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.     

Roles of SiH4 and SiF4 in growth and structural changes of poly-Si films

The structural properties of polycrystalline silicon films, prepared by plasma enhanced chemical vapor deposition system, with different flow rates of SiH₄/SiF₄ mixtures at 300 °C were investigated. This study indicates that the low hydrogen coverage on the growing surface, under optimum fluorine radicals, will be leaded to an improvement of crystallized area as compared with case of high hydrogen coverage surface. Moreover, the studies of the role of SiH₄ and SiF₄ radicals show that the SiH₄ radicals are important in the nucleation and growth of grains. However, SiF₄ radicals are effective in the structural change of grain boundaries regions and by this way, in the present system, establish the growth of grains under the dominant 〈1 1 0〉 direction. The stress investigation indicates that addition of high flow rate of SiF₄ in amorphous film, results in the nearly stress free films. Finally, we found that the changes in g-value reflect the changes in the intrinsic compressive and tensile stress in the both polycrystalline and amorphous silicon films.     

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.     

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.     

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     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Preparation and crystal structure ofexo-2,exo-6-dihydroxy-2,6-dimethyl-9-oxabicyclo[3.3.1]nonane

In a further exploration of the structural factors causing alicyclic diols such asexo-2,exo-6-dihydroxy-2,6-dimethylbicyclo[3.3.1]nonane (1) to adopt the helical tubuland inclusion host structure, the title compound (8) has been synthesized and its crystal structure determined. This 9-oxa analogue of (1) has a totally different structure [C₁₀H₁₈O₃; orthorhombic;P2₁2₁2;a 18.989(4),b 19.064(3),c 14.256(3) Å;Z 20; with finalR 0.065] due to involvement of the ether oxygen atom in the hydrogen bonding network. The structure of the diol (8) approximatesP¯42₁ c symmetry, and 16 of the 20 molecules per cell create a hostlike structure of this symmetry, which consists of tightly bound hydrogen bonded pillars parallel toc. The remaining guestlike molecules occupy inequivalent pseudo ¯4 sites separated byc/2 to form weakly bound columns parallel toc. Hydrogen bonds also occur between the pillars and columns. An ordered structure with sensible intermolecular contacts can be formed inP2₁2₁2₁ with thec axis doubled. A difference betweena andb axial lengths correlates with a difference in occupancies of pseudo-¯4-related sites for the guest-like component of the structure.