Coordination Bonds (coordination + bond)

Distribution by Scientific Domains

Selected Abstracts

Protein folding simulations: From coarse-grained model to all-atom model

IUBMB LIFE, Issue 6 2009
Jian Zhang
Abstract Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure,stability,function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein,protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based G,-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL, the development of discrete MD and its application in studying the ,,, conformational conversion and oligomer assembling process, and the modeling of metal ion involved protein folding. 2009 IUBMB IUBMB Life, 61(6): 627,643, 2009 [source]

Real time monitoring of drug metabolic enzyme response inside human hepatoma GS-3A4-HepG2 cells by means of electrochemical impedance measurement

Masaaki Kobayashi
Abstract Cytochrome P-450s (CYPs) are important biopolymers for the maintenance of cellular function. If metabolic activity of the CYP in the cells can be estimated, so can the function of metabolism, which is closer to the organism. In this research, the method of measuring the drug metabolic activity inside the cell by making use of an electrochemical technique was examined. Human hepatoma GS-3A4-HepG2 cells of which the cytochrome P-4503A4 (CYP3A4) drug metabolic activity is found to be the same as that of primary hepatocytes were used in the experiment. The GS-3A4-HepG2 cells were cultured on an indium-tin oxide (ITO) electrode until they became confluent. Substrate testosterone and inhibitor ketoconazole of CYP3A4 were exposed to cells cultured on an ITO electrode, and the reaction was observed by noting the electrochemical impedance measurement. Impedance was decomposed into the resistance component and the reactance component, and each was examined in detail. As a result, according to testosterone concentration change, there was a remarkable time change in the reactance component. A similar impedance measurement was done by using human hepatoma HepG2 cells in which the drug metabolic activity had extremely decreased. Nevertheless, no time change in the reactance component that was noticed in GS-3A4-HepG2 cells was observed. Next, the amount of metabolite in the solution after impedance measurement was measured by means of liquid chromatography-tandem mass spectroscopy (LC-MS/MS). In the experiment with GS-3A4-HepG2 cells, a testosterone concentration-dependent correlation was observed between the reactance component change and the amount of metabolite. But, in the impedance measurement by ketoconazole, the change in reactance components was not observed in either the GS-3A4-HepG2 cells or the HepG2 cells. Ketoconazole and the heme iron in CYP3A4 effect the coordination bond, but ketoconazole was not metabolized by CYP3A4. It was confirmed that the time change in the reactance component which was caused by the testosterone was detected neither in the cells that take up the substrate, nor in the coordination bond between the CYP enzyme and the drug. Therefore, the time change in the remarkable reactance component observed by this electrochemical impedance measurement is dependent on drug metabolic activity. An electrochemical drug metabolic activity measuring method with the human hepatoma GS-3A4-HepG2 cells was able to be established. Copyright 2004 John Wiley & Sons, Ltd. [source]

Synthesis, structure and biological activity of triorganotin 1H -tetrazolyl-1-acetates: cyclic hexamer and linkage coordination polymers

Yun-Fu Xie
Abstract Reaction of 1H -tetrazolyl-1-acetic acid (CHN4CH2CO2H) with (R3Sn)2O or R3SnOH yields triorganotin 1H -tetrazolyl-1-acetates [CHN4CH2CO2SnR3, R = Ph (1), p -tolyl (2), cyclohexyl (3), n -Bu (4) and Et (5)]. 1H -tetrazolyl-1-acetates in these triorganotin derivatives display remarkably different coordination modes, depending on the properties of the organic substituents bonded to the tin atoms. Complex 1 displays a rare cyclohexameric structure by the assembly of the SnN coordination bond, while complex 2 forms a linkage coordination polymer through the intermolecular SnN interactions. The structure of complex 3 is similar to that of complex 2, but the intermolecular SnN interactions are weaker in the former. However, in complex 4, the tetrazolyl nitrogen atoms do not coordinate to the tin atoms. This complex forms a polymeric chain by the unsymmetric bridging carboxylate group. All these complexes exhibit good antifungal activities in vitro against Alternaria solani, Cercospora arachidicola, Gibberella zeae, Physalospora piricola and Botrytis cinerea. The corresponding EC50 values of these complexes were tested. Copyright 2009 John Wiley & Sons, Ltd. [source]

Hyperstability and crystal structure of cytochrome c555 from hyperthermophilic Aquifex aeolicus

