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PubMed1992

[Function, molecular structure and gene expression of interferons].

Interferon is a key substance of the cytokine network, and is functioning not only as the virus inhibitory factor, but also as the factor for differentiation, development, and homeostasis of animals, including man. The molecular structure, induction mechanisms, interaction with receptor, and antiviral action mechanisms of IFN were reviewed. 1. Molecular structure of IFN IFNs are now divided into 4 types--alpha, beta, gamma, omega--according to antigenicities of IFN proteins, and to base sequence of their genes. The omega type was established officially on 1990 by the Nomenclature Committee of International Society for Interferon Research (ISIR). Also, the genes for HuIFNs were named as follows; HuIFN-A for HuIFN-alpha, HuIFN-B for HuIFN-beta, HuIFN-G for HuIFN-gamma, and HuIFN-W for HuIFN-omega. Nevertheless, the names of Type I IFN and Type II IFN are still valuable, since members of Type I IFN, alpha, beta, and omega, are similar in their molecular structures, and they share the common receptor (Type I IFN receptor), on the other hand, HuIFN-gamma (the only one member of Type II IFN) has different characteristics from the other IFNs, and binds to its specific receptor (Type II IFN receptor). However, it has been reported that both N-terminal and C-terminal of IFN protein of all types, participate in the binding of IFN to its receptor. 2. Induction mechanism of IFN. The factors, IRF-1 and IRF-2, were found to play an important role in IFN induction.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1991

Molecular structure and dynamics of tricyclic antidepressant drugs.

The molecular structure, electrostatic potentials and dynamics of imipramine, chlorimipramine, amitriptyline and nortriptyline were examined by computer graphics, molecular mechanical energy calculations and molecular dynamics simulations, using the AMBER all atom force field. Starting coordinates for amitriptyline and nortriptyline were generated by model building from the crystal structure of imipramine. The structures were refined by molecular mechanical energy minimization, and used as starting points for molecular dynamics simulations in vacuo and in aqueous solution. The simulations demonstrated considerable flexibility of the molecules, both in the side chain and in the ring system, where the angle between the phenyl rings varied between 90 degrees and 168 degrees. The most frequently observed conformations of imipramine, chlorimipramine and nortriptyline during the simulations had the side chain folded above one of the phenyl rings, while amitriptyline showed both folded and extended side chain conformations during the simulations. The results may provide increased understanding of the molecular recognition and specificity of tricyclic antidepressant drugs in interaction with neurotransmitter receptor molecules.

Antidepressive Agents, Tricyclic↗
PubMed1971

Molecular structures of DNA-dependent RNA polymerases (II) from calf thymus and rat liver.

DNA-dependent RNA polymerase II has been purified to high specific activity and apparent homogeneity from both calf thymus and rat liver. Two form II enzymes are present in rat-liver preparations, one with the molecular structure [(190,000)(1)(150,000)(1)(35,000)(1)(25,000)(1)], the other with a molecular structure of [(170,000)(1)(150,000)(1)(35,000)(1)(25,000)(1)] (molecular weights are within +/-5% but the absolute values are approximate). Inclusion of a proteolytic inhibitor during the isolation procedure decreases the proportion of the molecule containing the 170,000 subunit. Calf-thymus RNA polymerase preparations typically exhibit four components on polyacrylamide gels that contain sodium dodecyl sulfate, with an apparent molecular structure of [(190,000)(1)(150,000)(1)(35,000)(1)(25,000)(1)]. In addition, some calf-thymus polymerase II preparations contain small quantities of the [(170,000)(1)(150,000)(1)(35,000)(1)(25,000)(1)] species; the quantity of this species may also be increased from less than 5% in the normal preparation to at least 40% in an "aged" preparation. Thus, the 170,000 subunit may be derived from the 190,000 subunit in both tissues. Until unequivocal evidence is obtained on this point, however, the possibility that the large subunits are unique species should not be eliminated. The general structural similarity of the eukaryotic RNA polymerase II with that of the prokaryotic polymerase suggests that the modes of action and regulation may be analogous.

Acrylamides↗
PubMed1998

Molecular Structures of the Heavier Alkali Metal Salts of Supermesitylphosphane: A Systematic Investigation.

