binding free energy calculations identified P39 and P46 as potent binders due to favorable van der Waals and electrostatic interactions. M33 and P26 showed moderate affinity and high structural stability, making them promising leads. In contrast, P44 exhibited low stability and binding energy. Overall, this work offers valuable insights into thiazole-based DHODH inhibitor design and guides the development of selective therapeutic candidates.

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.