Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein

P-glycoprotein (Pgp) is a major efflux pump in humans, overexpressed in a variety of cancers and associated with the development of multi-drug resistance. Allosteric modulation by various ligands (e.g., transport substrates, inhibitors, and ATP) has been biochemically shown to directly influence structural dynamics, and thereby, the function of Pgp. However, the molecular details of such effects, particularly with respect to the role and involvement of the surrounding lipids, are not well established. Here, we employ all-atom molecular dynamics (MD) simulations to study the conformational landscape of Pgp in the presence of a high-affinity, third-generation inhibitor, tariquidar, in comparison to the nucleotide-free (APO) and the ATP-bound states, in order to characterize the mechanical effects of the inhibitor that might be of relevance to its blocking mechanism of Pgp. Simulations in a multi-component lipid bilayer show a dynamic equilibrium between open(er) and more closed inward-facing (IF) conformations in the APO state, with binding of ATP shifting the equilibrium towards conformations more prone to ATP hydrolysis and subsequent events in the transport cycle. In the presence of the inhibitor bound to the drug-binding pocket within the transmembrane domain (TMD), Pgp samples more open IF conformations, and the nucleotide binding domains (NBDs) become highly dynamic. Interestingly, and reproduced in multiple independent simulations, the inhibitor is observed to facilitate recruitment of lipid molecules into the Pgp lumen through the two proposed drug-entry portals, where the lipid head groups from the cytoplasmic leaflet penetrate into and, in some cases, translocate inside the TMD, while the lipid tails remain extended into the bulk lipid environment. These “wedge” lipids likely enhance the inhibitor-induced conformational restriction of the TMD leading to the differential modulation of coupling pathways observed with the NBDs downstream. We suggest a novel inhibitory mechanism for tariquidar, and potentially for related third-generation Pgp inhibitors, where lipids are seen to enhance the inhibitory role in the catalytic cycle of membrane transporters.

Lipid invasion of P-glycoprotein, enhanced by binding of an inhibitor.     

Carboxymethylation of corn starch and characterization using asymmetrical flow field-flow fractionation coupled with multiangle light scattering

Asymmetrical flow field-flow fractionation (AsFlFFF) was coupled online with multiangle light scattering (MALS) to study the changes in the molecular weight and the size distribution of the corn starch during carboxymethylation. A corn starch was derivatized with sodium chloroacetate in alcoholic medium under alkaline condition to produce carboxymethyl starches (CMS) having various degrees of substitution (DS). The change in thermal characteristics and granule structure of the native corn starch and CMS were compared using Thermogravimetric analysis and scanning electron microscope. The ionic strength of the carrier liquid (water with 0.02% NaN₃) was optimized by adding 50 mM NaNO₃ to minimize the interactions among the starch molecules and between the starch molecules and the AsFlFFF membrane. A field-programmed AsFlFFF allowed determination of the molecular weight distribution (MWD) of starches within about 25 min. It was found that carboxymethylation of starch results in reduction in the molecular weight due to molecular degradation by the alkaline treatment. The weight-average molecular weight (M_w) was reduced down to about 4.4 × 10⁵ from about 7.2 × 10⁶ when DS was 0.14. It seems AsFlFFF coupled with MALS (AsFlFFF/MALS) is a useful tool for monitoring the changes taking place in the molecular weight and the size of starch during derivatization.     

Direct use of unassigned resonances in NMR structure calculations with proxy residues

We present a method that significantly enhances the robustness of (automated) NMR structure determination by allowing the NOE data corresponding to unassigned NMR resonances to be used directly in the calculations. The unassigned resonances are represented by additional atoms or groups of atoms that have no interaction with the regular protein atoms except through distance restraints. These so-called "proxy" residues can be used to generate NOE-based distance restraints in a similar fashion as for the assigned part of the protein. If sufficient NOE information is available, the restraints are expected to place the proxies at positions close to the correct atoms for the unassigned resonance, which can facilitate subsequent assignment. Convergence can be further improved by supplying additional information about the possible identities of the unassigned resonances. We have implemented this approach in the widely used automated assignment and structure calculation protocols ARIA and CANDID. We find that it significantly increases the robustness of structure calculations with regard to missing assignments and yields structures of higher quality. Our approach is still able to find correctly folded structures with up to 30% randomly missing resonance assignments, and even when only backbone and beta resonances are present! This should be of significant value to NMR-based structural proteomics initiatives.     

