scholarly journals Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tomoaki Kawakami ◽  
Long-Jiang Yu ◽  
Tai Liang ◽  
Koudai Okazaki ◽  
Michael T. Madigan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrophobic Interactions ◽  
Electron Tunneling ◽  
Protein Complexes ◽  
Integral Membrane Protein ◽  
Molar Ratio ◽  
Binding Interface ◽  
Close Proximity ◽  
Sulfur Protein ◽  
Tetraheme Cytochrome

AbstractPhotosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems.

scholarly journals Crystallographic Studies of Human MitoNEET

2007 ◽  
Vol 282 (46) ◽  
pp. 33242-33246 ◽  
Author(s):  
Xiaowei Hou ◽  
Rujuan Liu ◽  
Stuart Ross ◽  
Eric J. Smart ◽  
Haining Zhu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mitochondrial Membrane ◽  
Hydrophobic Interactions ◽  
Water Molecules ◽  
Outer Mitochondrial Membrane ◽  
Protein Fold ◽  
Close Proximity ◽  
Diabetes Drug ◽  
Mitochondrial Membrane Protein ◽  
Novel Protein

MitoNEET was identified as an outer mitochondrial membrane protein that can potentially bind the anti-diabetes drug pioglitazone. The crystal structure of the cytoplasmic mitoNEET (residues 33–108) is determined in this study. The structure presents a novel protein fold and contains a [2Fe-2S] cluster-binding domain. The [2Fe-2S] cluster is coordinated to the protein by Cys-72, Cys-74, Cys-83, and His-87 residues. This coordination is also novel compared with the traditional [2Fe-2S] cluster coordinated by four cysteines or two cysteines and two histidines. The cytoplasmic mitoNEET forms homodimers in solution and in crystal. The dimerization is mainly mediated by hydrophobic interactions as well as hydrogen bonds coordinated by two water molecules binding at the interface. His-87 residue, which plays an important role in the coordination of the [2Fe-2S] cluster, is exposed to the solvent on the dimer surface. It is proposed that mitoNEET dimer may interact with other proteins via the surface residues in close proximity to the [2Fe-2S] cluster.

scholarly journals Very Few Substitutions in a Germ Line Antibody Are Required To Initiate Significant Domain Exchange

2010 ◽  
Vol 84 (20) ◽  
pp. 10700-10707 ◽  
Author(s):  
Michael Huber ◽  
Khoa M. Le ◽  
Katie J. Doores ◽  
Zara Fulton ◽  
Robyn L. Stanfield ◽  
...  
Keyword(s):  
Germ Line ◽  
Hydrophobic Interactions ◽  
Variable Region ◽  
Binding Interface ◽  
Close Proximity ◽  
Glycoprotein Gp120 ◽  
Human Igg1 ◽  
Anti Hiv ◽  
Conventional Antibody

ABSTRACT 2G12 is a broadly neutralizing anti-HIV-1 monoclonal human IgG1 antibody reactive with a high-mannose glycan cluster on the surface of glycoprotein gp120. A key feature of this very highly mutated antibody is domain exchange of the heavy-chain variable region (VH) with the VH of the adjacent Fab of the same immunoglobulin, which assembles a multivalent binding interface composed of two primary binding sites in close proximity. A non-germ line-encoded proline in the elbow between VH and CH1 and an extensive network of hydrophobic interactions in the VH/VH′ interface have been proposed to be crucial for domain exchange. To investigate the origins of domain exchange, a germ line version of 2G12 that behaves as a conventional antibody was engineered. Substitution of 5 to 7 residues for those of the wild type produced a significant fraction of domain-exchanged molecules, with no evidence of equilibrium between domain-exchanged and conventional forms. Two substitutions not previously implicated, AH14 and EH75, are the most crucial for domain exchange, together with IH19 at the VH/VH′ interface and PH113 in the elbow region. Structural modeling gave clues as to why these residues are essential for domain exchange. The demonstration that domain exchange can be initiated by a small number of substitutions in a germ line antibody suggests that the evolution of a domain-exchanged antibody response in vivo may be more readily achieved than considered to date.