Marii Obuchi
In order to elucidate the relationship between the stability and the structure of the monohaem cytochrome c555 (AA c555) from the hyperthermophilic bacterium Aquifex aeolicus, chemical denaturation and crystal structure determination were carried out. AA c555 exhibited higher stability than the thermophilic Hydrogenobacter thermophilus cytochrome c552 (HT c552), which is one of the most stable cytochromes c. The three-dimensional crystal structure of AA c555, which was determined using the multiple anomalous dispersion technique at 1.15, resolution, included a unique 14-residue extra helix, while the side-chain interactions of several amino-acid residues responsible for the stability of HT c552 were conserved in AA c555. The side chain of the Met61 residue in the extra helix was aligned towards the haem, forming a coordination bond between the Met S and haem Fe atoms. In other cytochromes c the corresponding regions always form , loops which also include the haem-liganding Met residue and are known to be involved in the initial step in cytochrome c denaturation. The formation of the extra helix in AA c555 results in the highest helix content, 59.8%, among the monohaem cytochromes c. The extra helix should mainly contribute to the hyperstability of AA c555 and is presumed to be a novel strategy of cytochromes c for adaptation to a hyperthermophilic environment. [source]

The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance

Laura S. Busenlehner
Abstract The SmtB/ArsR family of prokaryotic metalloregulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of di- and multivalent heavy metal ions. Derepression results from direct binding of metal ions by these homodimeric ,metal sensor' proteins. An evolutionary analysis, coupled with comparative structural and spectroscopic studies of six SmtB/ArsR family members, suggests a unifying ,theme and variations' model, in which individual members have evolved distinct metal selectivity profiles by alteration of one or both of two structurally distinct metal coordination sites. These two metal sites are designated ,3N (or ,3) and ,5 (or ,5C), named for the location of the metal binding ligands within the known or predicted secondary structure of individual family members. The ,3N/,3 sensors, represented by Staphylococcus aureus pI258 CadC, Listeria monocytogenes CadC and Escherichia coli ArsR, form cysteine thiolate-rich coordination complexes (S3 or S4) with thiophilic heavy metal pollutants including Cd(II), Pb(II), Bi(III) and As(III) via inter-subunit coordination by ligands derived from the ,3 helix and the N-terminal ,arm' (CadCs) or from the ,3 helix only (ArsRs). The ,5/,5C sensors Synechococcus SmtB, Synechocystis ZiaR, S. aureus CzrA, and Mycobacterium tuberculosis NmtR form metal complexes with biologically required metal ions Zn(II), Co(II) and Ni(II) characterized by four or more coordination bonds to a mixture of histidine and carboxylate ligands derived from the C-terminal ,5 helices on opposite subunits. Direct binding of metal ions to either the ,3N or ,5 sites leads to strong, negative allosteric regulation of repressor operator/promoter binding affinity, consistent with a simple model for derepression. We hypothesize that distinct allosteric pathways for metal sensing have co-evolved with metal specificities of distinct ,3N and ,5 coordination complexes. [source]

Polyphenylene Dendrimer-Templated In Situ Construction of Inorganic,Organic Hybrid Rice-Shaped Architectures

Xiaoying Qi
Abstract A novel dendrimer-templating method for the synthesis of CuO nanoparticles and the in situ construction of ordered inorganic,organic CuO,G2Td(COOH)16rice-shaped architectures (RSAs) with analogous monocrystalline structures are reported. The primary CuO nanoparticles are linked by the G2Td(COOH)16 dendrimer. This method provides a way to preserve the original properties of primary CuO nanoparticles in the ordered hybrid nanomaterials by using the 3D rigid polyphenylene dendrimer (G2Td(COOH)16) as a space isolation. The primary CuO nanoparticles with diameter of (6.3,,0.4) nm are synthesized via four successive reaction steps starting from the rapid reduction of Cu(NO3)2 by using NaBH4 as reducer and G2Td(COOH)16 as surfactant. The obtained hybrid CuO,G2Td(COOH)16 RSA, formed in the last reaction step, possesses a crystal structure analogous to a monocrystal as observed by transmission electron microscopy(TEM). In particular, the formation process of the RSA is monitored by UV,vis, TEM, and X-ray diffraction. Small angle X-ray scattering and Fourier transform infrared spectroscopy are used to investigate the role of the dendrimer in the RSA formation process. The obtained results illuminate that Cu2+COO, coordination bonds play an indispensable role in bridging and dispersing the primary CuO nanoparticles to induce and maintain the hybrid RSA. More importantly, the RSA is retained through the Cu2+COO,coordination bonds even with HCl treatment, suggesting that the dendrimers and Cu2+ ions may form rice-shaped polymeric complexes which could template the assembly of CuO nanoparticles towards RSAs. This study highlights the feasibility and flexibility of employing the peculiar dendrimers to in-situ build up hybrid architectures which could further serve as templates, containers or nanoreactors for the synthesis of other nanomaterials. [source]