The molecular structures of the rubidium and cesium derivatives of supermesitylphosphane [i.e., (2,4,6-(t)Bu(3)C(6)H(2))PH(2) = (t)Bu(3)MesPH(2)] as well as several base adducts of these are reported. Sodium hydride, potassium hydride, rubidium metal, and cesium metal react with (t)Bu(3)MesPH(2) in tetrahydrofuran solution at room temperature to produce MPRH salts 1-4 [M = Na (1), K (2), Rb (3), Cs (4); R = (t)Bu(3)Mes] in good yields. X-ray-quality crystals of 2 and 3 were obtained by slow evaporation of solutions of the corresponding MP(H)(t)Bu(3)Mes species dissolved in toluene/thf. Complex 4 was crystallized from hot toluene. On the other hand, slow evaporation of a toluene/tetrahydrofuran solution of CsP(H)(t)Bu(3)Mes (4) produces crystals of the composition {[CsP(H)(t)Bu(3)Mes](2)(&mgr;-THF)(0.9).toluene}(x)() (5). Crystallization of 4 in the presence of pyridine yields crystals of {[CsP(H)(t)Bu(3)Mes](2)(&mgr;-pyridine)}(x)() (6). Also, crystallization of complexes 3 and 4 from toluene/N-methylimidazole (N-MeIm) gives the isomorphous complexes {[RbP(H)(t)Bu(3)Mes](2)(&mgr;-N-MeIm)}(x)() (7) and {[CsP(H)(t)Bu(3)Mes](2)(&mgr;-N-MeIm)}(x)() (8), respectively. However, crystallization of 4 from toluene in the presence of bidentate or polydentate bases such as dimethoxyethane or pentamethyldiethylenetriamine does not result in incorporation of these bases into the lattice. Instead, the toluene solvate {[CsP(H)(t)Bu(3)Mes](2)(eta(3)-toluene)(0.5)}(x)() (9) is obtained. On the other hand, crystallization of 4 from toluene/ethylenediamine gives the base adduct {[CsP(H)(t)Bu(3)Mes](2)(&mgr;-ethylenediamine)}(x)() (10). Complex 3 crystallizes in the triclinic space group P&onemacr;. Crystal data for 3 at 218 K: a = 6.71320(10) Å, b = 10.5022(2) Å, c = 14.9733(3) Å, alpha = 91.3524(13) degrees, beta = 102.5584(13) degrees, gamma = 107.7966(14) degrees; Z = 1; R(1) = 6.55%. Complex 4 crystallizes in the triclinic space group P&onemacr;. Crystal data for 4 at 223 K: a = 7.0730(14) Å; b = 10.395(2) Å; c = 14.933(2) Å; alpha = 81.97(1) degrees; beta = 76.35(2) degrees; gamma = 71.824(14) degrees; Z = 1; R(1) = 4.56%. Complex 5 crystallizes in the monoclinic space group P2(1)/c. Crystal data for 5 at 243 K: a = 15.039(2) Å; b = 16.152(3) Å; c = 20.967(5) Å; beta = 91.53(2) degrees; Z = 4; R(1) = 4.83%. Complex 6 crystallizes in the orthorhombic space group Pbcn. Crystal data for 6 at 298 K: a = 14.686(2) Å; b = 21.295(5) Å; c = 28.767(5) Å; Z = 8; R(1) = 5.61%. Complex 7 crystallizes in the orthorhombic space group Pbcn. Crystal data for 7 at 218 K: a = 14.5533(2) Å; b = 21.4258(5) Å; c = 28.5990(5) Å; Z = 8; R(1) = 4.61%. Complex 8 crystallizes in the orthorhombic space group Pbcn. Crystal data for 8 at 219 K: a = 14.6162(2) Å; b = 21.3992(3) Å; c = 28.7037(2) Å; Z = 8; R(1) = 3.57%. Complex 9 crystallizes in the triclinic space group P&onemacr;. Crystal data for 9 at 293 K: a = 11.147(4) Å; b = 14.615(4) Å; c = 14.806(5) Å; alpha = 70.57(3) degrees; beta = 71.85(3) degrees; gamma = 72.93(2) degrees; Z = 2; R(1) = 5.13%. Complex 10 crystallizes in the triclinic space group P&onemacr;. Crystal data for 10 at 173 K: a = 10.5690(4) Å; b = 15.0376(5) Å; c = 15.3643(5) Å; alpha = 111.8630(10) degrees; beta = 100.4120(10) degrees; gamma = 97.4820(2) degrees; Z = 2; R(1) = 4.87%. A common feature of the molecular structures of complexes 2-10 is an infinitely extended polymeric ladder framework in the solid state. Both solution and solid-state NMR data are presented.

