Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P50583 (asymmetrical)
 12,197 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The structures of the protonated water cluster H+(H2O)8 have been globally explored by the scaled hypersphere search method. On the Hartree-Fock potential energy surface 174 isomers were found, among which 168 were computed to be minima at the B3LYP/6-31+G** level, and their energies were further refined at the level of MP2/6-311++G(3df,2p). The global minimum on the potential energy surface computed at the B3LYP/6-31+G** level shows a cagelike structure with the "Eigen" motif, while the lowest-free-energy isomer has a five-membered-ring structure at 170 K and a chain form at 273 K. The present results are well in line with previous experimental findings. In addition, the ADMP (atom-centered density matrix propagation) simulation indicates that the extra proton in the lowest-free-energy isomer (170 K), which has a five-membered ring and the "Zundel" feature, is often in an asymmetrical hydrogen bond.
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PMID:Quantum chemistry study of H+(H2O)8: a global search for its isomers by the scaled hypersphere search method, and its thermal behavior. 1788 37

The SL1 stem-loop is the dimerization initiation site for linking the two copies of the RNA forming the HIV-1 genome. The 26 nucleotides stem contains a defect consisting on a highly conserved G-rich 1-3 asymmetrical internal loop, which is a major site for nucleocapsid protein binding. Several NMR attempts were undertaken to determine the internal loop structure in the SL1 monomer. However, the RNA constructs used in the different studies were largely mutated, in particular with replacement of the nine nucleotides apical loop by a tetraloop, and divergent results were obtained ranging from a rigid structure to a particularly large flexibility. To investigate the reasons for such discrepancies, we used molecular dynamics simulation of the SL1 monomer to probe the effect of mutations on the conformational stability of the internal loop and of the whole stem. It is found that in the wild-type sequence, the internal loop displays conformational variability originating mainly from the nine nucleotides apical loop flexibility that causes large conformational fluctuations (without changing the average structure) in the 7 bp duplex linking the apical and internal loops. The large amplitude atomic motions in the duplex are transmitted to the internal loop in which they induce conformational changes characterized by a labile hydrogen bond network such as G5 successively H-bonded to A29 and G30. On the contrary, with a four nucleotides apical loop, conformational fluctuations in the duplex are reduced by a factor of 2 and are not sufficiently energizing for promoting changes in the internal loop structure at the time scale of the simulations.
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PMID:Insight into the intrinsic flexibility of the SL1 stem-loop from genomic RNA of HIV-1 as probed by molecular dynamics simulation. 1800 23

Intrigued by natural responsive systems based on a combination of macromolecules and non-covalent interactions, polymer scientists have mimicked such systems by the formation of supramolecular polymers based on ionic interaction, hydrogen bonding and metal coordination. In recent years, the focus has shifted from rather simple non-directional and self-complementary interactions to the use of asymmetrical directional supramolecular interactions that allow the formation of complex responsive macromolecular architectures such as block copolymers, star-shaped polymers and graft copolymers. This feature article covers these recent developments on the use of asymmetrical supramolecular interactions in polymer science. Special attention is given to the formation of complex macromolecular architectures using directional supramolecular interactions. In addition, the responsiveness of the resulting macromolecular systems is discussed based on the assembly and/or disassembly that can be triggered by changes in external conditions.
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PMID:Asymmetrical supramolecular interactions as basis for complex responsive macromolecular architectures. 1809 73

The title compound, [Cu(3)(C(9)H(17)N(3)O(3))(2)(NCS)(2)(CH(3)CN)(2)], contains two square-pyramidal Cu(II) units chelated by a transoid asymmetrical N-[3-(dimethylamino)propyl]-N'-(2-hydroxyethyl)oxamidate (dmapheoxd) dianion {H(2)dmapheoxd is N-[3-(dimethylamino)propyl]-N'-(2-hydroxyethyl)oxamide}, which coordinates to another Cu(II) ion in a square-planar environment lying on a crystallographic inversion center. Thus, the trans-oxamide ligand bridges two Cu(II) ions with different coordination numbers, and this is the first instance of such a zero-dimensional oxamide-bridged complex. The activated methyl group in the coordinated acetonitrile molecule is involved in a strong nonclassical C-H...O hydrogen bond, which contributes to a one-dimensional chain extending in the b direction. Considering the presence of weak bonding between the Cu atom and the uncoordinated hydroxyl O atoms, a two-dimensional structure is formed parallel to the ab plane.
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PMID:Diacetonitrile-1kappaN,3kappaN-bis{mu-trans-N-[3-(dimethylamino)propyl]-N'-(2-hydroxyethyl)oxamidato(2-)}-1:2kappa(5)N,N',O:O',N'';2:3kappa(5)O',N'':N,N',O-dithiocyanato-1kappaN,3kappaN-tricopper(II). 1839 74

