UNIPROT:Q86TM3 - FACTA Search

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Query: UNIPROT:Q86TM3 (cage)
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Following the solution of the structure of bovine rhodopsin by X-ray crystallography, it has been possible to build an improved homology model of the M(1) muscarinic acetylcholine receptor. This has been used to interpret the outcome of an extensive series of scanning and point mutagenesis studies on the transmembrane domain of the receptor. Potential intramolecular interactions enhancing the stability of the protein fold have been identified. The residues contributing to the binding site for the antagonist, N-methylscopolamine, and the agonist, acetylcholine have been mapped. The positively charged headgroups of these ligands appear to bind in a charge-stabilized aromatic cage formed by amino acid side chains in transmembrane (TM) helices 3, 6, and 7, while residues in TM 4 may participate in a peripheral docking site. Closure of the cage around the headgroup of acetylcholine may help to transduce binding energy into receptor activation, possibly disrupting a set of Van der Waals interactions between a set of residues underlying the binding site which help to constrain the receptor to the inactive state, in the absence of agonist. This may trigger the reorganization of a hydrogen bonding network between highly conserved residues in the core of the receptor, whose integrity is crucial for activation.
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PMID:Scanning mutagenesis studies of the M1 muscarinic acetylcholine receptor. 1289 35

How gas-phase materials become incorporated with cloud droplets has been an intriguing subject for decades, and considerable work has been done to understand the interactions between closed-shell molecules and liquid water. The interactions between open-shell radical species and liquid-phase cloud droplets, however, are not well understood. To probe these interactions we used quantum chemistry calculations to predict the energetics of the hydroperoxy radical (HO2) in the presence of an (H2O)20 spherical water cage. Our calculations show that it is energetically favorable for the radical to bind to the outside of the cage. This configuration has the hydrogen and the terminal oxygen of the radical as its primary bonding sites. Free-energy calculations suggest that, at atmospheric conditions, there will be a partitioning between HO2 radicals that are surface-bound and HO2 radicals that dissolve into the bulk. This may have important ramifications for our understanding of radical chemistry and may lend insight into the role that clouds and aerosols play in atmospheric chemical processes.
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PMID:On the interactions between atmospheric radicals and cloud droplets: a molecular picture of the interface. 1290 76

Formation of the donor-acceptor complexes of group 13 metal derivatives with nitriles and isonitriles X(3)M-D (M = Al,Ga,In; X = H,Cl,CH(3); D = RCN, RNC; R = H,CH(3)) and their subsequent reactions have been theoretically studied at the B3LYP/pVDZ level of theory. Although complexation with MX(3) stabilizes the isocyanide due to the stronger M-C donor-acceptor bond, this stabilization (20 kJ mol(-1) at most) is not sufficient to make the isocyanide form more favorable. Relationships between the dissociation enthalpy DeltaH degrees (298)(diss), charge-transfer q(CT), donor-acceptor bond energy E(DA), and the shift of the vibrational stretching mode of the CN group upon coordination Deltaomega(CN) have been examined. For a given metal center, there is a good correlation between the energy of the donor-acceptor bond and the degree of a charge transfer. Prediction of the DeltaH degrees (298)(diss) on the basis of the shift of CN stretching mode is possible within limited series of cyanide complexes (for the fixed M,R); in contrast, complexes of the isocyanides exhibit very poor Deltaomega(CN) - DeltaH degrees (298)(diss) correlation. Subsequent X ligand transfer and RX elimination reactions yielding monomeric (including donor-acceptor stabilized) and variety of oligomeric cage and ring compounds with [MN]n, [MC]n, [MNC]n cores have been considered and corresponding to thermodynamic characteristics have been obtained for the first time. Monomeric aluminum isocyanides X(2)AlNC are more stable compared to Al-C bonded isomers; for gallium and indium situation is reversed, in qualitative agreement with Pearson's HSAB concept. Substitution of X by CN in MX(3) increases the dissociation enthalpy of the MX(2)CN-NH(3) complex compared to that for MX(3)-NH(3), irrespective of the substituent X. Mechanisms of the initial reaction of the X transfer have been studied for the case X = R = H. The process of hydrogen transfer from the metal to the carbon atom in H(3)M-CNH is thermodynamically favorable and is likely to be intramolecular. By contrast, intramolecular hydrogen transfer in H(3)M-NCH has been definitely ruled out. Head-to-tail dimeric species [H(3)M-(NC)H](2) are formed exothermically and exhibit low H.H distances, which can assist in hydrogen transfer, and are likely to be the starting point for H(2) elimination. Elimination of H(2), CH(4), and C(2)H(6) from X(3)M-(NC)R adducts is very favorable thermodynamically; by contrast, elimination of HCl and CH(3)Cl is highly unfavorable even if formation of oligomer species takes place. Thus, high-temperature generation of gas-phase rings and clusters has been predicted viable in the cases X = H,CH(3) and their presence in the reactor media should not be neglected. Moderate stability of [HMCH(2)NH](4) clusters (especially in the cases M = Ga, In) makes these species viable intermediates of gas-phase reactions. Their formation may be responsible for the carbon contamination in the course of metal organic chemical vapor deposition processes of group 13 binary nitrides.
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PMID:Fascinating transformations of donor-acceptor complexes of group 13 metal (Al, Ga, In) derivatives with nitriles and isonitriles: from monomeric cyanides to rings and cages. 1291 63

