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Hydrogen-bond Network (hydrogen-bond + network)

Distribution by Scientific Domains
Chemistry93%
2 Other Domains7%
Distribution within Chemistry
Crystallography56%
General & Introductory Chemistry6%

Selected Abstracts

Hydrogen-Bond Networks in Water Clusters (H2O)20: An Exhaustive Quantum-Chemical Analysis

CHEMPHYSCHEM, Issue 2 2010
Andrei M. Tokmachev Dr.
Abstract Water aggregates allow for numerous configurations due to different distributions of hydrogen bonds. The total number of possible hydrogen-bond networks is very large even for medium-sized systems. We demonstrate that targeted ultra-fast methods of quantum chemistry make an exhaustive analysis of all configurations possible. The cage of (H2O)20 in the form of the pentagonal dodecahedron is a common motif in water structures. We calculated the spatial and electronic structure of all hydrogen-bond configurations for three systems: idealized cage (H2O)20 and defect cages with one or two hydrogen bonds broken. More than 3 million configurations studied provide unique data on the structure and properties of water clusters. We performed a thorough analysis of the results with the emphasis on the cooperativity in water systems and the structure-property relations. [source]

Deamidation of labile asparagine residues in the autoregulatory sequence of human phenylalanine hydroxylase

FEBS JOURNAL, Issue 5 2003
Structural, functional implications
Two dimensional electrophoresis has revealed a microheterogeneity in the recombinant human phenylalanine hydroxylase (hPAH) protomer, that is the result of spontaneous nonenzymatic deamidations of labile asparagine (Asn) residues [Solstad, T. and Flatmark, T. (2000) Eur. J. Biochem.267, 6302,6310]. Using of a computer algorithm, the relative deamidation rates of all Asn residues in hPAH have been predicted, and we here verify that Asn32, followed by a glycine residue, as well as Asn28 and Asn30 in a loop region of the N-terminal autoregulatory sequence (residues 19,33) of wt-hPAH, are among the susceptible residues. First, on MALDI-TOF mass spectrometry of the 24 h expressed enzyme, the E. coli 28-residue peptide, L15,K42 (containing three Asn residues), was recovered with four monoisotopic mass numbers (i.e., m/z of 3106.455, 3107.470, 3108.474 and 3109.476, of decreasing intensity) that differed by 1 Da. Secondly, by reverse-phase chromatography, isoaspartyl (isoAsp) was demonstrated in this 28-residue peptide by its methylation by protein- l -isoaspartic acid O -methyltransferase (PIMT; EC 2.1.1.77). Thirdly, on incubation at pH 7.0 and 37 °C of the phosphorylated form (at Ser16) of this 28-residue peptide, a time-dependent mobility shift from tR,,34 min to ,,31 min (i.e., to a more hydrophilic position) was observed on reverse-phase chromatography, and the recovery of the tR,,34 min species decreased with a biphasic time-course with t0.5 -values of 1.9 and 6.2 days. The fastest rate is compatible with the rate determined for the sequence-controlled deamidation of Asn32 (in a pentapeptide without 3D structural interference), i.e., a deamidation half-time of ,,1.5 days in 150 mm Tris/HCl, pH 7.0 at 37 °C. Asn32 is located in a cluster of three Asn residues (Asn28, Asn30 and Asn32) of a loop structure stabilized by a hydrogen-bond network. Deamidation of Asn32 introduces a negative charge and a partial ,-isomerization (isoAsp), which is predicted to result in a change in the backbone conformation of the loop structure and a repositioning of the autoregulatory sequence and thus affect its regulatory properties. The functional implications of this deamidation was further studied by site-directed mutagenesis, and the mutant form (Asn32,Asp) revealed a 1.7-fold increase in the catalytic efficiency, an increased affinity and positive cooperativity of L-Phe binding as well as substrate inhibition. [source]

Supramolecular catalysis induced by polysaccharides.

JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 8 2003
Homogeneous hydrolysis of p -nitrobenzyl amylose xanthate
Abstract p -Nitrobenzyl amylose xanthate (AmXNB) was synthesized and characterized by 13C NMR spectroscopy in solution and the solid state. The degree of substitution (DS), calculated from the sulfur content, was 7.0, and this value was similar to that obtained from solid-state 13C NMR using the signal of C-1 as internal standard. The hydrolysis of AmXNB was studied in 10% (v/v) DMSO with,µ,=,0.5 (KCl) at 25,°C. The basic hydrolysis was pseudo-first order, but the water-catalyzed hydrolysis in the pH range 7,9 showed a biphasic plot of ln (,Absorbance) vs time, as has been observed for cellulose xanthate esters, occurring through two parallel reactions with rate constants k,H2O (fast),=,5.3,×,10,5 s,1 and k,H2O (slow),=,3.3,×,10,6 s,1. The fast hydrolysis was more than three orders of magnitude faster than that of the O -ethyl analog. The activation parameters were ,H,,=,20.5,kcal,mol,1 and ,S,,=,+10 cal K,1,mol,1. They showed that the acceleration of the fast hydrolysis of AmXNB and cellulose analogs is due to an entropy of activation effect. There is a linear increase of logk,H2O (fast) with increase in the concentration of the small Li+ ion that produces an increase of the 3-D hydrogen-bond network of water while the large singly charged iodide ion has a considerable inverse effect. These results are strongly consistent with the theory that the supramolecular catalysis induced by modified polysaccharide esters is due to the 3-D hydrogen-bond network of the water in the solvation shell. Copyright © 2003 John Wiley & Sons, Ltd. [source]

A Self-Assembling Polythiophene Functionalised with a Cysteine Moiety

MACROMOLECULAR RAPID COMMUNICATIONS, Issue 9 2003
Adele Mucci
Abstract A new copolymer bearing a cysteine moiety, designed for molecular interaction, metal-ion detection, and chiral recognition, was synthesised starting from the dibromo derivative of methyl N -(tert -butoxycarbonyl)- S -thien-3-ylcysteinate and distannylthiophene through a Stille coupling reaction. UV-vis spectroscopy, circular dichroism, NMR spectroscopy, and gel permeation chromatography analyses evidenced that this polymer is able to form self-assembling structures, through the formation of a hydrogen-bond network, not only in the solid state but also in solution. [source]

L2, loop is critical for caspase-7 active site formation

PROTEIN SCIENCE, Issue 7 2009
Witold A. Witkowski
Abstract The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2,) from the other half of the dimer to bind substrate. In an inactive form, the two L2, loops form a cross-dimer hydrogen-bond network over the dimer interface. Although the L2, loop has been implicated as playing a central role in the formation of the active-site loop bundle, its precise role in catalysis has not been shown. A detailed understanding of the active and inactive conformations is essential to control the caspase function. We have interrogated the contributions of the residues in the L2, loop to catalytic function and enzyme stability. In wild-type and all mutants, active-site binding results in substantial stabilization of the complex. One mutation, P214A, is significantly destabilized in the ligand-free conformation, but is as stable as wild type when bound to substrate, indicating that caspase-7 rests in different conformations in the absence and presence of substrate. Residues K212 and I213 in the L2, loop are shown to be essential for substrate-binding and thus proper catalytic function of the caspase. In the crystal structure of I213A, the void created by side-chain deletion is compensated for by rearrangement of tyrosine 211 to fill the void, suggesting that the requirements of substrate-binding are sufficiently strong to induce the active conformation. Thus, although the L2, loop makes no direct contacts with substrate, it is essential for buttressing the substrate-binding groove and is central to native catalytic efficiency. [source]

Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: A special subgroup of the type III extradiol dioxygenases

