Elucidation of Metal‐Ion Accumulation Induced by Hydrogen Bonds on Protein Surfaces by Using Porous Lysozyme Crystals Containing RhIII Ions as the Model Surfaces

Metal‐ion accumulation on protein surfaces is a crucial step in the initiation of small‐metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh^III ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino‐acid residues to capture Rh^III ions. ii) Water molecules pre‐organized by hydrogen bonds can stabilize Rh^III coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino‐acid residues can be replaced by Rh^III ions to form polynuclear structures with the residues. iv) Rh^III aqua complexes are retained on amino‐acid residues through stabilizing hydrogen bonds even at low pH (≈2). These metal–protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.     

N‐Carboxy‐l‐aspartic anhydride benzyl ester

The structure of the title compound, benzyl (1,2,3,4‐tetra­hydro‐2,5‐dioxo‐1,3‐oxazol‐4‐yl)­acetate, C₁₂H₁₁NO₅, has been determined in an attempt to explain the polymerization observed in the solid state. The mol­ecules are linked by intermolecular hydrogen bonds between the imino group of the five‐membered ring and an adjacent carbonyl O atom, along the c axis. Intramolecular hydrogen bonds are also formed, between the imino group and the carbonyl O atom of the ester group. The five‐membered rings are arranged in a layer, sandwiched by layers incorporating the benzyl groups. This structure is thought to be preferable for the polymerization of the compound in the solid state, because the five‐membered rings can react with each other in the layer.     

Influence of Ester versus Amide Linkers on the Supramolecular Polymerization Mechanisms of Planar BODIPY Dyes

We report the H‐type supramolecular polymerization of two new hydrophobic BODIPY derivatives equipped with ester and amide linkages. Whereas the ester‐containing BODIPY derivative undergoes an isodesmic supramolecular polymerization in which the monomers are parallel‐oriented, the replacement of the ester by amide groups leads to a highly cooperative self‐assembly process into H‐type aggregates with a rotational displacement of the dye molecules within the stack. The dye organization imposed by simultaneous π–π and hydrogen bonding interactions is the driving force for the cooperative supramolecular polymerization, whereas the absence of additional hydrogen bonds for the ester‐containing moiety does not suffice to induce cooperative phenomena.     

用蛋白电泳和高效凝胶排阻色谱法分析还原脲变性蛋白溶菌酶稀释复性过程的集聚体

本文利用蛋白电泳和高效凝胶排阻层析法分析了还原脲变性蛋白溶菌酶稀释复性过程中的集聚体。当用复性液稀释复性还原脲变性蛋白溶菌酶时,会迅速产生可观量的沉淀。沉淀和上清液的不连续十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)和高效凝胶排阻层析分析结果表明,还原脲变性蛋白溶菌酶在稀释复性过程中除了能够复性成天然态蛋白溶菌酶分子外,还会形成可溶的蛋白溶菌酶分子二聚体和三聚体,二聚体和三聚体主要是靠分子间二硫键的错配连接而成的;可溶的蛋白溶菌酶分子二聚体之间通过非共价键相互作用而形成集聚体沉淀,而可溶的三聚体溶菌酶分子则仍处于复性液上清液中。     

A Competing Hydrogen Bonding Pattern to Yield a Thermo‐Thickening Supramolecular Polymer

Introduction of competing interactions in the design of a supramolecular polymer (SP) creates pathway complexity. Ester–bis‐ureas contain both a strong bis‐urea sticker that is responsible for the build‐up of long rod‐like objects by hydrogen bonding and ester groups that can interfere with this main pattern in a subtle way. Spectroscopic (FTIR and CD), calorimetric (DSC), and scattering (SANS) techniques show that such ester–bis‐ureas self‐assemble into three competing rod‐like SPs. The previously unreported low‐temperature SP is stabilized by hydrogen bonds between the interfering ester groups and the urea moieties. It also features a weak macroscopic alignment of the rods. The other structures form isotropic dispersions of rods stabilized by the more classical urea‐urea hydrogen bonding pattern. The transition from the low‐temperature structure to the next occurs reversibly by heating and is accompanied by an increase in viscosity, a rare feature for solutions in hydrocarbons.     

