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.     

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.     

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.     

Dendrimers and combinatorial chemistry—tools for fluorescent enhancement in protease assays

FRET based systems are some of the best methods available to detect and monitor proteolytic activity. To enhance fluorescent signals and hence assay sensitivity, two different systems were developed using two different dendrimeric constructs. In the first case, a triple branched dendrimer bearing three dansyl groups was used to enhance assay sensitivity and showed a significant enhancement of fluorescence following enzymatic cleavage. In another example, a tris-fluorescein probe, that undergoes self-quenching, was utilized in a combinatorial library synthesis to map the substrate specificity of proteases.     

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.     

头发锌含量测定的应用价值评价

以114例2－5岁儿童为对象，同时取其末梢血和头发，测定锌含量。以全血锌值为标准，评价头锌测定的应用价值。结果显示，头发锌测定的灵敏度可达86．1％，特异度为52．4％，符合率为73．7％。     

Classical Valence Similarity in Fullerene Derivatives

Summary.  The generalized Pauling bond order was enumerated in the C₆₀ fullerene cage molecule (truncated icosahedral symmetry). This index measures chemical similarity in fullerene derivatives such as dihydrofullerene (C₆₀H₂), anionized monohydrofullerene (C₆₀H⁻), N-substituted monohydrofullerene (C₅₉NH), the fullerene dimer ((C₆₀)₂), and the dianionic fullerene dimer ((C₆₀)₂ ²⁻). It is also useful in judging the chemical stability of isomers. Received October 9, 2001. Accepted November 9, 2001     

In silico engineering of tailored ink-binding ability at molecular printboards.

Molecular recognition between guest ink molecules and beta-cyclodextrin (beta-CD) cavities at self-assembled monolayers provides a molecular printboard for nanopatterning applications. We recently used molecular dynamics (MD) simulations to describe the specificity of ink-printboard binding and here extend the simulations to include charged cyclodextrin hosts, necessary to broaden the chemistry of molecular printboards and bind charged inks such as the ferrocenium cation. Shifting to high pH, or alternatively grafting a charged sidearm onto beta-CD, created three distinct types of anionic beta-CD cavity and we used electronic structure calculations and MD simulations to measure host-guest charge transfer and binding strengths. We find that steric recognition of uncharged organic molecules is retained at the charged printboards, and that improved guest-host electrostatic contacts can strengthen binding of larger inks while penalising small inks, enhancing the level of discrimination. A prudent choice of complementary host-guest shape and charge states thus provides a means of tuning both ink binding strength and specificity at molecular printboards.     

Aminolysis ofO-alkylO-4-nitropyenyl chloromethylphosphonates in reverse micellar solutions of the nonionic surfactant

The reaction ofn-hexylamine withO-alkylO-4-nitrophenyl chloromethylphosphonates in toluene solutions of poly(ethylene glycol)-600 monolaurate (PM) has been studied by spectrophotometry. The reverse micelles of the nonionic surfactant increase more than tenfold the observed rate constant of aminolysis. The catalytic activity of the surfactant is practically independent of the alkyl radical length of phosphonate. An increase in the concentration of amine results in a decrease in the catalytic efficiency. The character of the dependence of the rate constant on the concentration of PM is affected by the alkyl chain length of the substrate. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1735–1738, September, 1998.