The histone-like (HU) protein is one of the major nucleoid-associated proteins of the bacterial nucleoid, which shares high sequence and structural similarity with IHF but differs from the latter in ...DNA-specificity. Here, we perform an analysis of structural-dynamic properties of HU protein from Spiroplasma melliferum and compare its behavior in solution to that of another mycoplasmal HU from Mycoplasma gallisepticum. The high-resolution heteronuclear NMR spectroscopy was coupled with molecular-dynamics study and comparative analysis of thermal denaturation of both mycoplasmal HU proteins. We suggest that stacking interactions in two aromatic clusters in the HUSpm dimeric interface determine not only high thermal stability of the protein, but also its structural plasticity experimentally observed as slow conformational exchange. One of these two centers of stacking interactions is highly conserved among the known HU and IHF proteins. Second aromatic core described recently in IHFs and IHF-like proteins is considered as a discriminating feature of IHFs. We performed an electromobility shift assay to confirm high affinities of HUSpm to both normal and distorted dsDNA, which are the characteristics of HU protein. MD simulations of HUSpm with alanine mutations of the residues forming the non-conserved aromatic cluster demonstrate its role in dimer stabilization, as both partial and complete distortion of the cluster enhances local flexibility of HUSpm.
Monoclonal antibodies (mAbs) have revolutionized the biomedical field, directly influencing therapeutics and diagnostics in the biopharmaceutical industry, while continuing advances in computational ...efficiency have enabled molecular dynamics (MD) simulations to provide atomistic insight into the structure and function of mAbs. Despite the success of MD tools, further optimizations are still required to enhance the computational efficiency of complex mAb simulations. This issue can be tackled by changing the way the solvent system is modelled to reduce the number of atoms to be tracked but must be done without compromising the accuracy of the simulations. In this work, the structure of the IgG2a antibody was analyzed in three solvent systems: explicit water and ions, implicit water and ions, and implicit water and explicit ions. Root-mean-square distance (RMSD), root-mean-square fluctuations (RMSF), and interchain angles were used to quantify structural changes. The explicit system provides the most atomistic detail but is ~6 times slower in its exploration of configurational space and required ~4 times more computational time on our supercomputer than the implicit simulations. Overall, the behavior of the implicit and explicit simulations is quantifiably similar, with the inclusion of explicit ions in the implicit simulation stabilizing the antibody to reproduce well the statistical fluctuations of the fully explicit system. Therefore, this approach holds promise to maximize the use of computational resources to explore antibody behavior.
► The extra N-terminal α-helix of TIA-1 RRM3 is oriented in the two-domain RRM23 context. ► RRM3 is substantially destabilized by RRM2. ► TIA-1 RRM2 and RRM3 are tumbling together, with implications ...in RNA binding.
T-cell intracellular antigen-1 (TIA-1) plays a pleiotropic role in cell homeostasis through the regulation of alternative pre-mRNA splicing and mRNA translation by recognising uridine-rich sequences of RNAs. TIA-1 contains three RNA recognition motifs (RRMs) and a glutamine-rich domain. Here, we characterise its C-terminal RRM2 and RRM3 domains. Notably, RRM3 contains an extra novel N-terminal α-helix (α1) which protects its single tryptophan from the solvent exposure, even in the two-domain RRM23 context. The α1 hardly affects the thermal stability of RRM3. On the contrary, RRM2 destabilises RRM3, indicating that both modules are tumbling together, which may influence the RNA binding activity of TIA-1.
Molecular dynamics simulations were performed on both apo and copper forms of the human copper chaperone, Hah1. Wild-type Hah1 and a methionine (M10) to serine mutant were investigated. We have ...evidenced the central role of residue M10 in stabilizing the hydrophobic core of Hah1 as well as the internal structure of the metal-binding site. When copper(I) is bound, the mobility of Hah1 is reduced whereas mutation of M10 implies a drastic increase of the mobility of apoHah1, stressing the importance of this highly conserved hydrophobic residue for copper sequestration by the apoprotein.
Argonaute‐2 (AGO2), a member of the Argonaute family, is the only member possessing catalytic and RNA silencing activity. In here, a molecular dynamics (MDs) simulation was performed using the ...crystal structure of human AGO2 protein complex with miR‐20a. miR‐20a is involved with various kind of biological process like heart and lung development, oncogenic process, etc. In precise, MD simulation was carried out with AGO2 protein complex with wild type, two mutant sites and four mutant sites in guided microRNA (miRNA). It has been noted that root‐mean‐square deviation (RMSD) of atomic positions of nucleic acid for wild type and two mutant sites guided miRNA has the same pattern of fluctuations, which stabilizes around 0.27 nm after 2 ns. Cα atom of AGO2 protein in the complex shows that this complex with wild type and two mutant site mutation duplex has a stable RMSD value after 20 ns, ranging between 0.14 and 0.21 nm. From the root‐mean‐square fluctuation (RMSF), we observed an increased pattern of fluctuations for the atoms of four mutant complex of AGO2‐miR‐20a complex. This increased RMSF of non‐mutated nucleic acids is contributed by U‐A bond breaking at the site of the nucleotide of U2 of guided miRNA, as observed from the duplex structure taken at different time steps of the simulation. Superimposed structure of the miRNA‐mRNA duplex for the three complexes depicts that the three miRNA‐mRNA duplexes are stable during the simulation. Current work demonstrates the possible correlations between the conformational changes of this AGO2‐miR‐20a duplex structure and the interactions of different atoms.