The new cerium(III), lanthanum(III) and neodymium(III) complexes were synthesized in view of their application as cytotoxic agents. The complexes were characterized by different physicochemical methods: elemental analysis, mass spectrometry, (1)H NMR, (13)C NMR and IR spectroscopy. The spectra of the complexes were interpreted on the basis of comparison with the spectrum of the free ligand. The vibrational analysis showed that in the complexes the ligand coordinates to the metal ion through both deprotonated hydroxyl groups, however participation of the carbonyl groups in the coordination to the metal ion was also suggested. Geometry optimization of 3,3'-(ortho-pyridinomethylene)di-[4-hydroxycoumarin] H(2)(o-pyhc), (H(2)L) and its dianionic forms, o-pyhc(2-), (L(2-)) were carried out at AM1 and PM3 levels as well as using density functional theory with Becke's three parameter hybrid method and correlation functional of Lee, Yang and Parr (B3LYP) with 6-31G(d) basis set. The optimized geometries of the neutral ligand isomers were stabilized by two asymmetrical intramolecular O-H...O hydrogen bonds (HBs). The conformational search showed four low-energy dianionic species (o-pyhc(2-)) on the potential energy surface. Molecular electrostatic potential calculations showed that the most preferred sites for electrophilic attack in H(2)(o-pyhc) and o-pyhc(2-) are the carbonyl oxygen atoms. The evaluation of the cytotoxic activity of the novel lantanide complexes on HL-60 myeloid cells revealed, that they are potent cytotoxic agents. The cerium complex was found to exhibit superior activity in comparison to the lanthanum, and neodymium species, the latter being the least active. Taken together our data give us a reason to conclude that the newly synthesized lanthanide complexes should be a subset to further more detailed pharmacological and toxicological evaluation.
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PMID:Theoretical, spectral characterization and antineoplastic activity of new lanthanide complexes. 1856 22

Reactive nitrogen oxygen species (RNOS) contribute to the deleterious effects attributed to reacting with biomolecules. The mechanisms of the nitration and nitrosation of dimethylamine (DMA), which is the simplest secondary amine by N2O4, a member of RNOS, have been investigated at the CBS-QB3 level of theory. The nitration and nitrosation proceed via different pathways. The nitration of DMA follows three pathways. The first is the abstraction of the hydrogen atom of the amino group of DMA by the NO2 radical followed by a recombination reaction of the resulting aminyl radical with another NO2 radical. The second is DMA directly reacting with symmetrical O2NNO2 leading to dimethylnitramine via a concerted and a stepwise mechanism. The third is the reaction of DMA with asymmetrical ONONO2. By computation, the main pathway for the formation of dimethylnitramine in the gas phase is by DMA directly reacting with asymmetrical ONONO2. As to the nitrosation, a concerted mechanism for the reaction of DMA with asymmetrical ONONO2 plays a major role in nitrosodimethylamine (NDMA) formation. In addition, the solvent effect on these nitration and nitrosation reactions has been also studied by using the implicit polarizable continuum model. Two major pathways of the formation of dimethylnitramine in water were found, and they are the radical process involving NO2 and the concerted mechanism starting from symmetrical O2NNO2. The result of the nitrosation of DMA in water is consistent with that in the gas phase. Comparison of the energy barriers of each mechanism leads to the conclusion that the nitrosation is more favorable than the nitration in the reaction of DMA with N2O4. This conclusion is in good agreement with the experimental results. The results obtained here will help elucidate the mechanism of the lesions of biomolecules by RNOS.
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PMID:Theoretical investigation of nitration and nitrosation of dimethylamine by N2O4. 1861 60

The structure of liquid Cs(FH)(2.3)F was revealed using a combination of high-energy x-ray and neutron diffraction measurements. We found that the strongest intermolecular H-F hydrogen bonds at an average distance of 1.36 A are accompanied by the formation of a high degree of bending of the oligomer chain in the melt, with [angle]FHF=150 degrees . A reverse Monte Carlo simulation showed that the average number of atoms per chain is 4.4. A detailed chain analysis of the atomic configuration revealed that (FH)(2)F(-) oligomer chains are the major entities in the liquid, and asymmetrical FHF(-) are formed owing to the strong H-F hydrogen bonds. The results suggest that an average of one or two HF molecules bond to each of the 11 fluorine atoms surrounding a cesium ion.
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PMID:Very strong hydrogen bonds in a bent chain structure of fluorohydrogenate anions in liquid Cs(FH)2.3F. 1862 88

Uroporphyrinogen III synthase (U3S) catalyzes the asymmetrical cyclization of a linear tetrapyrrole to form the physiologically relevant uroporphyrinogen III (uro'gen III) isomer during heme biosynthesis. Here, we report four apoenzyme and one product complex crystal structures of the Thermus thermophilus (HB27) U3S protein. The overlay of eight crystallographically unique U3S molecules reveals a huge range of conformational flexibility, including a "closed" product complex. The product, uro'gen III, binds between the two domains and is held in place by a network of hydrogen bonds between the product's side chain carboxylates and the protein's main chain amides. Interactions of the product A and B ring carboxylate side chains with both structural domains of U3S appear to dictate the relative orientation of the domains in the closed enzyme conformation and likely remain intact during catalysis. The product C and D rings are less constrained in the structure, consistent with the conformational changes required for the catalytic cyclization with inversion of D ring orientation. A conserved tyrosine residue is potentially positioned to facilitate loss of a hydroxyl from the substrate to initiate the catalytic reaction.
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PMID:Structure and mechanistic implications of a uroporphyrinogen III synthase-product complex. 1865 50