Journal Article↗
PubMed2004

Characterization of molecular structures and properties of polyurethanes using molecular dynamics simulations.

Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the diisocyanates and diols, in particular changes in the mesogen, were investigated. Introduction of mesogenic segments into the polymers suppresses the ordering. Stiff end substituents (phenyl and alkoxy groups) of the mesogens stabilize the mesophases to such an extent that the negative influence of long polymer chains is compensated and the liquid-crystalline properties are recovered. All-atom molecular dynamics simulations in the Cerius2 modeling environment were carried out to characterize the structures of the polymers. Analysis of the dynamic trajectories at 20, 100, 120 and 170 degrees C revealed changes in conformation of macromolecules, which correlate with DSC measurements.

Calorimetry↗
PubMed2000

Quantitative structure-property relationships for the prediction of vapor pressures of organic compounds from molecular structures

A quantitative structure-property relationship (QSPR) is developed to relate the molecular structures of 420 diverse organic compounds to their vapor pressures at 25 degrees C expressed as log(vp), where vp is in pascals. The log(vp) values range over 8 orders of magnitude from -1.34 to 6.68 log units. The compounds are encoded with topological, electronic, geometrical, and hybrid descriptors. Statistical and computational neural network (CNN) models are built using subsets of the descriptors chosen by simulated annealing and genetic algorithm feature selection routines. An 8-descriptor CNN model, which contains only topological descriptors, is presented which has a root-mean-square (rms) error of 0.37 log unit for a 65-member external prediction set. A 10-descriptor CNN model containing a larger selection of descriptor types gives an improved rms error of 0.33 log unit for the external prediction set.

Journal Article↗
PubMed1993

The crystal and molecular structure of trichosanthin at 2.6 A resolution.

The crystallographic refinement of trichosanthin has been performed at 2.6 A resolution. The crystal and molecular structure of trichosanthin is described in detail in this paper. On summarizing the regularity of the amino acid sequences of eight kinds of ribosome inactivating proteins and combining with the crystal and molecular structure of trichosanthin, fifteen most conservative amino acid residues are analyzed. It is found that four most conservative polar amino acid residues Gln156, Glu160, Arg163 and Glu189 gather on the molecular surface on the boundary of the large and small domains, thus forming the active center of the protein molecule.

Amino Acid Sequence↗
PubMed1988

Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

Cyclic AMP↗
PubMed2002

MOSBY: a molecular structure viewer program with portability and extensibility.

A molecular structure viewer program, MOSBY has been developed for studies that use atomic coordinates to understand the structures of protein molecules. The program is designed to be portable with a comprehensive user interface by our high-throughput graphics library. In addition, it cooperates with extension modules customized for individual research topics and analysis. For example, an electron density module loads and displays electron density maps derived in X-ray crystallographic analysis superimposed to an atomic model. A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure. These plug-in modules are devised to function without modification to the MOSBY program. For variations of analysis and calculations with atomic coordinates, the portability and extensibility illustrated by MOSBY play an important rule in scientific computational tools with active software development.

Computer Graphics↗
PubMed2005

Reinvestigation of molecular structure and barrier to internal rotation of pyridinium N-phenolate betaine dye.

In the present paper, the results of a systematic theoretical study of the molecular structure of 4-(1-pyridinium-1-yl)phenolate betaine are reported. The ground-state molecular structure and the barrier to internal rotation of the betaine dye molecule were calculated ab inito (with Hartree-Fock theory and the second-order of Möller-Plesset method) and with density functional theory (DFT). In order to estimate the complete basis set limit, the calculations of barriers to internal rotations were performed using correlation-consistent basis sets with a maximal cardinal number of four. It was determined that electron correlation is crucial in order to obtain reliable geometries and rotational barriers of the molecule investigated. For the sake of comparison, the results of calculations using the AM1 Hamiltonian are also presented. [Figure: see text]. Investigated betaine dye.

