Journal of Biomolecular Structure & Dynamics最新文献

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.

Apolipoprotein E3 (ApoE3) plays crucial role in binding with lipids, heparin and lipid receptors to initiate the essential signaling cascade responsible for lipid metabolism. To execute these roles, apoE3 requires unique conformational attributes, including the association of the N-terminal (NT) and C-terminal (CT) domains, stability, helical amphipathicity and specific inter-residue interactions within the heparin binding site. Glycation in ApoE3 impairs the inter domain (NT and CT) association, stability and alters the helical amphipathicity and residue interaction of heparin binding site. Glycation destabilizes ApoE3 by disrupting the helixC1 lock and LoopN1 tethering, which triggers conformation alteration in CT domain and inter domain (NT and CT) interface. Furthermore, it perturbs the residue interaction network pattern of NT domain and helical orientation of helix4 and helixC2, which leads to conformational changes in NT domain and inter-domain interface respectively. The separation of the NT and CT domains reduces the dipolar environment of the lipid binding region and changes the amphipathicity of the heparin binding helical segment and also changes the residue interaction pattern of K143 and K146, which are necessary features of heparin binding. Free energy landscape (FEL) analysis confirms multiple energetically favorable conformational states in glycated systems, with expanded gap region distances between NT and CT domains, indicating impaired lipid-binding ability. Centrality analysis of residue interaction networks further underscores glycation induced reorganization of structural hubs, particularly within helix 4. These findings provide detailed molecular insights into glycation-induced structural destabilization and functional impairment of ApoE3, contribute to lipid metabolism disorders in diabetic conditions.

Keratin derived from human hair has garnered significant attention for its biomedical applications. While ionic liquids (ILs) and keratinases independently facilitate hair hydrolysis, their synergistic use remains largely unexplored. Here, we computationally investigate the possibility of combining the use of ionic liquids and keratinases. We present here the structure of kerF and kerC, two keratinases identified from literature as promising candidates for human hair degradation, predicted using AlphaFold2. Subsequently, we performed molecular dynamics simulations to investigate the stability of these keratinases in water and six ionic liquids, chosen based on their recorded human hair degradation efficiency. The stability analysis was conducted using key metrics such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and number of intra-protein hydrogen bonds. Computational data indicate that kerF exhibits stability in both water and two ionic liquids: 1-Allyl-3-methylimidazolium chloride [AMIM]Cl, and 1-butyl-3-methylimidazolium bromide [BMIM]Br. kerC remains stable in [AMIM]Cl. The results suggest the potential utility of these two keratinases in environmentally friendly keratin extraction processes from human hair waste. This study aims to identify suitable keratinases and advances the understanding of their stability in non-conventional ionic liquid solvent systems, supporting the development of sustainable, eco-friendly strategies for the extraction of valuable human hair keratin.

This theoretical study examines the interaction between dacarbazine (DTIC) and a select group of amino acids-lysine (Lys), histidine (His), threonine (Thr), and isoleucine (Ile)-utilizing density functional theory (DFT) calculations. The research offers a comprehensive analysis of the noncovalent interactions that dictate the stability of DTIC-amino acid complexes, including hydrogen bonding, electrostatic forces, and hydrophobic contacts. The findings indicate that hydrogen bonding plays a crucial role in stabilizing these complexes, with the DTIC-His interaction demonstrating the highest stability energy of -19.89 kcal/mol. Natural bond orbital (NBO) calculations further substantiate this observation, revealing a significant second-order perturbation energy of 34.55 kcal/mol, highlighting the strong electronic interactions between DTIC and histidine. Additional insights from the Quantum Theory of Atoms in Molecules (QTAIM) and global reactivity descriptors affirm the presence of robust hydrogen bonds, particularly in the DTIC-His complex. The study also investigates the optical properties of these complexes through UV-vis calculations, identifying distinct characteristic wavelengths. Notably, the DTIC-His complex absorbs at 321.36 nm, while DTIC-Ile exhibits absorption at 329.61 nm. This research underscores the critical role of histidine in binding to dacarbazine, providing quantitative insights into the binding affinities and electronic properties of these interactions. These findings enhance the understanding of the molecular mechanisms underlying DTIC-amino acid complexes, with potential implications for drug design and biochemical applications.