PROTEIN SCIENCE, Issue 4 2006
Xiaowu Li
Abstract 3-Hydroxyanthranilic acid 3,4-dioxygenase (3HAO) is a non-heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes the conversion of 3-hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an endogenous neurotoxin, via the activation of N-methyl-D-aspartate (NMDA) receptors and the precursor of NAD+ biosynthesis. The crystal structure of 3HAO from S. cerevisiae at 2.4 Å resolution shows it to be a member of the functionally diverse cupin superfamily. The structure represents the first eukaryotic 3HAO to be resolved. The enzyme forms homodimers, with two nickel binding sites per molecule. One of the bound nickel atoms occupies the proposed ferrous-coordinated active site, which is located in a conserved double-strand ,-helix domain. Examination of the structure reveals the participation of a series of residues in catalysis different from other extradiol dioxygenases. Together with two iron-binding residues (His49 and Glu55), Asp120, Asn51, Glu111, and Arg114 form a hydrogen-bonding network; this hydrogen-bond network is key to the catalysis of 3HAO. Residues Arg101, Gln59, and the substrate-binding hydrophobic pocket are crucial for substrate specificity. Structure comparison with 3HAO from Ralstonia metallidurans reveals similarities at the active site and suggests the same catalytic mechanism in prokaryotic and eukaryotic 3HAO. Based on sequence comparison, we suggest that bicupin of human 3HAO is the first example of evolution from a monocupin dimer to bicupin monomer in the diverse cupin superfamilies. Based on the model of the substrate HAA at the active site of Y3HAO, we propose a mechanism of catalysis for 3HAO. [source]

Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimer

PROTEIN SCIENCE, Issue 11 2003
Terence C. Flynn
Abstract The crystal structures of lactose repressor protein (LacI) provide static endpoint views of the allosteric transition between DNA- and IPTG-bound states. To obtain an atom-by-atom description of the pathway between these two conformations, motions were simulated with targeted molecular dynamics (TMD). Strikingly, this homodimer exhibited asymmetric dynamics. All asymmetries observed in this simulation are reproducible and can begin on either of the two monomers. Asymmetry in the simulation originates around D149 and was traced back to the pre-TMD equilibrations of both conformations. In particular, hydrogen bonds between D149 and S193 adopt a variety of configurations during repetitions of this process. Changes in this region propagate through the structure via noncovalent interactions of three interconnected pathways. The changes of pathway 1 occur first on one monomer. Alterations move from the inducer-binding pocket, through the N-subdomain ,-sheet, to a hydrophobic cluster at the top of this region and then to the same cluster on the second monomer. These motions result in changes at (1) side chains that form an interface with the DNA-binding domains and (2) K84 and K84', which participate in the monomer,monomer interface. Pathway 2 reflects consequent reorganization across this subunit interface, most notably formation of a H74-H74rsquo; ,-stacking intermediate. Pathway 3 extends from the rear of the inducer-binding pocket, across a hydrogen-bond network at the bottom of the pocket, and transverses the monomer,monomer interface via changes in H74 and H74rsquo;. In general, intermediates detected in this study are not apparent in the crystal structures. Observations from the simulations are in good agreement with biochemical data and provide a spatial and sequential framework for interpreting existing genetic data. [source]

l -2-Aminobutyric acid: two fully ordered polymorphs with Z, = 4

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010
Carl Henrik Görbitz
The crystal structure of l -2-aminobutyric acid, an l -alanine analogue with an ethyl rather than a methyl side chain, has proved elusive owing to problems growing diffraction quality crystals. Good diffraction data have now been obtained for two polymorphs, in space groups P21 and I2, revealing surprisingly complex, yet fully ordered crystalline arrangements with Z, = 4. The closely related structures are divided into hydrophilic and hydrophobic layers, the latter being the thinnest ever found for an amino acid (other than ,-glycine). The hydrophobic layers furthermore contain conspicuous pseudo-centers-of-symmetry, leading to overall centrosymmetric intensity statistics. Uniquely, the four molecules in the asymmetric unit can be divided into two pairs that each forms an independent hydrogen-bond network. [source]

Tautomerism and hydrogen bonding in guaninium phosphite and guaninium phosphate salts

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2007
El-Eulmi Bendeif
The crystal structures of three similar guaninium salts, guaninium monohydrogenphosphite monohydrate, C5H6N5O+·H2O3P,·H2O, guaninium monohydrogenphosphite dihydrate, C5H6N5O+·H2O3P,·2H2O, and guaninium dihydrogenmonophosphate monohydrate, C5H6N5O+·H2O4P,·H2O, are described and compared. The crystal structures have been determined from accurate single-crystal X-ray data sets collected at 100,(2),K. The two phosphite salts are monoclinic, space group P21/c, with different packing and the monophosphate salt is also monoclinic, space group P21/n. An investigation of the hydrogen-bond network in these guaninium salts reveals the existence of two ketoamine tautomers, the N9H form and an N7H form. [source]