Betaine↗
PubMed1991

Alteration in molecular structure of cytoskeleton proteins in griseofulvin-treated mouse liver: a pressure tuning infrared spectroscopy study.

Different liver diseases are associated with modifications in hepatocyte cytoskeletal organization and formation of Mallory bodies (MBs). Since the structure of a protein is critical for its function, we studied the changes in the molecular structure of the cytoskeletal protein in the liver from mice fed griseofulvin (GF), which is a good animal model for studying liver disease. Using pressure-tuning infrared spectroscopy we compared the infrared spectra of the cytoskeletal proteins from control liver and griseofulvin treated liver. The results show that the overall structure of the cytoskeletal protein was modified by the griseofulvin treatment. A relative increase in the amount of alpha-helices to beta-sheets was observed in the liver cytoskeleton from the GF-treated mice. Moreover, the random coil and the turn segments were dramatically decreased compared to controls. Pressure-induced modifications including denaturation were irreversible in the control samples whereas they were reversible in the griseofulvin-treated samples. These changes reflect important fundamental modifications in the molecular structure of the cytoskeletal proteins in the griseofulvin-treated hepatocytes. We suggest that these changes are related to the modification of the organization of intermediate filaments and the formation of MBs that occur in the GF-treated liver.

Animals↗
PubMed2006

Relationship between incoherent excitation energy migration processes and molecular structures in zinc(II) porphyrin dendrimers.

Multiporphyrin dendrimers are among the most promising architectures to mimic the oxygenic light-harvesting complex because of their structural similarities and synthetic convenience. The overall geometries of dendrimers are determined by the core structure, the type of dendron, and the number of generations of interior repeating units. The rigid core and bulky volume of exterior porphyrin units in multiporphyrin dendrimers give rise to well-ordered three-dimensional structures. As the number of generations of interior repeating units increases, however, the overall structures of dendrimers become disordered and randomized due to the flexibility of the repeating units. To reveal the relationship between molecular structure and processes of excitation-energy migration in multiporphyrin dendrimers, we calculated the molecular structure and measured the time-resolved transient absorption and fluorescence anisotropy decays for various hexaarylbenzene-anchored polyester zinc(II) porphyrin dendrimers along with three types of porphyrin dendrons as references. We found that the congested two-branched type dendrimers exhibit more efficient energy migration processes than one- or three-branched type dendrimers because of multiple energy migration pathways, and the three-dimensional packing efficiency of dendrimers strongly depends on the type of dendrons.

Dendrimers↗
PubMed1975

The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-A resolution.

The structure of the variable portions of a K-type Bence-Jones protein REI forming a dimer has been determined by X-ray diffraction to a resolution of 2.0 A. The structure has been refined using a constrained crystallographic refinement procedure. The final R value is 0.24 for 15000 significantly measured reflections; the estimated standard deviation of atomic positions is 0.09 A. A more objective assessment of the error in the atomic positions is possible by comparing the two independently refined monomers. The mean deviation of main-chain atoms of the two chains in internal segments in 0.22 A, of main-chain dihedral angles 6.3 degrees for these segments. The unrefined molecular structure of the VREI dimer has been published (Epp, O., Colman, P., Fehlhammer, H., Bode, W., Schiffer, M., Huber, R., and Palm, W. (1974), Eur. J. Biochem. 45, 513). Now a detailed analysis is presented in terms of hydrogen bonds and conformational angles. Secondary structural elements (antiparallel beta structure, reverse turns) are defined. A more precise atomic arrangement of the amino acid residues forming the contact region and the hapten binding site is given as well as the localization of solvent molecules. Two cis-prolines (Pro-8 and Pro-95) were detected. The intrachain disulfide bridge (Cys-23-Cys-88) occurs statistically in two alternative conformations. The structure suggests reasons for strong conservation of several amino acid residues. The knowledge of the refined molecular structure enables crystal structure analyses of related molecules to be made by Patterson search techniques. The calculated phases based on the refined structure are much improved compared to isomorphous phases. Therefore the effects of hapten binding on the molecular structure can be analyzed by the difference Fourier technique with more reliability. Hapten binding studies have been started.

Amino Acid Sequence↗
PubMed2003

Physicochemical effects in the representation of molecular structures for drug designing.