The cellular immune responses associated with multiple sclerosis are triggered when T-lymphocyte receptors interact with the MOG epitope-MHC complex. By inhibiting the formation of this harmful trimeric complex (MHC-epitope-TCR), it is possible to alleviate the symptoms of MS. In this research, one of the human neuroantigenic epitopes (hMOG_37-46) involved in MS was bound to mouse MHC, forming a dimer complex (mMHC-hMOG). Subsequently, 12 peptides derived from honey bee venom were selected. Each peptide underwent a separate 100 ns molecular dynamics (MD) simulation before being docked into the binding cleft of the dimer complex, facilitating the identification of the most favorable complex. These trimer complexes were then subjected to an additional 100 ns MD simulation, and the binding free energy for each bee peptide to the dimer complex was computed using the MM/PBSA and quasi-harmonic methods. The findings indicated that Secapin 53-77 (YIIDVPPRCPPGSKFIKNRCRVIVP) demonstrated a greater binding affinity to the dimer complex. An examination of the binding site for this peptide within the dimer complex revealed a close similarity to the binding site of MHC with TCR, suggesting that this bee peptide can effectively obstruct the interaction between the mMHC-hMOG complex and TCR, thus preventing the onset of MS-related reactions. Also, another MD simulation showed that this peptide can bind to the complex human MHC-human MOG properly. Furthermore, based on the simulation results, a novel peptide (YIIKVHHRCHHGSKVIKNRCRVIVH) was designed, which also exhibited favorable interactions with the mMHC-hMOG complex. Finally, the residence times of these two peptides were determined through RAMD simulation.

To date, the treatment for Alzheimer's disease (AD) has focused on the cholinergic hypothesis, particularly through the inhibition of acetylcholinesterase (AChE). Asiatic acid, madecassic acid, asiaticoside, and madecassoside, which are triterpenoid derivatives from Centella asiatica, have previously been reported to exhibit the AChE inhibitory activity. This study aimed to investigate their binding modes and to determine efficient computational methods for analyzing their interactions with AChE. Molecular dynamics simulations demonstrated that most of their equilibrated structures remained within the AChE binding site. Principal component analysis and free energy landscape (FEL) confirmed their stability of the binding. Among the evaluated methods, the MM-(ALPB)SA binding energies, when combined with ligand surface binding efficiency index, showed the best correlation with experimental binding free energy. Density functional theory (DFT) calculations revealed the common key interaction between triterpenoids and AChE, including hydrogen bonds (Tyr124, Arg296, Tyr337, and Tyr341), H-π (Tyr341) and van der Waals (Trp86) interactions. Additionally, pharmacokinetics and drug-likeness predictions indicated that madecassic acid and asiatic acid are promising candidates for drug development. This study highlights the potential of triterpenoid derivatives in AChE inhibition and provides valuable insights into their binding efficiency, which could contribute to future drug discovery targeting Alzheimer's disease.

Dengue virus, an arbovirus belongs to the Flavivirus genus is the causative agent of Dengue fever, Dengue Hemorrhagic fever and Dengue Shock Syndrome, and accounts for thousands of lives every year. Here, we have characterized three such Dengue virus proteins (NS2A, NS2B and M) which have been previously shown to possess porin like functions. An exhaustive review of the literature and multiple in silico techniques were used to identify the protein segments that are capable of generating pores. Using independent sets of Molecular Dynamics (MD) simulations and post-simulation assessments, followed by hydration analysis of the channel interiors, the potential oligomeric status of the pore-forming segments was determined. The most likely ion conducting conformation and oligomeric status were chosen after the ion conductivity mechanism of the various oligomeric topologies was examined using computational electrophysiology MD simulations. The structure of the ion channel topologies as well as their electrical characteristics, such as conductance and current through the channel, were thoroughly described. The structure-function link of the porin activity of the three Dengue virus proteins is explained in depth by this work. The data gathered from this investigation could assist target these proteins for therapeutic intervention and support future research on the ion channel function of the Dengue virus proteins.

Tuberculosis (TB) remains a major global health issue, with growing challenges posed by drug resistance, highlighting the urgent need to identify new drug targets. This study examines the conservation pattern of the dapB gene, which encodes Dihydrodipicolinate reductase (DapB), a key enzyme in the lysine biosynthesis pathway of Mycobacterium tuberculosis (Mtb), a pathway absent in humans. The dapB gene was amplified from 72 Indian clinical isolates, sequenced and analysed for mutations. Further, the genomic data of 310 isolates from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database were also analysed. Further, atomistic simulations were performed in triplicate for the wild-type and mutant proteins to assess the impact of mutations on protein structure and function. Sequence analysis identified a single DapB mutation (DapB_65), among clinical isolates. Analysis of BV-BRC isolates revealed two synonymous mutations and one non-synonymous mutation (DapB_89). The mutations were mapped on the surface of the protein and were found to be more than 1.0 nm away from the active site. Simulations reveal no significant difference in the overall structure or the binding pocket dimensions and volumes between the native and mutant proteins. This study thus highlights the potential of DapB as a conserved drug target for future drug development efforts aimed at TB.