UV-vis-Induced Vitrification of a Molecular Crystal,

T. Naito
Abstract A charge-transfer complex of 2,5-dimethyl- N,N,-dicyanoquinonediimine (DM) with silver (crystalline Ag(DM)2, defined as ,) is irreversibly transformed by UV-vis illumination. Depending on the illumination conditions, three new types of solids (defined as ,, ,, and ,) with different structural and physical properties are obtained and examined by a variety of analytical techniques, including solid-state, high-resolution, cross-polarization magic angle spinning (CP-MAS) 13C,NMR, elemental analysis (EA), mass spectrometry (MS), X-ray absorption fine structure (XAFS), and powder X-ray diffraction (XRD). The CP-MAS, EA, MS, and XAFS results indicate that compound , is a glass state of Ag(DM)2. The transformation from crystalline (,) to amorphous (,) solid Ag(DM)2 is an irreversible exothermic glass transition (glass-transition temperature 155.2,C; ,H,=,,126.8,kJ,mol,1), which implies that the glass form is thermodynamically more stable than the crystalline form. Compound , (Ag(DM)1.5) consists of silver nanoparticles (diameter (7,,2),nm ) dispersed in a glassy matrix of neutral DM molecules. The N,CN,Ag coordination bonds of the , form are not maintained in the , form. Decomposition of , by intense illumination results in a white solid (,), identified as being composed of silver nanoparticles (diameter (60,,10),nm). Physical and spectroscopic (XAFS) measurements, together with XRD analysis, indicate that the silver nanoparticles in both , and , are crystalline with lattice parameters similar to bulk silver; however, the magnetic susceptibilities differ from bulk silver. [source]

Coordination Polymers: Organization of Coordination Polymers on Surfaces by Direct Sublimation (Adv. Mater.

Sublimation and surface reassembly of coordination polymers is introduced by Felix Zamora and co-workers on page 2025. This striking phenomenon is achieved due to the reversibility of the coordination bonds, which allows the polymers to be sublimated in form of small oligomers and reassembled on the surface. Temperature-controlled transition to a 1D organization reflecting the 1D bulk structure of the coordination compound is observed by atomic force microscopy. [source]

Organization of Coordination Polymers on Surfaces by Direct Sublimation

Lorena Welte
Sublimation and surface reassembly of coordination polymers is achieved due to the reversibility of the coordination bonds. Atomic force microscopy images show linear structures on surfaces, as expected for a 1D coordination polymer [source]

Heavy atom motions and tunneling in hydrogen transfer reactions: the importance of the pre-tunneling state

Hans-Heinrich Limbach
Abstract Arrhenius curves of selected hydrogen transfer reactions in organic molecules and enzymes are reviewed with the focus on systems exhibiting temperature-independent kinetic isotope effects. The latter can be rationalized in terms of a ,pre-tunneling state' which is formed from the reactants by heavy atom motions and which represents a suitable molecular configuration for tunneling to occur. Within the Bell,Limbach tunneling model, formation of the pre-tunneling state dominates the Arrhenius curves of the H and the D transfer even at higher temperatures if a large energy Em is required to reach the pre-tunneling state. Tunneling from higher vibrational levels and the over-barrier reaction via the transition state which lead to temperature-dependent kinetic isotope effects dominate the Arrhenius curves only if Em is small compared to the energy of the transition state. Using published data on several hydrogen transfer systems, the type of motions leading to the pre-tunneling state is explored. Among the phenomena which lead to large energies of the pre-tunneling state are (i) cleavage of hydrogen bonds or coordination bonds of the donor or acceptor atoms to molecules or molecular groups in order to allow the formation of the pre-tunneling state, (ii) the occurrence of an energetic intermediate on the reaction pathway within which tunneling takes place, and (iii) major reorganization of a molecular skeleton, requiring the excitation of specific vibrations in order to reach the pre-tunneling state. This model suggests a solution to the puzzle of Kwart's findings of temperature-independent kinetic isotope effects for hydrogen transfer in small organic molecules. Copyright 2010 John Wiley & Sons, Ltd. [source]

catena -Poly[bis[silver(I)-,2 -4,4,-bipyridine-,2N:N,] naphthalene-2,6-dicarboxylate tetrahydrate]: self-assembly of a supramolecular framework via coordination bonds and supramolecular interactions

Di Sun
The ultrasonic reaction of AgNO3, 4,4,-bipyridine (bipy) and naphthalene-2,6-dicarboxylic acid (H2NDC) gives rise to the title compound, {[Ag2(C10H8N2)2](C12H6O4)4H2O}n. The NDC dianion is located on an inversion centre. The AgI centre is coordinated in a linear manner by two N atoms from two bipy ligands. The crystal structure consists of one-dimensional AgI,bipy cationic chains and two-dimensional NDC,H2O anionic sheets, constructed by coordination bonds and supramolecular interactions, respectively. [source]