A gradient elution HPLC method with a wavelength switch technique was developed to simultaneously analyze the beta-lactam ticarcillin and the beta-lactamase inhibitor clavulanate in rabbit serum and tissue cage fluid (TCF). A C18 reversed-phase column with a programmable UV detector changing the wavelength from 218 to 254 nm at 9 min was used for chromatographic separation. The mobile phase consisted of acetonitrile, phosphate buffer and tetrabutylammonium hydrogen sulfate by following a gradient elution program at a flow-rate of 1 ml/min. Sample processing was carried out with liquid-liquid extraction. Good linearity, recoveries, precision and accuracy were obtained. The ranges of the standard curves were 1-100 microg/ml for ticarcillin, and 0.2-20 microg/ml for clavulanate. This assay has been successfully applied to analyze ticarcillin and clavulanate in rabbit serum and tissue cage fluid samples from a pharmacokinetic study.
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PMID:Simultaneous determination of ticarcillin and clavulanate in rabbit serum and tissue cage fluid by liquid chromatography. 1295 75

Low-temperature (-78 degrees C) ozonation of 1,2-diphenylhydrazine in various oxygen bases as solvents (acetone-d(6), methyl acetate, tert-butyl methyl ether) produced hydrogen trioxide (HOOOH), 1,2-diphenyldiazene, 1,2-diphenyldiazene-N-oxide, and hydrogen peroxide. Ozonation of 1,2-dimethylhydrazine produced besides HOOOH, 1,2-dimethyldiazene, 1,2-dimethyldiazene-N-oxide and hydrogen peroxide, also formic acid and nitromethane. Kinetic and activation parameters for the decomposition of the HOOOH produced in this way, and identified by (1)H, (2)H, and (17)O NMR spectroscopy, are in agreement with our previous proposal that water participates in this reaction as a bifunctional catalyst in a polar decomposition process to produce water and singlet oxygen (O(2), (1)delta(g)). The possibility that hydrogen peroxide is, besides water, also involved in the decomposition of hydrogen trioxide is also considered. The half-life of HOOOH at room temperature (20 degrees C) is 16 +/- 1 min in all solvents investigated. Using a variety of DFT methods (restricted, broken-symmetry unrestricted, self-interaction corrected) in connection with the B3LYP functional, a stepwise mechanism involving the hydrotrioxyl (HOOO(*)) radical is proposed for the ozonation of hydrazines (RNHNHR, R = H, Ph, Me) that involves the abstraction of the N-hydrogen atom by ozone to form a radical pair, RNNHR(*) (*)OOOH. The hydrotrioxyl radical can then either abstract the remaining N(H) hydrogen atom from the RNNHR(*) radical to form the corresponding diazene (RN=NR), or recombines with RNNHR(*) in a solvent cage to form the hydrotrioxide, RN(OOOH)NHR. The decomposition of these very labile hydrotrioxides involves the homolytic scission of the RO-OOH bond with subsequent "in cage" formation of the diazene-N-oxide and hydrogen peroxide. Although 1,2-diphenyldiazene is unreactive toward ozone under conditions investigated, 1,2-dimethyldiazene reacts with relative ease to yield 1,2-dimethyldiazene-N-oxide and singlet oxygen (O(2), (1)delta(g)). The subsequent reaction sequence between these two components to yield nitromethane as the final product is discussed. The formation of formic acid and nitromethane in the ozonolysis of 1,2-dimethylhydrazine is explained as being due to the abstraction of a methyl H atom of the CH(3)NNHCH(3)(*) radical by HOOO(*) in the solvent cage. The possible mechanism of the reaction of the initially formed formaldehyde methylhydrazone (and HOOOH) with ozone/oxygen mixtures to produce formic acid and nitromethane is also discussed.
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PMID:Mechanism of formation of hydrogen trioxide (HOOOH) in the ozonation of 1,2-diphenylhydrazine and 1,2-dimethylhydrazine: an experimental and theoretical investigation. 1312 58