scholarly journals Crystal structure of Pistol, a class of self-cleaving ribozyme

2017 ◽  
Vol 114 (5) ◽  
pp. 1021-1026 ◽  
Author(s):  
Laura A. Nguyen ◽  
Jimin Wang ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Nonbridging Oxygen ◽  
Close Proximity ◽  
Domains Of Life ◽  
Guanine Base ◽  
A Minor

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2′-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5′ leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

Effect of Complexing Agent on Morphology and Crystal Structure of La1-xCexCoO3 (x=0, 0.2, and 0.4) Perovskite-Type Mixed Oxides Catalyst Prepared by Sol-Gel Method

2010 ◽  
Vol 658 ◽  
pp. 29-32 ◽  
Author(s):  
Kanit Soongprasit ◽  
Duangdao Aht-Ong ◽  
Viboon Sricharoenchaikul ◽  
Duangduen Atong
Keyword(s):  
Crystal Structure ◽  
Polyvinyl Alcohol ◽  
Mixed Oxides ◽  
Sol Gel ◽  
Value Added ◽  
Molar Ratio ◽  
Complexing Agent ◽  
Nitrate Hexahydrate ◽  
Mixed Oxide Catalysts ◽  
Perovskite Type

. La1-xCexCoO3 (x=0, 0.2, and 0.4) perovskite-type mixed oxides using polyvinyl alcohol (PVA) as complexing agent at two molar ratio of metal ion to PVA (1:1 and 1:2) were successfully prepared by sol-gel process. The precursor included lanthanum (II) nitrate hexahydrate, cerium (II) nitrate hexahydrate, and cobalt (II) nitrate hexahydrate where polyvinyl alcohol was added as complexing agent. The suitable condition of Cerium (Ce) substitution and PVA molar ratio were established for further application in hydrocarbon conversion to high value added products. TGA thermogram of as-prepared precursor showed that PVA absolutely decomposed at temperature higher than 500°C. XRD patterns of calcined catalyst showed both LaCoO3 rhombohedral and CeO2 cubic structures that confirmed the formation of mixed crystal structure. Nevertheless, Co3O4 slightly appeared with low peak intensity which came from the oxidation reaction of as-prepared catalyst during calcinations. XRD showed that PVA did not effect to crystal structure of synthesized catalyst. Higher PVA content added in the precursor cause the reduction of crystal growth of catalyst in calcinations step. In contrast, morphology of catalyst is directly related with PVA content such that the spongy and sheet-like structure were formed with increasing PVA content which prevented the agglomeration of particles. The results showed that PVA content play an important role in morphology of perovskite-type mixed oxide catalysts but did not affected to their crystal structures.

scholarly journals Crystal structure of the new hybrid material bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate

2015 ◽  
Vol 71 (11) ◽  
pp. 1384-1387
Author(s):  
Marwen Chouri ◽  
Habib Boughzala
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Molar Ratio ◽  
Water Molecules ◽  
Site Symmetry ◽  
Two Dimensional ◽  
Slow Evaporation ◽  
Solution Ph

The title compound bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate, (C6H14N2)2[Bi2Cl10]·2H2O, was obtained by slow evaporation at room temperature of a hydrochloric aqueous solution (pH = 1) containing bismuth(III) nitrate and 1,4-diazabicyclo[2.2.2]octane (DABCO) in a 1:2 molar ratio. The structure displays a two-dimensional arrangement parallel to (100) of isolated [Bi2Cl10]4−bioctahedra (site symmetry -1) separated by layers of organic 1,4-diazoniabicyclo[2.2.2]octane dications [(DABCOH2)2+] and water molecules. O—H...Cl, N—H...O and N—H...Cl hydrogen bonds lead to additional cohesion of the structure.