Anisotropic crystal structure distortion of the monoclinic polymorph of acetaminophen at high hydrostatic pressures

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2000
E. V. Boldyreva
The anisotropy of structural distortion of the monoclinic polymorph of acetaminophen induced by hydrostatic pressure up to 4.0,GPa was studied by single-crystal X-ray diffraction in a Merrill,Bassett diamond anvil cell (DAC). The space group (P21/n) and the general structural pattern remained unchanged with pressure. Despite the overall decrease in the molar volume with pressure, the structure expanded in particular crystallographic directions. One of the linear cell parameters (c) passed through a minimum as the pressure increased. The intramolecular bond lengths changed only slightly with pressure, but the changes in the dihedral and torsion angles were very large. The compressibility of the intermolecular hydrogen bonds NH,O and OH,O was measured. NH,O bonds were shown to be slightly more compressible than OH,O bonds. The anisotropy of structural distortion was analysed in detail in relation to the pressure-induced changes in the molecular conformations, to the compression of the hydrogen-bond network, and to the changes in the orientation of molecules with respect to each other in the pleated sheets in the structure. Dirichlet domains were calculated in order to analyse the relative shifts of the centroids of the hydrogen-bonded cycles and of the centroids of the benzene rings with pressure. [source]

2,-Deoxy-5-propynyluridine: a nucleoside with two conformations in the asymmetric unit

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009
Simone Budow
The title compound, 1-(2-deoxy-,- d - erythro -pentofuranosyl)-5-(prop-1-ynyl)pyrimidin-2,4(1H,3H)-dione, C12H14N2O5, shows two conformations in the crystalline state: conformer 1 adopts a C2,- endo (close to 2E; S -type) sugar pucker and an anti nucleobase orientation [, = ,134.04,(19)°], while conformer 2 shows an S sugar pucker (twisted C2,- endo,C3,- exo), which is accompanied by a different anti base orientation [, = ,162.79,(17)°]. Both molecules show a +sc (gauche, gauche) conformation at the exocyclic C4,,C5, bond and a coplanar orientation of the propynyl group with respect to the pyrimidine ring. The extended structure is a three-dimensional hydrogen-bond network involving intermolecular N,H...O and O,H...O hydrogen bonds. Only O atoms function as H-atom acceptor sites. [source]

5-Amino-2,4,6-tribromoisophthalic acid: the MAD triangle for experimental phasing

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009
Tobias Beck
The title compound, C8H4Br3NO4, shows an extensive hydrogen-bond network. In the crystal structure, molecules are linked into chains by COO,H...O bonds, and pairs of chains are connected by additional COO,H...O bonds. This chain bundle shows stacking interactions and weak N,H...O hydrogen bonds with adjacent chain bundles. The three Br atoms present in the molecule form an equilateral triangle. This can be easily identified in the heavy-atom substructure when this compound is used as a heavy-atom derivative for experimental phasing of macromolecules. The title compound crystallizes as a nonmerohedral twin. [source]

Sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2007
Moolya B. Narayana
The title compound, Na+·3C2H6NO2+·2SiF62,·3C2H5NO2, arose from an unexpected reaction of glycine and HF with the glass container. It is an unusual hybrid organic,inorganic network built up from chains of vertex-sharing NaF4O2 and SiF6 octahedra. A pair of glycinium/glycine molecules bridges the chains into a sheet via a centrosymmetric O...H...O link. The other organic species interact with the network by an extensive N,H...F hydrogen-bond network, including bifurcated and trifurcated bonds. Finally, an extremely short C,H...O interaction (H...O = 2.25,Å) is seen in the crystal structure. The Na atom has site symmetry . [source]

Three related benzoannelated diazapolyether macrocycles: effects of macrocycle ring size and position of benzo groups on hydrogen bonding of the amine H atoms