After the identification of a biological target, drug design is to analyze the relationships between the structure of potential ligands and their biological activity. A hierarchy of structure representation is presented here considering either the constitution of a molecule, its 3D structure, or the molecular surface. At each level, a variety of physicochemical effects can be accounted for. Furthermore, the special requirements of learning algorithm, such as neural networks, are taken into consideration. Application to problems from combinatorial chemistry, lead identification, high-throughput screening, and prediction of ADME-Tox properties are given.

Chemical Phenomena↗
PubMed2006

Molecular structures and vibrational frequencies of 2-, 3- and 4-pyridine carboxaldehydes by ab initio Hartree-Fock and density functional theory calculations.

The optimised molecular structures, vibrational frequencies and corresponding vibrational assignments of the cis and trans conformers of 2-, 3- and 4-pyridine carboxaldehydes have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d, p) basis set. The calculations were adapted to the C(S) symmetries of all the molecules. The mean vibrational deviations between the vibrational frequency values of the two conformers of all the compounds have been seen to increase while the relative energies increase and it was concluded the more different the molecular structure of the two conformers is the higher the relative energy is between them, and thus a bigger mean vibrational deviation.

Aldehydes↗
PubMed1983

Self base pairing in a complementary deoxydinucleoside monophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3'-5')-deoxyguanosine.

The molecular structure of ammonium deoxycytidylyl-(3'-5')-deoxyguanosine, crystallized from aqueous acetone near pH 4, was determined for X-ray diffraction data. The crystals were tetragonal, space group P43212 with a = b = 11.078 (1) A and c = 45.826 (4) A. The structure was solved by tangent expansion of phases based on a derived phosphorus position and refined to R = 0.060 by full matrix least squares. Molecules related by a 2-fold symmetry axis are connected by hydrogen bonds between the bases and form parallel right-handed duplexes. Pairs of cytosines share a proton at N(3) and are joined by three hydrogen bonds: N(4)-H...O(2)...H-N(4), and N(3)-H...N(3). Guanines are joined by two hydrogen bonds: N(2)-H...N(3) and N(3)...H-N(2). Base-stacking interactions within the duplex are weak with the cytosine and guanine ring planes inclined at 24 degrees to each other in each monomer. Despite the unusual arrangement of the molecules, the sugar phosphate backbone has the g-g- conformation normally associated with right-handed double helical structures. Conformational parameters of the nucleosides are also typical with both sugars C(2')-endo and glycosidic torsion angles 55 degrees for cytidine and 94 degrees for guanosine. The bonding geometry of the bases is influenced by hydrogen bonding and charge-transfer networks in the crystal lattice. The solvent molecules interact with the dimer in three fused circular hydrogen bonding domains with a single disordered ammonium cation per d(CpG) dimer. Parallels with the formation of self base pairs and their implications in molecular biology are discussed.

Base Composition↗
PubMed1983

Activated cyclophosphamide anticancer drugs: molecular structures of cis- and trans-4-hydroperoxyisophosphamides.

Molecular structures of two stereoisomers of 4-hydroperoxyisophosphamide (HPIPA) have been determined by single-crystal X-ray diffraction. These isomers are active cytostatic agents closely related to an active metabolite of the antitumor drug isophosphamide, an analogue of cyclophosphamide. Both isomers crystallize in monoclinic space group P21/c with cell dimensions for cis-HPIPA of a = 8.999 (2), b = 8.743 (2), c = 17.078 (4) A; beta = 107.91 (2) degrees, and Z = 4 molecules per unit cell, and cell dimensions for trans-HPIPA of a = 15.184 (3), b = 10.345 (3), c = 18.205 (3) A, beta = 114.15 (1) degrees, and Z = 8. The structures were solved by direct methods and refined by anisotropic least squares to a discrepancy index R = 0.048 for cis-HPIPA and R = 0.065 for trans-HPIPA. In both isomers the 4-hydroperoxy group is situated axial to the ring. The phosphoryl oxygen atom is situated axial to the ring and, thus, cis to the C(4) oxygen in the cis-HPIPA isomer. In the trans-HPIPA isomer, the phosphoryl oxygen is equatorial to the ring and trans to the C(4) oxygen.

Chemical Phenomena↗