Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Carbon deposition on a Ni/α-Al2O3 catalyst

The kinetics of carbon deposition over a Ni/α-Al₂O₃ commercial catalyst, has been studied using CH₄−H₂ gas mixtures in the range of 748–873 K. A Hougen-Watson type model gives good agreement with the experimental rates.     

Time-resolved gas-phase kinetic and quantum chemical studies of the reaction of silylene with nitric oxide

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with NO. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 299-592 K. The second-order rate constants at 10 Torr fitted the Arrhenius equation log(k/cm3 molecule(-1) s(-1)) = (-11.66 +/- 0.01) + (6.20 +/- 0.10 kJ mol(-1))/RT ln 10 The rate constants showed a variation with pressure of a factor of ca. 2 over the available range, almost independent of temperature. The data could not be fitted by RRKM calculations to a simple third body assisted association reaction alone. However, a mechanistic model with an additional (pressure independent) side channel gave a reasonable fit to the data. Ab initio calculations at the G3 level supported a mechanism in which the initial adduct, bent H2SiNO, can ring close to form cyclo-H2SiNO, which is partially collisionally stabilized. In addition, bent H2SiNO can undergo a low barrier isomerization reaction leading, via a sequence of steps, ultimately to dissociation products of which the lowest energy pair are NH2 + SiO. The rate controlling barrier for this latter pathway is only 16 kJ mol(-1) below the energy of SiH2 + NO. This is consistent with the kinetic findings. A particular outcome of this work is that, despite the pressure dependence and the effects of the secondary barrier (in the side reaction), the initial encounter of SiH2 with NO occurs at the collision rate. Thus, silylene can be as reactive with odd electron molecules as with many even electron species. Some comparisons are drawn with the reactions of CH2 + NO and SiCl2 + NO.     

Copolymeric nano/microgels of N-isopropylacrylamide and carboxyalkyl methacrylamides: Effect of methylene chains and the ionization state of the weak acids on size and sensitivity to pH and temperature

ABSTRACT

We prepared nano/microgels by precipitation copolymerization of N-isopropylacrylamide (NIPAAm), and one of three different carboxyalkyl methacrylamides [methacryloylamido hexanoic acid (M₅), 8-methacryloylamido octanoic acid (M₇), and 11-methacryloylamido undecanoic acid (M₁₀)], either in the acid forms or as carboxylates (potassium salts). The hydrodynamic diameter (Dh) of the nano/microgels prepared with the carboxylates was smaller (≈100 nm for M₁₀ copolymers), compared to the size of homopolymeric NIPAAm microgels prepared by dispersion polymerization (around 600 nm), indicating that the carboxylates act as surfactants reducing the size of the seeds during the polymerization process. These materials presented a swollen-shrunken transition temperature (T _tr) similar to the T _tr of the homopolymeric NIPAAm microgels, without pH sensitivity. On the other hand, the copolymeric microgels prepared from the acid form of the comonomers have a similar or bigger size than NIPAAm microgels. For these copolymers, the T _tr can be tuned by the type and proportion of acid comonomer used and present pH sensitivity. This is important for biomedical applications such as positive temperature control release. Polyelectrolyte titration demonstrates that the nano/microgels prepared with the carboxylates behave as hard spheres, while the microgels prepared with the weak acid behave as porous materials.     

Search space pruning and global optimisation of multiple gravity assist spacecraft trajectories

We introduce and describe the Multiple Gravity Assist problem, a global optimisation problem that is of great interest in the design of spacecraft and their trajectories. We discuss its formalization and we show, in one particular problem instance, the performance of selected state of the art heuristic global optimisation algorithms. A deterministic search space pruning algorithm is then developed and its polynomial time and space complexity derived. The algorithm is shown to achieve search space reductions of greater than six orders of magnitude, thus reducing significantly the complexity of the subsequent optimisation. This work was partially funded under the Ariadna scheme of the European Space Agency, contract number 18138/04/NL/MV.     

Factors Influencing the Isothermal Retention Indices of 51 Solutes on 12 Stationary Phases of Different Polarity: Applicability of the Solvation Parameter Model

Isothermal retention indices (I) at 333–413 K on 12 stationary phases (SPs) covering a wide polarity range of a variety of volatile solutes belonging to 7 one-heteroatom chemical function series and 10 non-series solutes have been determined. The I values were computed with a method (LQG method) which does not require the determination of holdup times of the chromatographic column. I values of some compounds never before studied are reported. The influence on the retention indices of the column temperature, methylene number, and polarity of both the stationary phase and the solute has been studied. The solvation parameter model (SPM) as a function of I has been used for predicting I values, and for unraveling the influence of the polarity of stationary phase and solute on the retention indices. Seeley et al.’s formulation of the SPM has been used for quantifying the influence of polar and non-polar interactions on the I, and for checking the agreement between calculated and experimental values. According to our results, the I values obtained by the modified SPM can be considered equal to the experimental I values at the 99 % confidence level.

     

Gas phase kinetic and theoretical studies of reactions of germylenes and dimethylstannylene

The results of time resolved gas phase studies of labile germylenes (GeH₂ and GeMe₂) and dimethylstannylene (SnMe₂) reactions reported to date are considered together with data of quantum-chemical investigations of the potential energy surfaces of these systems. Reaction mechanisms are discussed. A comparison of reactivity in the series of carbene analogs, ER₂ (E = Si, Ge, Sn, R = H, Me), is made.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 477–505, March, 2005.     

Surprisingly slow reaction of dimethylsilylene with dimethylgermane: time-resolved kinetic studies and related quantum chemical calculations

Time-resolved studies of silylene, SiH2, and dimethylsilylene, SiMe2, generated by the 193 nm laser flash photolysis of appropriate precursor molecules have been carried out to obtain rate constants for their bimolecular reactions with dimethylgermane, Me2GeH2, in the gas phase. SiMe2 + Me2GeH2 was studied at five temperatures in the range 299-555 K. Problems of substrate UV absorption at 193 nm at temperatures above 400 K meant that only three temperatures could be used reliably for rate constant measurement. These rate constants gave the Arrhenius parameters log(A/cm3 molecule(-1) s(-1)) = -13.25 +/- 0.16 and E(a) = -(5.01 +/- 1.01) kJ mol(-1). Only room temperature studies of SiH2 were carried out. These gave values of (4.05 +/- 0.06) x 10(-10) cm3 molecule(-1) s(-1) (SiH2 + Me2GeH2 at 295 K) and also (4.41 +/- 0.07) x 10(-10) cm3 molecule(-1) s(-1) (SiH2 + MeGeH3 at 296 K). Rate constant comparisons show the surprising result that SiMe2 reacts 12.5 times slower with Me2GeH2 than with Me2SiH2. Quantum chemical calculations (G2(MP2,SVP)//B3LYP level) of the model Si-H and Ge-H insertion processes of SiMe2 with SiH4/MeSiH3 and GeH4/MeGeH3 support these findings and show that the lower reactivity of SiMe2 with Ge-H bonds is caused by a higher secondary barrier for rearrangement of the initially formed complexes. Full details of the structures of intermediate complexes and the discussion of their stabilities are given in the paper. Other, related, comparisons of silylene reactivity are also presented.