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2007
Gary L. N. Smith
The benzoannelated diazapolyether macrocycles 6,7,9,10,17,18-hexahydro-5H,11H -8,16,19-trioxa-5,11-diazadibenzo[a,g]cyclopentadecene, C18H22N2O3, (I), 6,7,9,10,12,13,20,21-octahydro-5H,14H -8,11,19,22-tetraoxa-5,14-diazadibenzo[a,g]cyclooctadecene, C20H26N2O4, (II), and 6,7,9,10,17,18,20,21-octahydro-16H,22H -5,8,11,19-tetraoxa-16,22-diazadibenzo[a,j]cyclooctadecene 0.3-hydrate, C20H26N2O4·0.304H2O, (III), show different patterns of hydrogen bonding. In (I), the amine H atoms participate only in intramolecular hydrogen bonds with ether O atoms. In (II), the amine H atoms form intramolecular hydrogen bonds with the phenoxy ether O atoms and intermolecular hydrogen bonds with alkyl ether O atoms in an adjacent molecule, forming a chain linking the macrocycles together via an R22(10) motif. Molecules of (II) were found on a crystallographic twofold axis. In (III), the amine H atoms participate in a hydrogen-bond network with adjacent ether O atoms and with a water molecule [having a partial occupancy of 0.304,(6)] that links the molecules together via a C22(7) motif. [source]

Transition metal complexes with ­thiosemicarbazide-based ligands.

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2002
XLIII.
In the title compound, [ZnCl(C2H7N3S)2]Cl, the ZnII ion is five-coordinated in a distorted trigonal,bipyramidal arrangement, with the hydrazine N atoms located in the apical positions. The structure is stabilized by N,H,Cl hydrogen bonds, which involve both the Cl atoms and all the hydrogen donors, except for one of the two thio­amide N atoms. A comparison of the geometry of thio­semicarbazide and S -­methyl­iso­thio­semicarbazide complexes with ZnII, CuII and NiII shows the pronounced influence of the hydrogen-bond network on the coordination geometry of ZnII compounds. [source]

A new crystalline phase of nitric acid dihydrate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2001
Nathalie Lebrun
The crystal structure of a new high-temperature phase of nitric acid dihydrate, HNO3·2H2O, has been determined at 225,K by single-crystal X-ray diffraction. The H atom of the nitric acid is delocalized to one water mol­ecule, leading to an association of equimolar NO3, and H5O2+ ionic groups. The asymmetric unit contains two mol­ecules of HNO3·2H2O. The two independent mol­ecules are related by a pseudo-twofold c axis, by a translation of 0.54 (approximately ½) along b, with a mean atomic distance difference of 0.3,Å, except for one H atom of the water mol­ecules (1.5,Å), because of their different orientations in the two mol­ecules. The two independent mol­ecules, linked by strong hydrogen bonds, are arranged in layers. These layers are linked by weaker hydrogen bonds oriented approximately along the c axis. A three-dimensional hydrogen-bond network is observed. [source]

Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3,-monophosphate

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010
Shuji Noguchi
Aspartates in proteins are isomerized non-enzymatically to isoaspartate via succinimide in vitro and in vivo. In order to elucidate the mechanism of isoaspartate formation within the Asp45-Glu46 sequence of Ustilago sphaerogena ribonuclease U2 based on three-dimensional structure, crystal structures of ribonuclease U2 complexed with adenosine 3,-monophosphate have been solved at 0.96 and 0.99,Å resolution. The crystal structures revealed that the C, atom of Asp45 is located just beside the main-chain N atom of Glu46 and that the conformation which is suitable for succinimide formation is stabilized by a hydrogen-bond network mediated by water molecules 190, 219 and 220. These water molecules are suggested to promote the formation of isoaspartate via succinimide: in the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid. The purine-base recognition scheme of ribonuclease U2 is also discussed. [source]

pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera)

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010
Takao Kuwada
Haemoglobin component V (Hb,V) from the midge larva Propsilocerus akamusi exhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb,V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb,V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb,V retains its functional properties by adapting to the structural changes caused by amino-acid replacements. [source]

Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010
Jeremy D. Wilbur
Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility. [source]

