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.     

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.     

Structure and protonation of some indolizine derivatives studied by ab initio MO calculations

Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed ¹³C and ¹⁵N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.     

Spectroscopic properties of the photoproducts of pyridoxal-5′-P irradiation: Catalytic site recognition of ribonuclease A

Photoproducts of pyridoxal-5-P, i.e., 4-pyridoxic-5-P and bis-pyridoxal-5-P, have been studied by spectroscopic methods. The spectroscopic properties of bis-pyridoxal-5-P (bis-PLP) resemble those of pyridoxal-5-P (PLP) under similar experimental conditions. The coupling of methylen hydrogens to the phosphorus atom has been shown by NMR spectroscopy. The singlet in the³¹P-NMR spectra and the triplet in¹H-undecoupled experiments confirm the presence of the phosphate group in the 5 position of the structure of the vitamin. The effect of pH and solvent composition on the relative distribution of species of bis-pyridoxine-5-P (bis-PNP) has been investigated by absorption and fluorescence spectroscopy. The acid-base dissociation of the phosphate group is easily detected by emission spectroscopy. Bis-PNP and bis-PLP bind to the enzyme RNase A and they behave as competitive inhibitors with respect to the substrate cytidine-2-3-cyclic phosphate. The natural forms of vitamin B₆, pyridoxine, and pyridoxine-5-P have no effect on the catalytic activity of the protein. Experimental evidence derived from fluorescence and inhibition experiments is consistent with the hypothesis that bis-PNP recognizes the catalytic site of RNase A.