Most of the cancer-associated mutations in the tumor suppressor p53 map to its DNA-binding core domain. Many of them inactivate p53 by decreasing its thermodynamic stability. We have previously designed the superstable quadruple mutant M133L/V203A/N239Y/N268D containing the second-site suppressor mutations N239Y and N268D, which specifically restore activity and stability in several oncogenic mutants. Here we present the x-ray structure of this quadruple mutant at 1.9 A resolution, which was solved in a new crystal form in the absence of DNA. This structure reveals that the four point mutations cause only small local structural changes, whereas the overall structure of the central beta-sandwich and the DNA-binding surface is conserved. The suppressor mutation N268D results in an altered hydrogen bond pattern connecting strands S1 and S10, thus bridging the two sheets of the beta-sandwich scaffold in an energetically more favorable way. The second suppressor mutation N239Y, which is located in close proximity to the DNA-binding surface in loop L3, seems to reduce the plasticity of the structure in large parts of loop L3 as indicated by decreased crystallographic temperature factors. The same is observed for residues in the vicinity of the N268D substitution. This increase in rigidity provides the structural basis for the increase in thermostability and an understanding how N268D and N239Y rescue some of the common cancer mutants.
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PMID:Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations. 1453 97

Four new silver(I) double salts (L(2)H)(4)[Ag(10)(C(2))(CF(3)CO(2))(12)(L)(2)].5H(2)O (1), [Ag(8)(C(2))(CF(3)CO(2))(6)(L)(6)] (2), [(Ag(2)C(2))(AgC(2)F(5)CO(2))(6)(L)(3)(H(2)O)].H(2)O (3), and (L.H(3)O)(2)[Ag(11)(C(2))(2)(C(2)F(5)CO(2))(9)(H(2)O)(2)].H(2)O (4) incorporating the hitherto unexplored ligand 4-hydroxyquinoline (L) have been synthesized by the hydrothermal method. Compound 1 features an unprecedented bicapped square-antiprismatic Ag(10) silver cage with an embedded C(2)(2-) moiety, whereas the discrete supermolecule 2 bears a rhombohedral Ag(8) core similar to that previously found in Ag(2)C(2).6AgNO(3). Compound 3 contains a discrete supramolecular complex whose core is a (C(2))(2)@Ag(16) double cage constructed from the edge-sharing of two monocapped square antiprisms, which is completely surrounded by 12 pentafluoropropionate, 6 4-hydroxyquinoline, and 2 aqua ligands. The layer structure in 4 is constructed from a sinuous anionic silver column composed of fused irregular monocapped trigonal antiprisms each encapsulating a C(2)(2-) dianion, with L.H(3)O(+) species serving as hydrogen-bond connectors to adjacent columns.
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PMID:Self-assembled silver polyhedra with embedded acetylide dianion stabilized by perfluorocarboxylate and 4-hydroxyquinoline ligands. 1463 3

The stability of the recently characterized type II hydrogen clathrate [Mao, W. L., Mao, H.-K., Goncharov, A. F., Struzhkin, V. V., Guo, Q., et al. (2002) Science 297, 2247-2249] with respect to hydrogen occupancy is examined with a statistical mechanical model in conjunction with first-principles quantum chemistry calculations. It is found that the stability of the clathrate is mainly caused by dispersive interactions between H2 molecules and the water forming the cage walls. Theoretical analysis shows that both individual hydrogen molecules and nH2 guest clusters undergo essentially free rotations inside the clathrate cages. Calculations at the experimental conditions--2,000 bar (1 bar = 100 kPa) and 250 K confirm multiple occupancy of the clathrate cages with average occupations of 2.00 and 3.96 H2 molecules per D-5(12) (small) and H-5(12)6(4) (large) cage, respectively. The H2-H2O interactions also are responsible for the experimentally observed softening of the H[bond]H stretching modes. The clathrate is found to be thermodynamically stable at 25 bar and 150 K.
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PMID:Thermodynamic stability of hydrogen clathrates. 1465 91