Common fixed point theorems for self-mappings in Menger PM-spaces with nonlinear contractive condition

The purpose of this paper is to prove some common fixed point theorems for a pair of self-mappings defined on Menger PM-spaces with nonlinear contractive condition in the sense of Fang (Fuzzy Set Syst 267:86–99, 2015). Following Pant and Pant (Filomat (31)(11):3495–3499, 2017), we define semi R-commutativity for a pair of self-mappings for Menger PM-spaces. Using this notion and the notion of orbital continuity introduced by ?iri? (Publ Inst Math (12)(26):19–26, 1971), we obtain the main results. These results generalize some known results. Some examples and comments according to the preceding results are given.     

Effect of positional substitution of methyl group on the fluorescence properties of quinolinium ion

In the present study we have investigated the effect of methyl substitution at various positions on the spectral and decay behavior of some quinolinium ions. The spectra reveal marked differences when methyl group is present at 7th and 8th positions. The non-radiative deactivation is also considerably affected by the substituent position. The results are explained by considering the modulation (decrease as compared to the unsubstituted quinolinium) in nonradiative rate (intersystem crossing) due to substitution.     

Characterization and transport properties of 10BaO–xAg<Subscript>2</Subscript>O–(85-x)V<Subscript>2</Subscript>O<Subscript>5</Subscript>–5TeO<Subscript>2</Subscript> glass system

Silver-based quaternary glasses were prepared by splat quenching technique. X-ray diffraction and differential scanning calorimetry were done for confirming their amorphous nature. The conductivity of the glasses was measured in the frequency range from 1 Hz to 32 MHz from room temperature to 373 K. Conductivity data, which obeys the Arrhenius type behavior, shows minimum at 30 mol% Ag₂O, suggesting that the conductivity mechanisms are different above and below these two regions. The minimum in conductivity is accompanied by an inverse behavior of activation energy. Experimental data suggests that a polaron hopping mechanism operates in the electronically conducting domain of 20 ≤ × ≤ 30, and an interstitial pair mechanism operates in the ionically conducting domain of 35 ≤ × ≤ 55.     

New mutation schemes for differential evolution algorithm and their application to the optimization of directional over-current relay settings

Differential evolution is a novel evolutionary approach capable of handling non-differentiable, nonlinear and multimodal objective functions. It has been consistently ranked as one of the best search algorithm for solving global optimization problems in several case studies. In the present study we propose five new mutation schemes for the basic DE algorithm. The corresponding versions are termed as MDE1, MDE2, MDE3, MDE4 and MDE5. These new schemes make use of the absolute weighted difference between the two points and instead of using a fixed scaling factor F, use a scaling factor following the Laplace distribution. The performance of the proposed schemes is validated empirically on a suit of ten benchmark problems having box constraints. Numerical analysis of results shows that the proposed schemes improves the convergence rate of the DE algorithm and also maintains the quality of solution. Efficiency of the proposed schemes is further validated by applying it to a real life electrical engineering problem dealing with the optimization of directional over-current relay settings. It is a highly constrained nonlinear optimization problem. A constraint handling mechanism based on repair methods is used for handling the constraints. Once again the simulation results show the compatibility of the proposed schemes for solving the real life problem.     

Synthesis of conformationally diverse tetrathiacalix[4]arene(amido)crowns and tetrathiacalix[4]arene amides with pendant amine functions

A series of conformationally diverse novel tetrathiacalix[4]arene(amido)crowns and amides from tetrakis((ethoxycarbonyl)methoxy)p-tert-butyl tetrathiacalix[4]arene and its debutylated analog have been prepared by their reaction with diamines [H₂N(CH₂)_nNH₂; n=2,3,4, and 6] and polyamines. It has been determined that the length of the alkyl spacer in diamines is pivotal for the formation of either the tetrathiacalix[4]arene bis(amido)crowns or tetrathiacalix[4]arene amides with pendant amine functions. The synthesized compounds represent potential building blocks for achieving sophisticated molecular assemblies for molecular organization and recognition. Single crystal X-ray analysis of tetrathiacalix[4]arene bis(amido)crown 6a revealed that it has a 1,3-alternate conformation, which forms supramolecular complexes with chloroform.     

Polymer micro-environmental effects on the fluorescence characteristics of 5-aminoquinoline and 3-aminoquinoline

In this paper we report the spectral and decay behavior of two probes viz. 5-aminoquinoline (5AQ) and 3-aminoquinoline (3AQ) in three different polymeric systems viz. poly methyl methacrylate (PMMA), polyvinyl alcohol (PVA) and cellulose acetate (CA). Absorption spectra are nearly identical for all the polymers but the emission shows larger shift in case of CA as compared to PMMA and PVA. The behavior is explained on the basis of higher hydrogen bond donating ability in case of CA because of the presence of cellulosic hydrogens. Observed multiexponential decays are explained on the basis of free as well as hydrogen-bonded species and also trapping in various excited state geometries of the matrix.