Structure of a highly stable mutant of human fibroblast growth factor 1

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2009
Anna Szlachcic
Fibroblast growth factors (FGFs) are involved in diverse cellular processes such as cell migration, angiogenesis, osteogenesis, wound healing and embryonic and foetal development. Human acidic fibroblast growth factor (FGF-1) is the only member of the FGF family that binds with high affinity to all four FGF receptors and thus is considered to be the human mitogen with the broadest specificity. However, pharmacological applications of FGF-1 are limited owing to its low stability. It has previously been reported that the introduction of single mutations can significantly improve the stability of FGF-1 and its resistance to proteolytic degradation. Here, the structure of the Q40P/S47I/H93G triple mutant of FGF-1, which exhibits much higher stability, a prolonged half-life and enhanced mitogenic activity, is presented. Compared with the wild-type structure, three localized conformational changes in the stable triple mutant were observed, which is in agreement with the perfect energetic additivity of the single mutations described in a previous study. The huge change in FGF-1 stability (the denaturation temperature increased by 21.5,K, equivalent to ,,Gden = 24.3,kJ,mol,1) seems to result from the formation of a short 310 -helix (position 40), an improvement in the propensity of amino acids to form ,-sheets (position 47) and the rearrangement of a local hydrogen-bond network (positions 47 and 93). [source]

Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2,Å resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004
Masakazu Sugishima
Photoactive yellow protein from Ectothiorhodospira halophila is a photoreceptor protein involved in the negative phototaxis of this bacterium. Its chromophore (p -coumaric acid) is deprotonated in the ground state, which is stabilized by a hydrogen-bond network between Tyr42, Glu46 and Thr50. Glu46 is a key residue as it has been suggested that the proton at Glu46 is transferred to the chromophore during its photoconversion from the dark state to the signalling state. The structure of E46Q mutant protein was determined at 1.2,Å resolution, revealing that the phenolic O atom of p -­coumaric acid is hydrogen bonded to NH2 of Gln46 in E46Q with a longer distance (2.86 ± 0.02,Å) than its distance (2.51,Å) to Glu46,OH in the wild type. This and the decreased thermal stability of E46Q relative to the wild type show that this hydrogen bond is weakened in the E46Q mutant compared with the corresponding bond in the wild type. Several characteristic features of E46Q such as an alkali shift in the pKa and the rapid photocycle can be explained by this weakened hydrogen bond. Furthermore, the red shift in the absorption maximum in E46Q can be explained by the delocalization of the electron on the phenolic oxygen of p -­coumaric acid owing to the weakening of this hydrogen bond. [source]

Theoretical design of bioinspired macromolecular electrets based on anthranilamide derivatives

BIOTECHNOLOGY PROGRESS, Issue 4 2009
M. K. Ashraf
Abstract Polypeptide helices possess considerable intrinsic dipole moments oriented along their axes. While for proline helices the dipoles originate solely from the ordered orientation of the amide bonds, for 310, and ,-helices the polarization resultant from the formation of hydrogen-bond network further increases the magnitude of the macromolecular dipoles. The enormous electric-field gradients, generated by the dipoles of ,-helices (which amount to about 5 D per residue with 0.15 nm residue increments along the helix), play a crucial role in the selectivity and the transport properties of ion channels. The demonstration of dipole-induced rectification of vectorial charge transfer mediated by ,-helices has opened a range of possibilities for applications of these macromolecules in molecular and biomolecular electronics. These biopolymers, however, possess relatively large bandgaps. As an alternative, we examined a series of synthetic macromolecules, aromatic oligo- ortho -amides, which form extended structures with amide bonds in ordered orientation, supported by a hydrogen-bond network. Unlike their biomolecular counterparts, the extended ,-conjugation of these macromolecules will produce bandgaps significantly smaller than the polypeptide bandgaps. Using ab initio density functional theory calculations, we modeled anthranilamide derivatives that are representative oligo- ortho -amide conjugates. Our calculations, indeed, showed intrinsic dipole moments oriented along the polymer axes and increasing with the increase in the length of the oligomers. Each anthranilamide residue contributed about 3 D to the vectorial macromolecular dipole. When we added electron donating (diethylamine) and electron withdrawing (nitro and trifluoromethyl) groups for n- and p-doping, respectively, we observed that: (1) proper positioning of the electron donating and withdrawing groups further polarized the aromatic residues, increasing the intrinsic dipole to about 4.5 D per residue; and (2) extension of the ,-conjugation over some of the doping groups narrowed the band gaps with as much as 1 eV. The investigated bioinspired systems offer alternatives for the development of broad range of organic electronic materials with nonlinear properties. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source]

