Binding motif of taxol in WT and mutated tubulins.

<p>The drug-receptor complexes were obtained by simulating the lowest energy docked complexes for 10 ns in explicit water. Taxol is shown in licorice and the tubulin residues involved in interactions are colored according to atom type – green: C, red: O, blue: N, white: H. Results shown for - a) WT b) T274I c) R282Q d) Q292E. Mutations resulted in altered mode of drug binding and loss of characteristic drug-receptor contacts.</p

Nanostructural Reorganization Manifests in <i>Sui-Generis</i> Density Trend of Imidazolium Acetate/Water Binary Mixtures

Ionic liquids (ILs) are emerging as a novel class of solvents in chemical and biochemical research. Their range of applications further expands when a small quantity of water is added. Thus, the past decade has seen extensive research on IL/water binary mixtures. While the thermophysical properties of most of these mixtures exhibited the expected trend, few others have shown deviations from the general course. One such example is the increase in density of the 1-alkyl-3-methyl imidazolium acetate ([R_<i>n</i>mim]­[Ac])-based ILs with the addition of low to moderate concentrations of water. Although such a unique trend was observed for imidazolium cations of different tail lengths and also from independent experiments, the molecular basis of this unique behavior remains unknown. In this study, we examine the nanostructural reordering in [R_<i>n</i>mim]­[Ac] (<i>n</i> = 2–6) ILs due to added water by means of molecular dynamics simulations, and correlate the observed changes to the <i>sui-generis</i> density trend. Results suggest that the initial rise in density in these ILs mainly pertains to the water-induced increased spatial correlation among the polar components, where high basicity of the acetate anion plays a key role. At moderate water concentration, the density can rise further for ILs with longer cation tails due to hydrophobic clustering. Thus, while [emim]­[Ac]/water mixtures exhibit the density turnover at <i>X</i>_w = 0.5, [bmim]­[Ac] and [hmim]­[Ac] show the turnover at <i>X</i>_w = 0.7. The detailed understanding provided here could help the preparation of optimal IL/water binary mixtures for various biochemical applications

Understanding the Basis of Drug Resistance of the Mutants of αβ-Tubulin Dimer <em>via</em> Molecular Dynamics Simulations

<div><p>The vital role of tubulin dimer in cell division makes it an attractive drug target. Drugs that target tubulin showed significant clinical success in treating various cancers. However, the efficacy of these drugs is attenuated by the emergence of tubulin mutants that are unsusceptible to several classes of tubulin binding drugs. The molecular basis of drug resistance of the tubulin mutants is yet to be unraveled. Here, we employ molecular dynamics simulations, protein-ligand docking, and MMPB(GB)SA analyses to examine the binding of anticancer drugs, taxol and epothilone to the reported point mutants of tubulin - T274I, R282Q, and Q292E. Results suggest that the mutations significantly alter the tubulin structure and dynamics, thereby weaken the interactions and binding of the drugs, primarily by modifying the M loop conformation and enlarging the pocket volume. Interestingly, these mutations also affect the tubulin distal sites that are associated with microtubule building processes.</p> </div

Toward Greater DNA Stability by Leveraging the Proton-Donating Ability of Protic Ionic Liquids

Deoxyribonucleic acid (DNA) stability is a prerequisite in many applications, ranging from DNA-based vaccines and data storage to gene therapy. However, the strategies to enhance DNA stability are limited, and the underlying mechanisms are poorly understood. Ionic liquids (ILs), molten salts of organic cations and organic/inorganic anions, are showing tremendous prospects in myriads of applications. With a judicious choice of constituent ions, the protic nature of ILs can be tuned. In this work, we investigate the relative stability of full-length genomic DNA in aqueous IL solutions of increasing protic nature. Our experimental measurements show that the protic ionic liquids (PILs) enhance the DNA melting temperature significantly while unaltering its native B-conformation. Molecular dynamics simulations and quantum mechanical calculation results suggest that the intramolecular Watson–Crick H-bonding in DNA remains unaffected and, in addition, the PILs induce stronger H-bonding networks in solution through their ability to make multiple intermolecular H-bonds with the nucleobases and among its constituent ions, thus aiding greater DNA stability. The detailed understanding obtained from this study could bring about the much-awaited breakthrough in improved DNA stability for its sustained use in the aforesaid applications

Dynamical Network of HIV‑1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity

HIV-1 protease variants resist drugs by active and non-active-site mutations. The active-site mutations, which are the primary or first set of mutations, hamper the stability of the enzyme and resist the drugs minimally. As a result, secondary mutations that not only increase protein stability for unhindered catalytic activity but also resist drugs very effectively arise. While the mechanism of drug resistance of the active-site mutations is through modulating the active-site pocket volume, the mechanism of drug resistance of the non-active-site mutations is unclear. Moreover, how these allosteric mutations, which are 8–21 Å distant, communicate to the active site for drug efflux is completely unexplored. Results from molecular dynamics simulations suggest that the primary mechanism of drug resistance of the secondary mutations involves opening of the flexible protease flaps. Results from both residue- and community-based network analyses reveal that this precise action of protease is accomplished by the presence of robust communication paths between the mutational sites and the functionally relevant regions: active site and flaps. While the communication is more direct in the wild type, it traverses across multiple intermediate residues in mutants, leading to weak signaling and unregulated motions of flaps. The global integrity of the protease network is, however, maintained through the neighboring residues, which exhibit high degrees of conservation, consistent with clinical data and mutagenesis studies

Binding motif of epothilone A in WT and mutated tubulins.

<p>The drug-receptor complexes were obtained by simulating the lowest energy docked complexes for 10 ns in explicit water. Results shown for - a) WT b) T274I c) R282Q d) Q292E. Epothilone A is shown in yellow.</p

Resistant β-tubulin mutations selected for computational study.

<p>Resistant β-tubulin mutations selected for computational study.</p

Binding energetics of taxol in wild type and mutated tubulins using the MMPBSA and MMGBSA methods.

<p>The error bars calculated from four separate windows are included.</p

Binding energetics of epothilone A in wild-type and mutated tubulins from docking studies.

<p>Binding energies are obtained from the lowest energy epothilone-tubulin docked complexes. For WT tubulin, the experimental K_I = 1.4 µM <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042351#pone.0042351-Kowalski1" target="_blank">[43]</a>. Also listed are the RMSD values of the protein and ligand, relative to the crystal structure.</p

Binding energetics of taxol in wild type and mutated tubulins from docking studies.

<p>Binding energies are obtained from the lowest energy taxol-tubulin docked complexes. For WT tubulin, the experimental K_I = 2.5 µM <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042351#pone.0042351-Li1" target="_blank">[42]</a>. Also listed are the RMSD values of the protein and ligand, relative to the crystal structure.</p