The study demonstrates the possible correlations between the conformational changes of AGO2‐miR‐20a duplex structure and the interactions of different atoms. Molecular dynamic study by us might contribute to the future molecular research studying molecular interaction during miRNA‐mRNA interferences.
•Synthesis and exploring biological potential of 2-Chloroquinoline-based-Thiosemicarbazones.•In vitro studies of monoamine oxidase (MAO) and cholinesterase (ChE) inhibitors.•Applications of ...2-Chloroquinoline-based-Thiosemicarbazones as anti-alzheimer agents.•In silico docking study, molecular dynamics Simulations, and RMSF analyses.
Neurodegenerative diseases can be treated more effectively with multitarget approaches. monoamine oxidases (MAOs) acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are promising agents for cognitive decline. Here, a series of novel 2-chloroquinoline-3-carbaldehyd thiosemicarbazone derivatives (3a-r) were synthesized via a single-pot reaction. In-vitro testing results showed four compound 3c, 3o, 3g and 3l having chloro, fluoro, methyl and ethyl functional groups showed high potency against MAO-A, MAO-B, AChE and BChE, with an IC50 value 0.549 ± 0.045, 0.340 ± 0.02, 0.280 ± 0.135 and 2.77 ± 0.62 µM, respectively. Compounds 3g exhibited maximum inhibitory potential against all four targeted enzymes. Density functional theory (DFT) was used to evaluate the reaction profiles of the potent derivatives. We found that compounds 3c, 3o, 3l, and 3g exhibited strong reactivity because their LUMO/HOMO energy gaps were narrow. In addition, the molecular docking studies revealed excellent docking scores, ligands were well accommodated in the active site of targeted enzymes and produced stable protein-ligand complexes. The stability of the protein-ligand complex was confirmed by molecular dynamic (MD) simulations which revealed stable and equilibrated protein-ligand complexes. While compounds 3p, 3q and 3r were less effective than the whole series against the targeted enzymes. This integrated approach enhances the findings' comprehensiveness and reliability. The finding of In-vitro and In-silico studies suggested compound 3g as a promising multi-targeted compound that can be act as a molecule for AD treatment.
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GH11 xylanases are versatile small-molecular-weight single-polypeptide chain monofunctional enzymes. This family of glycoside hydrolases has important applications in food, feed and chemical ...industries. We designed mutants for improved thermal stability with substitutions in the first six residues of the N-terminal region and evaluated the stability in silico. The first six residues RTITNN of native xylanase have been mutated accordingly to introduce β structure, increase hydrophobic clusters and enhance conformational rigidity in the molecule. To design stable mutants, the approach consisted of constructing root mean square fluctuation (RMSF) plots of both mesophilic and thermophilic xylanases to check the localized backbone displacement maxima, identify the hydrophobic interaction cluster in and around the peaks of interest, construct mutants by substituting appropriate residues based on beta propensity, hydrophobicity, side chain occupancy and conformational rigidity. This resulted in the decreased number of possible substitutions from 19 to 6 residues. Introduction of conformational rigidity by substitution of asparagine residues at 5th and 6th residue position with proline and valine enhanced the stability. Deletion of N-terminal region increased the stability probably by reducing entropic factors. The structure and stability of GH11 xylanase and resultant mutants were analyzed by root mean square deviation, RMSF, radius of gyration and solvent accessible surface area analysis. The stability of the mutants followed the order N-del > Y1P5 >Y1V5 > ATRLM. The contribution of N-terminal end to overall stability of the molecule is significant because of the proximity of the C-terminal end to the N-terminal end which reinforces long-range interactions.
Communicated by Ramaswamy H. Sarma
Tankyrase (TNKS) enzymes remained central biotargets to treat Wnt-driven colorectal cancers. The success of Olaparib posited the druggability of PARP family enzymes depending on their role in tumor ...proliferation. In this work, an MD-simulation-based comparative assessment of the protein-ligand interactions using the best-docked poses of three selected compounds (two of the designed and previously synthesized molecules obtained through molecular docking and one reported TNKS inhibitor) was performed for a 500 ns period. The PDB:ID-7KKP and 3U9H were selected for TNKS1 and TNKS2, respectively. The Molecular Mechanics Generalized Born Surface Area (MM-GBSA) based binding energy data exhibited stronger binding of compound-15 (average values of −102.92 and −104.32 kcal/mol for TNKS1 and TNKS2, respectively) as compared to compound-22 (average values of −82.99 and −85.68 kcal/mol for TNKS1 and TNKS2, respectively) and the reported compound-32 (average values of −81.89 and −74.43 kcal/mol for TNKS1 and TNKS2, respectively). Compound-15 and compound-22 exhibited comparable or superior binding to both receptors forming stable complexes when compared to that of compound-32 upon examining their MD trajectories. The key contributors were hydrophobic stacking and optimum hydrogen bonding allowing these molecules to occupy the adenosine pocket by interfacing D-loop residues. The results of bond distance analysis, radius of gyration, root mean square deviation, root mean square fluctuation, snapshots at different time intervals, LUMO-HUMO energy differences, electrostatic potential calculations, and binding free energy suggested better binding efficiency for compound-15 to TNKS enzymes. The computed physicochemical and ADMET properties of compound-15 were encouraging and could be explored further for drug development.
Communicated by Ramaswamy H. Sarma
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