Understanding Promiscuous Amidase Activity of an Esterase from Bacillus subtilis

CHEMBIOCHEM, Issue 1 2008
Robert Kourist
Water works. Bacillus subtilis esterase BS2 is a promiscuous esterase that shows amidase activity. This amidase activity was shown to depend on a hydrogen-bond network with the substrate amide hydrogen (indicated by arrow). When this stabilising hydrogen bond network was removed by a point mutation, the amide activity was significantly lowered in comparison with the esterase activity. [source]

Hydrogen-Bonding Cooperativity: Using an Intramolecular Hydrogen Bond To Design a Carbohydrate Derivative with a Cooperative Hydrogen-Bond Donor Centre

CHEMISTRY - A EUROPEAN JOURNAL, Issue 17 2004
Virginie Vicente Dr.
Abstract Neighbouring groups can be strategically located to polarise HO,,,OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO,,,OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3 -cis- diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1,3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule. [source]

Folding Dynamics of 10-Residue ,-Hairpin Peptide Chignolin

CHEMISTRY - AN ASIAN JOURNAL, Issue 5 2007
Atsushi Suenaga Dr.
Abstract Short peptides that fold into ,-hairpins are ideal model systems for investigating the mechanism of protein folding because their folding process shows dynamics typical of proteins. We performed folding, unfolding, and refolding molecular dynamics simulations (total of 2.7,,s) of the 10-residue ,-hairpin peptide chignolin, which is the smallest ,-hairpin structure known to be stable in solution. Our results revealed the folding mechanism of chignolin, which comprises three steps. First, the folding begins with hydrophobic assembly. It brings the main chain together; subsequently, a nascent turn structure is formed. The second step is the conversion of the nascent turn into a tight turn structure along with interconversion of the hydrophobic packing and interstrand hydrogen bonds. Finally, the formation of the hydrogen-bond network and the complete hydrophobic core as well as the arrangement of side-chain,side-chain interactions occur at approximately the same time. This three-step mechanism appropriately interprets the folding process as involving a combination of previous inconsistent explanations of the folding mechanism of the ,-hairpin, that the first event of the folding is formation of hydrogen bonds and the second is that of the hydrophobic core, or vice versa. [source]

Chiral discrimination of 2-arylalkanoic acids by (1S,2S)-1-aminoindan-2-ol and (1S,2S)-2-aminoindan-1-ol: Correlation of the relative configuration of the amino and hydroxy groups with the pattern of a supramolecular hydrogen-bond network in the less-soluble diastereomeric salt

CHIRALITY, Issue 6 2003
Kazushi Kinbara
Abstract The diastereomeric resolution of 2-arylalkanoic acids with enantiopure trans -1-aminoindan-2-ol and trans -2-aminoindan-1-ol were studied. Enantiopure trans -1-aminoindan-2-ol had a moderate resolving ability for 2-arylalkanoic acids having a naphthyl group as an aryl substituent at the ,-position, while enantiopure trans -2-aminoindan-1-ol had a moderate-to-high resolving ability for a wide variety of the acids having a methyl group as an alkyl substituent at the ,-position. The crystal structures of the corresponding less-soluble salts revealed that a reinforced columnar hydrogen-bond network was formed in the less-soluble salts with trans -1-aminoindan-2-ol, while a rather stable hydrogen-bond sheet was generated with the assistance of water molecules in the less-soluble salts with trans -2-aminoindan-1-ol. These results suggest that not only the relative configuration but also the position of the hydrogen-bonding groups in resolving agents have a considerable effect on the structure of the less-soluble salts. The difference in favorable hydrogen-bond structure determined the adaptivity to the structural feature of target racemic 2-arylalkanoic acids in the resolution by trans -1-aminoindan-2-ol and trans -1-aminoindan-2-ol, respectively. Chirality 15:564,570, 2003. © 2003 Wiley-Liss, Inc. [source]

Hydrophobic `lock and key' recognition of N -4-nitrobenzoylamino acid by strychnine