Structure and activity transition of lysozyme on interacting with and releasing from polyelectrolyte with different hydrophobicity

The complexes of lysozyme with poly(isobutylene‐alt‐maleic acid) (PIMA) and poly(1‐tetradecene‐alt‐maleic acid) (PTMA) at pH 7.4 were characterized using static and dynamic light scattering. The electrostatic interaction of PIMA with lysozyme results in a loose complex structure, while the electrostatic and hydrophobic interactions between PTMA and lysozyme produce a compact complex structure. Lysozyme in PIMA complex particles remains a part of activity and structure analyzed by circular dichroism and substrate hydrolysis. However, lysozyme loses its tertiary structure and activity completely in PTMA complex. NaCl is more effective to dissociate PIMA–lysozyme complex by screening the electrostatic interaction, whereas GdHCl is more effective to dissociate PTMA–lysozyme complex by forming GdHCl–PTMA precipitates through extra hydrophobic interactions. In the release process, the denatured lysozyme molecules are able to avoid hydrophobic aggregation and fully regenerate their native structure and activity. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4681–4690, 2008     

Hexaaquanickel(II) bis[2‐carboxylato‐2‐(isothiouronium‐S‐ylmethyl)propane‐1,3‐diyl phosphate] hexahydrate

In the title complex, [Ni(H₂O)₆](C₆H₁₀N₂O₆PS)₂·6H₂O, the asymmetric unit consists of one‐half of an Ni atom (which lies on an inversion centre) with three coordinated water molecules, one complete 2‐carboxylato‐2‐(isothiouronium‐S‐ylmethyl)propane‐1,3‐diyl phosphate anion and three noncoordinated water molecules. The hexaaquanickel(II) cations have distorted octahedral coordination and are connected via water chains to form two‐dimensional supramolecular networks parallel to the ab plane. The phosphate ester anion is linked via N—H...O and O—H...O hydrogen bonds, thus creating various ring, dimer and chain hydrogen‐bonding patterns, and building up a second two‐dimensional supramolecular network parallel to the ab plane. The crystal structure is further stabilized by an intra‐ and interlayer hydrogen‐bond network. This work illustrates that a carboxylate with a caged phosphate ester can open its ring in the presence of dichloridotetrakis(thiourea)nickel, and the resulting polyfunctional anion can be used for constructing a complex hydrogen‐bonding scheme.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Structural Effects of Multiple Pathogenic Mutations Suggest a Model for the Initiation of Misfolding of the Prion Protein

A molecular understanding of the prion diseases requires delineation of the origin of misfolding of the prion protein (PrP). An understanding of how different disease‐linked mutations affect the structure and dynamics of native monomeric PrP can provide a clue about how misfolding commences. In this study, hydrogen–deuterium exchange mass spectrometry was used to show that several disease‐linked mutant variants, which are thermodynamically destabilized, share a common structural perturbation in their native states: helix 1 is destabilized to an extent that correlates well with the destabilization of the native protein. The mutant variants misfold and form oligomers faster than does the wild‐type protein, at rates that increase exponentially with the extent to which helix 1 is destabilized in the native protein. It appears, therefore, that the loss of helix 1 structure marks the beginning of PrP misfolding and oligomerization.     

N‐Acetyl‐l‐tyrosine methyl ester monohydrate at 293 and 123 K

The crystal structure of a protected l ‐tyrosine, namely N‐acetyl‐l ‐tyrosine methyl ester monohydrate, C₁₂H₁₅NO₄·H₂O, was determined at both 293 (2) and 123 (2) K. The structure exhibits a network of O—H...O and N—H...O hydrogen bonds, in which the water molecule plays a crucial role as an acceptor of one and a donor of two hydrogen bonds. Molecules of water and of the protected l ‐tyrosine form hydrogen‐bonded layers perpendicular to [001]. C—H...π interactions are observed in the hydrophobic regions of the structure. The structure is similar to that of N‐acetyl‐l ‐tyrosine ethyl ester monohydrate [Soriano‐García (1993). Acta Cryst. C 49 , 96–97].     

