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.     

In-time motion adjustment in laser cladding manufacturing process for improving dimensional accuracy and surface finish of the formed part

This paper presents in-time motion adjustment in laser cladding manufacturing process as a means to improve dimensional accuracy and surface finish of the built part. Defects occurring during laser cladding degrade the part quality such as dimensional accuracy and surface finish. In this paper, in-time motion adjustment strategy was presented to remedy and eliminate defects occurring during laser cladding to improve the dimensional accuracy and surface finish. Based on the relationship between the motion of laser head relative to the growing part and other parameters in effects on clad profile, the laser traverse speed, stand-off distance and laser approach orientation to the existing clad layer were adjusted by instructions from a close-loop control system in real time to remedy and eliminate defects. The results of the experiments verified the effects of in-time motion adjustment on dimensional accuracy and surface finish.     

Investigations of He implantation and subsequent annealing effects in InP

The influence of 70 keV He⁺ ion implantation and subsequent annealing of Cz-indium phosphide (InP) samples has been investigated using a slow positron beam-based Doppler broadening spectrometer. Three samples with ion fluences of 1 × 10¹⁶, 5 × 10¹⁶ and 1 × 10¹⁷ cm⁻² were studied in the as-implanted condition as well as after annealing at 640 °C for times between 5 and 40 min. It was found that the line-shape parameter of the positron-electron annihilation peak in the implanted layer increases after 5 min annealing, then after longer annealing times it starts to decline gradually until it reaches a value close to the value of the as-grown sample. This implies that vacancy-like defects can be created in InP by He implantation followed by short-thermal annealing at T > 600 °C. Comparison of the results with a study where cavities were observed in He-implanted InP has been carried out.     

Quadrupole interactions at 57Fe and 119Sn in 3d-metal antimonides

3d-metal antimonides: Fe_1+x Sb, N_+x Sb, Co_+x Sb and the (Ni_1?y Fe _y )Sb solid solution have been studied by the Mössbauer effect method at ⁵⁷Fe and ¹¹⁹Sn. It was found that the quadrupole interactions at the Fe and Sn nucleus in 3d-metal antimonides are very sensitive to the filling of different crystallographic sites with metal atoms. The metal atoms in trigonal-bipyramidal sites have a strong effect on the quadrupole splitting of ¹¹⁹Sn. They are nearest to anions (Sb or Sn) with the typical axial ratio of c/a = 1.25. The QS(x) dependence of ¹¹⁹ Sn in 3d-metal antimonides in the 0 ≤ x ≤ 0.1 concentration range can be used to determine x – the concentration of transition metal excess relative to the stoichiometric composition.     

Structural manipulation of pyrochlores: Thermal evolution of metastable Gd2(Ti1−yZry)2O7 powders prepared by mechanical milling

The structural and microstructural characteristics of metastable Gd₂(Ti_1−yZr_y)₂O₇ powders prepared by mechanical milling have been studied by a combination of XRD and Raman spectroscopy. Irrespective of their Zr content, as-prepared powder phases present an anion-deficient fluorite-type of structure as opposed to the pyrochlore equilibrium configuration obtained for the same solid solution by other synthetic routes. These fluorites are stable versus thermal activation, at least up to temperatures of 800 °C. For the Ti-rich compositions, thermal treatments at higher temperatures facilitate the rearrangement of the cation and anion substructures and the relaxation of mechanochemically induced defects whereas for compositions with high Zr content, the fluorite crystal structure is retained even at temperatures as high as 1200 °C. Interestingly enough, transient pyrochlores showing a very unusual cation distribution were observed during the thermally induced defect-recovery process.     

Fluorescence line narrowed spectra of Zn and metal-free cytochrome c

Fluorescence line narrowing (FLN) spectroscopy was used to study the role of the polypeptide chain in influencing the spectrum of Zn-substituted cytochrome c (Zn cyt c) and metal-free cyt c (porphyrin cyt c). For both derivatives the spectra show characteristics of relaxed fluorescence from an inhomogeneously broadened sample. Zero phonon lines and phonon wings can be clearly distinguished, and vibrational frequencies of the ground and excited states were identified. The inhomogeneous distribution width for porphyrin cyt c is slightly wider than that of Zn cyt c and a second population of molecules was apparent in the porphyrin cyt c. The phonon coupling was greater for Zn cyt c than for porphyrin cyt c, which may be due to the extra coupling to the polypeptide chain by metal ligation.This work has been done in partial fulfillment of the requirements for the Doctor of Philosophy degree.     

Slow positron beam study of corrosion-related defects in pure iron

Corrosion-related defects of pure iron were investigated by measuring Doppler broadening energy spectra (DBES) of positron annihilation and positron annihilation lifetime (PAL). Defect profiles of the S-parameter from DBES as a function of positron incident energy up to 30 keV (i.e. ∼1 μm depth) were analyzed. The DBES data show that S-parameter increases as a function of positron incident energy (mean depth) after corrosion, and the increase in the S-parameter is larger near the surface than in the bulk due to corrosion. Furthermore, information on defect size from PAL data as a function of positron incident energy up to 10 keV (i.e. ∼0.2 μm depth) was analyzed. In the two-state trapping model, the lifetime τ₂ = 500 ps is ascribed to annihilation of positrons in voids with a size of the order of nanometer. τ₁, which decreases with depth from the surface to the bulk, is ascribed to the annihilation of positrons in dislocations and three-dimensional vacancy clusters. The corroded samples show a significant increase in τ₁ and the intensity I₂, and near the surface the corroded iron introduces both voids and large-size three-dimensional vacancy clusters. The size of vacancy clusters decreases with depth.     

Identity of defect causing nonideality in nearly ideal Au/n-Si Schottky barriers

We have proposed a mechanism of nonideality, i.e., the temperature dependence of the ideality factor, in nearly ideal Au/n-Si Schottky barriers. Because of the nature of metal-induced gap states, positively ionized defects close to the interface are considered to cause local lowering of the Schottky barrier height (SBH) due to downward bending of the energy band. These positively charged defects become neutralized in equilibrium with the Fermi level due to the band bending, when they are very close to the interface. However, because the SBH lowering disappears by the neutralization of donor, the energy level of donor with a usual energy level scheme rises above the Fermi level after the neutralization. This contradiction to the equilibrium neutralization is resolved by Si self-interstitial with a large negative-U property, which is generated by the fabrication process. The energy level of the donor estimated from the SBH lowering is in good agreement with that of theoretical calculation of Si self-interstitial. Thus, the defect is concluded to be the Si self-interstitial, which is distributed to more than 10 Å depth from the interface.     

Quantum chemistry investigation on the active site of Mn-SOD

In this paper, we carried out a theoretical study on the active site structures of the Mn-SOD with ab initio Hartree–Fock SCF method, and analyzed the molecular orbital energies, charges and atomic orbital contribution to the frontier molecular orbital.