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2006
Zbigniew Ciunik
During racemic resolution of N -4-nitrobenzoyl- dl -amino acids (alanine, serine and aspartic acid) by a fractional crystallization of strychninium salts, crystals of both diastereo­meric salts were grown, and the crystal structures of strychninium N -4-nitrobenzoyl- l -alaninate methanol disolvate (1a), strychninium N -4-nitrobenzoyl- d -alaninate dihydrate (1b), strychninium N -4-nitrobenzoyl- d -serinate dihydrate (2a), strychninium N -4-nitrobenzoyl- l -serinate methanol solvate hydrate (2b), strychninium hydrogen N -4-nitrobenzoyl- l -aspartate 3.75 hydrate (3a) and strychninium hydrogen N -4-nitrobenzoyl- d -aspartate 2.25 hydrate (3b) were determined. The strychninium cations form corrugated layers, which are separated by hydrogen-bonded anions and solvent molecules. Common features of the corrugated layers are deep hydrophobic grooves at their surfaces, which are occupied by the 4-nitro­benzoyl groups of suitable anions. The hydrophobic `lock and key' recognition of 4-nitrobenzoyl groups of amino acid derivatives in deep grooves of the strychnine self-assembly causes the resulting surface to have more hydrophilic properties, which are more appropriate for interactions in the hydrophilic environments from which strychninium salts were crystallized. In the crystal structure of (2a) and (3a), such hydrophobic `lock and key' recognition is responsible for the lack of N,H+,O, hydrogen bonds that are usually formed between the protonated tertiary amine N atom of the strychninium cation and the deprotonated carboxyl group of the resolved acid. In the crystal structure of (2a) and (3a), the protonated amine N atom is a donor of hydrogen bonds, while the hydroxyl group of the serine derivative and water molecules are their acceptors. In light of the hydrophobic recognition, chiral discrimination depends on the nature of the hydrogen-bond networks, which involve anions, solvent molecules and the protonated amine N atom of strychninium cations. [source]

N,H...O and O,H...O hydrogen-bonded supramolecular networks in 4-chloroanilinium, 2-hydroxyanilinium and 3-hydroxyanilinium hydrogen phthalates

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009
R. Jagan
The title salts, 4-chloroanilinium hydrogen phthalate (PCAHP), C6H7ClN+·C8H5O4,, 2-hydroxyanilinium hydrogen phthalate (2HAHP), C6H8NO+·C8H5O4,, and 3-hydroxyanilinium hydrogen phthalate (3HAHP), C6H8NO+·C8H5O4,, all crystallize in the space group P21/c. The asymmetric unit of 2HAHP contains two independent ion pairs. The hydrogen phthalate ions of 2HAHP and 3HAHP show a short intramolecular O,H...O hydrogen bond, with O...O distances ranging from 2.3832,(15) to 2.3860,(14),Å. N,H...O and O,H...O hydrogen bonds, together with short C,H...O contacts in PCAHP and 3HAHP, generate extended hydrogen-bond networks. PCAHP forms a two-dimensional supramolecular sheet extending in the (100) plane, whereas 2HAHP has a supramolecular chain running parallel to the [100] direction and 3HAHP has a two-dimensional network extending parallel to the (001) plane. [source]

Hydrogen-Bond Networks in Water Clusters (H2O)20: An Exhaustive Quantum-Chemical Analysis

CHEMPHYSCHEM, Issue 2 2010
Andrei M. Tokmachev Dr.
Abstract Water aggregates allow for numerous configurations due to different distributions of hydrogen bonds. The total number of possible hydrogen-bond networks is very large even for medium-sized systems. We demonstrate that targeted ultra-fast methods of quantum chemistry make an exhaustive analysis of all configurations possible. The cage of (H2O)20 in the form of the pentagonal dodecahedron is a common motif in water structures. We calculated the spatial and electronic structure of all hydrogen-bond configurations for three systems: idealized cage (H2O)20 and defect cages with one or two hydrogen bonds broken. More than 3 million configurations studied provide unique data on the structure and properties of water clusters. We performed a thorough analysis of the results with the emphasis on the cooperativity in water systems and the structure-property relations. [source]