Triclinic and orthorhombic polymorphs of 2‐iodo‐4‐nitro­aniline: interplay of hydrogen bonds,nitro⃛I interactions and aromatic π–π‐stacking interactions

In the triclinic polymorph of 2‐iodo‐4‐nitro­aniline, C₆H₅IN₂O₂, space group P, the mol­ecules are linked by paired N—­H?O hydrogen bonds into C(8)[R(6)] chains of rings. These chains are linked into sheets by nitro?I interactions, and the sheets are pairwise linked by aromatic π–π‐stacking interactions. In the orthorhombic polymorph, space group Pbca, the mol­ecules are linked by single N—H?O hydrogen bonds into spiral C(8) chains; the chains are linked by nitro?O interactions into sheets, each of which is linked to its two immediate neighbours by aromatic π–π‐stacking inter­actions, so producing a continuous three‐dimensional ­structure.     

Stability and Unfolding Mechanism of the N‐terminal β‐Hairpin from [2Fe‐2S] Ferredoxin I by Molecular Dynamics Simulations

The stability and unfolding mechanism of the N‐terminal β‐hairpin of the [2Fe‐2S] ferredoxin I from the blue‐green alga Aphanothece sacrum in pure methanol, 40% (v/v) methanol‐water, and pure water systems were investigated by 10 ns molecular dynamics simulations under periodic boundary conditions. The β‐hairpin was mostly in its native‐like state in pure methanol, whereas it unfolds dramatically following the ‘zip‐up’ mechanism when it was placed in pure water. Both interstrand and inside‐turn hydrogen bonds account for the stability of the β‐hairpin in its native‐like conformation, whereas hydrophobic interactions among nonpolar side chains are responsible for maintaining its stable loop‐like intermediate structures in 40% (v/v) methanol‐water. Reducing solvent polarity seems to increase the stability of the β‐hairpin in its native‐like structure. Methanol is likely to mimic the partially hydrophobic environment around the N‐terminal β‐hairpin by the subsequent α‐helix.     

Synthesis of a 1,2,7,8-Tetraoxa-spiro[5.5]undecane

Synthesis of a new spiro organic peroxide is described. The peroxy bonds were incorporated into the substrate framework via an acid-catalyzed ketal exchange reaction using hydrogen peroxide as the source of peroxy linkage. The hydroperoxyl groups were then bonded at the OH ends via Hg（II）-induced electrophilic additions to the C-C double bonds, giving a novel sprio structure with one peroxy bond in each of the two six-membered rings. The ester functionalities in the side chains also make it possible to conduct further structural modifications.     

A hydrogen‐bonded chain of rings in 5‐amino‐1‐(4‐methoxybenzoyl)‐3‐methylpyrazole and a three‐dimensional hydrogen‐bonded framework in 5‐amino‐3‐methyl‐1‐(2‐nitrobenzoyl)pyrazole

The molecules of 5‐amino‐1‐(4‐methoxybenzoyl)‐3‐methylpyrazole, C₁₂H₁₃N₃O₂, (I), and 5‐amino‐3‐methyl‐1‐(2‐nitrobenzoyl)pyrazole, C₁₁H₁₀N₄O₃, (II), both contain intramolecular N—H...O hydrogen bonds. The molecules of (I) are linked into a chain of rings by a combination of N—H...N and N—H...π(arene) hydrogen bonds, while those of (II) are linked into a three‐dimensional framework structure by N—H...N and C—H...O hydrogen bonds.     

Triphenylsilanol–4,4′‐bipyridyl (4/1): the Z′ = 4 polymorph revisited

A fully ordered structure is reported for the polymorph of triphenylsilanol–4,4′‐bipyridyl (4/1), 4C₁₈H₁₆OSi·C₁₀H₈N₂, having Z′ = 4. The asymmetric unit contains four similar but distinct five‐molecule aggregates, in which the central bipyridyl unit is linked to two molecules of triphenylsilanol via O—H...N hydrogen bonds, with a further pair of triphenylsilanol molecules linked to the first pair via O—H...O hydrogen bonds. An extensive series of C—H...π(arene) hydrogen bonds links these aggregates into complex sheets. This structure is compared with a previously reported structure [Bowes, Ferguson, Lough & Glidewell (2003). Acta Cryst. B 59 , 277–286], which was based on an erroneous disordered structural model arising from a false direct‐methods solution with reference to a strong pseudo‐inversion centre.     