Strong hydrogen-bonding forces between the Thr26 and Thr26' of the protease stabilize the internal cage of the dimeric triad of the aspartyl HIV-1 protease (Asp25Thr26Gly27 and Asp25' Thr26'Gly27', respectively). The interaction of reversible inhibitors of HIV-1 protease is based on (i) strong hydrogen-bonding forces between the main chain (--CONH--) oxygen atoms of Gly27 and/or Gly27' and hydrogen-bond donating moieties of a drug, and (ii) hydrogen bonds between the oxygen of the catalytic Asp25 and/or Asp25' carboxylates and aliphatic hydroxyl groups of a drug. The free entry of natural substrates into the active-site cavity is sterically hindered by inhibitors, so that the catalytic Asp carboxylates cannot interact with natural substrates. Irreversible inhibitors interact with the nucleophilic carboxylate moiety of Asp25 of HIV-1 protease by covalent bonding.
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PMID:Interactions of the dimeric triad of HIV-1 aspartyl protease with inhibitors. 1467 43

The 10-vertex phosphadicarbaboranes, 6-R-arachno-6,8,9-PC(2)B(7)H(11) (1) (R = Ph 1a or Me 1b) and 6-R-arachno-6,5,7-PC(2)B(7)H(11) (2) (R = Ph 2a or Me 2b) have been synthesized using in situ dehydrohalogenation reactions of RPCl(2) (R = Ph or Me) with the arachno-4,5-C(2)B(7)H(13) and arachno-4,6-C(2)B(7)H(13) carboranes, respectively. X-ray crystallographic determinations in conjunction with DFT/GIAO/NMR calculations and NMR spectroscopic studies have established that both 1 and 2 have open cage structures based on an icosahedron missing two vertexes. The two isomeric compounds differ in the positions of the carbons and bridging hydrogens on the open face. Studies of the reactions of 2a with BH(3).THF, S(8), and hydrogen peroxide demonstrated that 2a shows strong donor properties yielding the compounds endo-6-H(3)B-exo-6-Ph-arachno-6,5,7-PC(2)B(7)H(11) (3), endo-6-S-exo-6-Ph-arachno-6,5,7-PC(2)B(7)H(11) (4), and endo-6-O-exo-6-Ph-arachno-6,5,7-PC(2)B(7)H(11) (5) in which the BH(3), S, and O substitutents are bonded to an electron lone pair localized at the phosphorus endo-position. The reaction of 2a with an excess of S(8) results in the loss of a framework boron to produce the unique open-cage compound micro(7,8)-[HS(Ph)P]-hypho-7,8-C(2)B(6)H(11) (6). 2a also formed the donor complexes cis-(eta(1)-[6-Ph-arachno-6,5,7-PC(2)B(7)H(11)])(2)PtBr(2) (7) and trans-(eta(1)-[6-Ph-arachno-6,5,7-PC(2)B(7)H(11)])(2)PdBr(2) (8) in which the metal fragment is bonded in an eta(1)-fashion at the phosphorus endo-position. In these complexes, 2a is functioning as a two-electron sigma donor to the metals and can thus be considered as an analogue of the PR(3) ligands in the classical cis-(PPh(3))(2)PtBr(2) and trans-(PPh(3))(2)PdBr(2) coordination complexes. Although 1a did not show the donor properties exhibited by 2a, its dianion 6-Ph-6,8,9-PC(2)B(7)H(9)(2)(-) (1a(2)()(-)()) readily formed eta(4)-coordinated complexes with late transition metals including 8-Ph-7-(Ph(3)P)(2)-nido-7,8,10,11-PtPC(2)B(7)H(9) (9), 7-Ph-11-(eta(5)-C(5)H(5))-nido-11,7,9,10-CoPC(2)B(7)H(9) (10), and commo-Ni-(7-Ni-8'-Ph-nido-8',10',11'-PC(2)B(7)H(9))(7-Ni-8-Ph-nido-8,10,11-PC(2)B(7)H(9)) (11).
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PMID:Syntheses, characterizations, and coordination chemistry of the 10-vertex phosphadicarbaboranes 6-R-arachno-6,8,9-PC2B7H11 and 6-R-arachno-6,5,7-PC2B7H11. 1467 98

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