Four enantiomerically pure 3D chiral POM-based compounds, [Ni(2)(bbi)(2)(H(2)O)(4)V(4)O(12)]2 H(2)O (1 a and 1 b) and [Co(bbi)(H(2)O)V(2)O(6)] (2 a and 2 b) (bbi=1,1'-(1,4-butanediyl)bisimidazole) based on the achiral ligand, different vanadate chains, and different metal centers have been synthesized by hydrothermal methods. Single-crystal X-ray diffraction analyses revealed that 1 a and 1 b, and 2 a and 2 b, respectively, are enantiomers. In 1 a and 1 b two kinds of vanadate chains with different screw axes link Ni cations to generate 3D chiral inorganic skeletons, which are connected by the achiral bbi ligands to form complicated 3D 3,4-connected chiral self-penetrating frameworks with (7(2)8)(7(2)8(2)9(2))(7(3)8(2)10) topology. They represent the first examples of chiral self-penetrating frameworks known for polyoxometalate (POM) systems. Contrary to 1 a and 1 b, in 2 a and 2 b the vanadate chains link Co(II) cations to generate 3D chiral inorganic skeletons, which are assembled from two kinds of heterometallic helical units of opposite chirality along the c axes. The chiral inorganic skeletons are connected by bbi to form 3D 3,4-connected chiral POM-based frameworks with (6(2)8)(2)(6(2)8(2)10(2)) topology. It is believed that the asymmetrical coordination modes of the metal cations in 1 a-2 b generate the initial chiral centers, and that the formation of the various helical units and the hydrogen bond interactions are responsible for preservation of the chirality and spontaneous resolution when the chirality is extended into the homochiral 3D-networks. This is the first known report of chiral POM-based compounds consisting of 3D chiral inorganic skeletons being obtained by spontaneous resolution upon crystallization in the absence of any chiral source, which may provide a rational strategy for synthesis of chiral POM-based compounds by using achiral ligands and POM helical units.
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PMID:Spontaneous resolution of chiral polyoxometalate-based compounds consisting of 3D chiral inorganic skeletons assembled from different helical units. 1881 Jul 44

The microscopic origin and quantum effects of the low barrier hydrogen bond (LBHB) in the proton-bound ammonia dimer cation N(2)H(7) (+) were studied by means of ab initio and density-functional theory (DFT) methods. These results were analyzed in the framework of vibronic theory and compared to those obtained for the Zundel cation H(5)O(2) (+). All geometry optimizations carried out using wavefunction-based methods [Hartree-Fock, second and fourth order Moller-Plesset theory (MP2 and MP4), and quadratic configuration interaction with singles and doubles excitations (QCISD)] lead to an asymmetrical H(3)N-H(+)cdots, three dots, centeredNH(3) conformation (C(3v) symmetry) with a small energy barrier (1.26 kcalmol in MP4 and QCISD calculations) between both equivalent minima. The value of this barrier is underestimated in DFT calculations particularly at the local density approximation level where geometry optimization leads to a symmetric H(3)Ncdots, three dots, centeredH(+)cdots, three dots, centeredNH(3) structure (D(3d) point group). The instability of the symmetric D(3d) structure is shown to originate from the pseudo-Jahn-Teller mixing of the electronic (1)A(1g) ground state with five low lying excited states of A(2u) symmetry through the asymmetric alpha(2u) vibrational mode. A molecular orbital study of the pseudo-Jahn-Teller coupling has allowed us to discuss the origin of the proton displacement and the LBHB formation in terms of the polarization of the NH(3) molecules and the transfer of electronic charge between the proton and the NH(3) units (rebonding). The parallel study of the H(5)O(2) (+) cation, which presents a symmetric single-well structure, allows us to analyze why these similar molecules behave differently with respect to proton transfer. From the vibronic analysis, a unified view of the Rudle-Pimentel three-center four-electron and charge transfer models of LBHBs is given. Finally, the large difference in the N-N distance in the D(3d) and C(3v) configurations of N(2)H(7) (+) indicates a large anharmonic coupling between alpha(2u)-alpha(1g) modes along the proton-transfer dynamics. This issue was explored by solving numerically the vibrational Schrodinger equation corresponding to the bidimensional E[Q(alpha(2u)),Q(alpha(1g))] energy surface calculated at the MP46-311++G(**) level of theory.
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PMID:Pseudo-Jahn-Teller origin of the low barrier hydrogen bond in N(2)H(7) (+). 1904 29


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