Poly[triaqua(,4 -4-carboxybenzenesulfonato-,4O:O,:O,,:O,,,)(4-carboxybenzenesulfonato-,O)strontium(II)]

G. Prochniak
This study presents the coordination modes and two-dimensional network of a novel strontium(II) coordination polymer, [Sr(C7H5O5S)2(H2O)3]n. The eight-coordinate Sr2+ ion is in a distorted bis-disphenoidal coordination environment, surrounded by four sulfonate and one carboxyl O atom from five benzenesulfonate ligands, two of which are symmetry unique, and by three O atoms from three independent aqua ligands. The compound exhibits a monolayer structure with coordination bonds within and hydrogen bonds between the layers. The ,4 acid ligand bridges the metal ions in two dimensions to form a thick undulating monolayer with a hydrophobic interior and hydrophilic surfaces. A second independent monoanion is arranged outward from both sides of the monolayer and serves to link adjacent monolayers via carboxyl,water and water,carboxyl hydrogen bonds. [source]

Calcium chloride rhenate(VII) dihydrate

Urszula Jarek
The crystal structure of calcium chloride rhenate(VII) dihydrate, CaCl(ReO4)2H2O, investigated at 85,K, consists of calcium cations, chloride anions, rhenate(VII) anions and water molecules. In the nearly tetrahedral rhenate(VII) anion, all constituent atoms lie on special positions of m2m (Re) and m (O) site symmetries. The Cl, anion and water O atom lie on special positions of m2m and 2 site symmetries, respectively. The Ca2+ ion, also on a special position (m2m), is eight-coordinated in a distorted square-antiprismatic coordination mode. The crystal has a layered structure stabilized by Ca,O coordination bonds and O,H...Cl hydrogen bonds. [source]

Caged and clustered structures of endothelin inhibitor BQ123, cyclo(- d -Trp- d -Asp, -Pro- d -Val-Leu-),Na+, forming five and six coordination bonds between sodium ions and peptides

Mitsunobu Doi
BQ123 is a cyclic pentapeptide and a potent endothelin-1 inhibitor. The crystal structure of the BQ123 sodium salt was determined as the first example of an endothelin inhibitor. Four independent molecules and many solvent molecules were found in the asymmetric unit; the total weight was about 3000,Da. The precise structure including the solvent molecules was determined using high-resolution data collected on a synchrotron source. Sodium ions formed unique structures with five and six coordination bonds and their forms were distinguished into three classes. An ion was sandwiched by two BQ123 molecules. This peptide,sodium (2:1) complex showed a cage-like structure and octahedral coordination was observed. Sodium ions also formed a cluster composed of hydrated water molecules and peptides. Two sodium ions were contained in this cluster, making five coordination bonds. Despite having the same coordination numbers, these ions were distinguishable by differences in the polyhedra. One was trigonal bipyramidal (having six planes) and the other was square pyramidal (having five planes). Both shapes were very similar to each other, although the synchrotron data clearly revealed slight geometrical differences. [source]

Modification of Supramolecular Binding Motifs Induced By Substrate Registry: Formation of Self-Assembled Macrocycles and Chain-Like Patterns

Leslie-Anne Fendt
Abstract The self-assembly properties of two ZnII porphyrin isomers on Cu(111) are studied at different coverage by means of scanning tunneling microscopy (STM). Both isomers are substituted in their meso -positions by two voluminous 3,5-di(tert -butyl)phenyl and two rod-like 4,-cyanobiphenyl groups, respectively. In the trans -isomer, the two 4,-cyanobiphenyl groups are opposite to each other, whereas they are located at right angle in the cis -isomer. For coverage up to one monolayer, the cis- substituted porphyrins self-assemble to form oligomeric macrocycles held together by antiparallel CN,,,CN dipolar interactions and CN,,,H-C(sp2) hydrogen bonding. Cyclic trimers and tetramers occur most frequently but everything from cyclic dimers to hexamers can be observed. Upon annealing of the samples at temperatures >150,C, dimeric macrocyclic structures are observed, in which the two porphyrins are bridged by Cu atoms, originating from the surface, under formation of two CN,,,Cu,,,NC coordination bonds. The trans -isomer builds up linear chains on Cu(111) at low coverage, whereas for higher coverage the molecules assemble in a periodic, densely packed structure. Both cis - and trans -bis(4,-cyanobiphenyl)-substituted ZnII porphyrins behave very differently on Cu(111) compared to similar porphyrins in literature on less reactive surfaces such as Au(111) and Ag(111). On the latter surfaces, there is no signal visible between molecular orientation and the crystal directions of the substrate, whereas on Cu(111), very strong adsorbate,substrate interactions have a dominating influence on all observed structures. This strong porphyrin,substrate interaction enables a much broader variety of structures, including also less favorable intermolecular bonding motifs and geometries. [source]