The Structural Basis of Mycobacterium tuberculosis RpoB Drug-Resistant Clinical Mutations on Rifampicin Drug Binding

Tuberculosis (TB), caused by the Mycobacterium tuberculosis infection, continues to be a leading cause of morbidity and mortality in developing countries. Resistance to the first-line anti-TB drugs, isoniazid (INH) and rifampicin (RIF), is a major drawback to effective TB treatment. Genetic mutations in the β-subunit of the DNA-directed RNA polymerase (rpoB) are reported to be a major reason of RIF resistance. However, the structural basis and mechanisms of these resistant mutations are insufficiently understood. In the present study, thirty drug-resistant mutants of rpoB were initially modeled and screened against RIF via a comparative molecular docking analysis with the wild-type (WT) model. These analyses prioritized six mutants (Asp441Val, Ser456Trp, Ser456Gln, Arg454Gln, His451Gly, and His451Pro) that showed adverse binding affinities, molecular interactions, and RIF binding hinderance properties, with respect to the WT. These mutant models were subsequently analyzed by molecular dynamics (MD) simulations. One-hundred nanosecond all-atom MD simulations, binding free energy calculations, and a dynamic residue network analysis (DRN) were employed to exhaustively assess the impact of mutations on RIF binding dynamics. Considering the global structural motions and protein–ligand binding affinities, the Asp441Val, Ser456Gln, and His454Pro mutations generally yielded detrimental effects on RIF binding. Locally, we found that the electrostatic contributions to binding, particularly by Arg454 and Glu487, might be adjusted to counteract resistance. The DRN analysis revealed that all mutations mostly distorted the communication values of the critical hubs and may, therefore, confer conformational changes in rpoB to perturb RIF binding. In principle, the approach combined fundamental molecular modeling tools for robust “global” and “local” level analyses of structural dynamics, making it well suited for investigating other similar drug resistance cases.     

High-order multipolar hyperpolarizabilities with imaginary frequency for H and He

Calculations are reported of X³_zz,zz,z,z(−iω;iω,0,0), X³_zz,zz,x,x(−iω;iω,0,0), X³_zzz,z,z,z(−iω;iω,0,0), X⁴_zz,z,z,z,z(−iω;iω,0,0,0), and X⁴_zz,x,x,z,z(−iω;iω,0,0,0) for H and He. These are the independent components of the atomic (quadrupole)²-(dipole)², (octupole)-(dipole)³, and (quadrupole)-(dipole)⁴ hyperpolarizability tensors for an imaginary frequency iω. The first three quantities have been used for the determination of the R⁻⁸ dispersion contribution to the H-H, H-He, and He-He collision-induced pair polarizability functions. The last two quantities will be needed in future calculations of the leading order (R⁻⁷) dispersion contributions to the collision-induced first hyperpolarizability (β) for the H-He pair. The calculations were based on sum-over-states formulations with near-exact wave functions for H and highly accurate explicitly electron-correlated wave functions for He. For this reason we believe them to be of benchmark quality. © 1996 John Wiley & Sons, Inc.     

Optimization of chromatographic buffer conditions for the simultaneous analysis of phosphatidylinositol and phosphatidylinositol phosphate species in canola

The phosphatidylinositols and phosphatidylinositol phosphates are a set of closely related lipids known to influence various cellular functions. Irregular distributions of these molecules have been correlated with the development and progression of multiple diseases, including Alzheimer's, bipolar disorder, and various cancers. As a result, there is continued interest regarding the speciation of these compounds, with specific consideration on how their distribution may differ between healthy and diseased tissue. The comprehensive analysis of these compounds is challenging due to their varied and unique chemical characteristics, and current generalized lipidomics methods have proven unsuitable for phosphatidylinositol analysis and remain incapable of phosphatidylinositol phosphate analysis. Here we improved upon current methods by enabling the sensitive and simultaneous analysis of phosphatidylinositol and phosphatidylinositol phosphate species, whilst enhancing their characterization through chromatographic resolution between isomeric species. A 1 mM ammonium bicarbonate and ammonia buffer was determined optimal for this goal, enabling the identification of 148 phosphatidylinositide species, including 23 lyso-phosphatidylinositols, 51 phosphatidylinositols, 59 oxidized-phosphatidylinositols, and 15 phosphatidylinositol phosphates. As a result of this analysis, four distinct canola cultivars were differentiated based exclusively on their unique phosphatidylinositide-lipidome, indicating analyses of this type may be of use when considering the development and progression of the disease through lipidomic profiles.     

The behavior of the structure function at large wavevectors for polymers in different regimes

Off‐lattice Monte Carlo simulations employing the pivot algorithm are used to generate ideal and excluded volume linear polymers in three dimensions. The structure function at large wavevectors is calculated from the resulting configurations. This is compared to the exact equation for ideal chains and to experimental data and both scaling and renormalization group predictions for excluded volume chains. It is found that using the des Cloizeaux form for the distance distribution function in an analytic calculation of the structure function leads to close agreement with the experimental and Monte Carlo data.