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

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.     

Three‐dimensional hydrogen‐bonded framework structures in flunarizinium nicotinate and flunarizinediium bis(4‐toluenesulfonate) dihydrate

The structures of two salts of flunarizine, namely 1‐bis[(4‐fluorophenyl)methyl]‐4‐[(2E)‐3‐phenylprop‐2‐en‐1‐yl]piperazine, C₂₆H₂₆F₂N₂, are reported. In flunarizinium nicotinate {systematic name: 4‐bis[(4‐fluorophenyl)methyl]‐1‐[(2E)‐3‐phenylprop‐2‐en‐1‐yl]piperazin‐1‐ium pyridine‐3‐carboxylate}, C₂₆H₂₇F₂N₂⁺·C₆H₄NO₂⁻, (I), the two ionic components are linked by a short charge‐assisted N—H...O hydrogen bond. The ion pairs are linked into a three‐dimensional framework structure by three independent C—H...O hydrogen bonds, augmented by C—H...π(arene) hydrogen bonds and an aromatic π–π stacking interaction. In flunarizinediium bis(4‐toluenesulfonate) dihydrate {systematic name: 1‐[bis(4‐fluorophenyl)methyl]‐4‐[(2E)‐3‐phenylprop‐2‐en‐1‐yl]piperazine‐1,4‐diium bis(4‐methylbenzenesulfonate) dihydrate}, C₂₆H₂₈F₂N₂²⁺·2C₇H₇O₃S⁻·2H₂O, (II), one of the anions is disordered over two sites with occupancies of 0.832 (6) and 0.168 (6). The five independent components are linked into ribbons by two independent N—H...O hydrogen bonds and four independent O—H...O hydrogen bonds, and these ribbons are linked to form a three‐dimensional framework by two independent C—H...O hydrogen bonds, but C—H...π(arene) hydrogen bonds and aromatic π–π stacking interactions are absent from the structure of (II). Comparisons are made with some related structures.     

Hydrogen bonding and π–π inter­actions in a laminar structure: benzene‐1,3‐dicarboxylic acid–4‐methyl­pyridine (1/2)

The title complex, C₈H₆O₄·2C₆H₇N, consists of two crystallographically independent 1:2 clusters of benzene‐1,3‐­dicarboxylic acid and 4‐methyl­pyridine. Each cluster, the components of which are linked by O—H⋯N hydrogen bonds, is almost planar by alignment of C—H⋯O hydrogen bonds. Herring‐bone ribbons of clusters are formed by other C—H⋯O hydrogen bonds, and these ribbons are further packed to form a laminar structure by π–π inter­actions.     

Methyl 2‐(4‐bromophenyl)‐1‐(5‐tert‐butyl‐1H‐pyrazol‐3‐yl)‐1H‐benzimidazole‐5‐carboxylate: a hydrogen‐bonded chain of edge‐fused centrosymmetric rings

In the title compound, C₂₂H₂₁BrN₄O₂, the imidazole and pyrazole rings are almost orthogonal to each other, but the ester unit is effectively coplanar with the adjacent aryl rings. The molecules are linked into a chain of edge‐fused centrosymmetric rings by a combination of N—H...O and C—H...π(arene) hydrogen bonds.     

A novel crystal form of metacetamol: the first example of a hydrated form

We report the crystal structure and crystallization conditions of a first hydrated form of metacetamol (a hemihydrate), C₈H₉NO₂·0.5H₂O. It crystallizes from metacetamol‐saturated 1:1 (v/v) water–ethanol solutions in a monoclinic structure (space group P2₁/n) and contains eight metacetamol and four water molecules per unit cell. The conformations of the molecules are the same as in polymorph II of metacetamol, which ensures the formation of hydrogen‐bonded dimers and R₂²(16) ring motifs in its crystal structure similar to those in polymorph II. Unlike in form II, however, these dimers in the hemihydrate are connected through water molecules into infinite hydrogen‐bonded molecular chains. Different chains are linked to each other by metacetamol–water and metacetamol–metacetamol hydrogen bonds, the latter type being also present in polymorph I. The overall noncovalent network of the hemihydrate is well developed and several types of hydrogen bonds are responsible for its formation.