Synthese und Kristallstruktur des 2.4-Di-terf-butoxy-2,4-di-terfbutylcyclodisilazans / Synthesis and Crystal Structure of 2.4-Di-terf-butoxy-2,4-di-terrbutylcyclodisilazane

1995 ◽  
Vol 50 (5) ◽  
pp. 844-847 ◽  
Author(s):  
Sven Dielkus ◽  
Dorothee Großkopf ◽  
Regine Herbst-Irmer ◽  
Uwe Klingebiel
Keyword(s):  
Crystal Structure ◽  
Molar Ratio ◽  
Synthesis And Crystal Structure ◽  
Lithium Derivative ◽  
Nitrogen Ring

Abstract Me3CSiHal3 react with LiOCMe3 to give Me3CO(Me3C)SiHal2 (HaI = F (1), Cl (3)). The aminofluorosilane, Me3CO(Me3C)SiFNH2 (2), is formed in the reaction of 1 with LiNH2. The diaminosilane Me3CO(Me3C)Si(NH2)2 (4) is obtained from the reaction of 2 with ammonia. 4 reacts with LiC4H9 to give the lithium derivative Me3CO(Me3C)Si(NHLi)NH2 (5). In a molar ratio 1:1 the reaction of 5 and 1 leads to the formation of the 1-amino-3-fluoro-disilazane Me3CO(Me3C)SiF- NH - SiNH2(CMe3)OCMe3 (6) and in a molar ratio 2:1 to the four-membered silicon nitrogen ring [Me3CO(M e3C)Si-NH]2 (7). The crystal structure of 7 was determined.

scholarly journals Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation

2018 ◽  
Vol 116 (2) ◽  
pp. 528-533 ◽  
Author(s):  
Ivan B. Lomakin ◽  
Sergey E. Dmitriev ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Translation Initiation ◽  
Zinc Ion ◽  
Zinc Binding ◽  
Ion Binding ◽  
Binding Interface ◽  
Zinc Binding Site ◽  
Reading Frames ◽  
Zinc Ion Binding

The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR’s MCT-1–binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

On the dimorphism of Pr6Mo10O39

2017 ◽  
Vol 72 (11) ◽  
pp. 765-774
Author(s):  
Daniel Rudolph ◽  
Sonja Laufer ◽  
Ingo Hartenbach
Keyword(s):  
Crystal Structure ◽  
Thermal Decomposition ◽  
Single Crystals ◽  
Main Product ◽  
Molar Ratio ◽  
Coordination Environment ◽  
Space Group ◽  
Coordination Numbers ◽  
Dense Modification

AbstractAttempts to synthesize Pr4Mo7O27 using Pr, Pr6O11 and MoO3 in a molar ratio of 8:6:77 led to a main product of scheelite-type Pr0.667[MoO4] and few single crystals of the triclinic A-type Pr6Mo10O39. The latter crystallizes in space group P1̅ (a=945.25(1), b=1058.49(2), c=1815.16(3) pm; α=104.149(1), β=95.220(1), γ=102.617(1)°, Z=2). Its crystal structure comprises six crystallographically independent Pr3+ cations, eight tetrahedral [MoO4]2− units, and one [Mo2O7]2− entity. The cations display coordination numbers of seven (1×) and eight (5×), while the [MoO4]2− tetrahedra are surrounded by five Pr3+ cations each. The [Mo2O7]2− anions exhibit a coordination environment of seven Pr3+ cations. The attempt to synthesize PrF[MoO4] using PrOF (from in situ thermal decomposition of PrF[CO3]) as reagent did not lead to the desired product but to monoclinic B-type Pr6Mo10O39. This slightly less dense modification compared to its triclinic analogue crystallizes in space group C2/c (a=1247.93(3), b=1989.68(6), c=1392.52 (4) pm, β=100.505(2)°, Z=4) with three crystallographically independent Pr3+ cations, four [MoO4]2− tetrahedra, and again one [Mo2O7]2− unit in the crystal structure. Thus, both Pr6Mo10O39 modifications are better described with the structured formula Pr6[MoO4]8[Mo2O7]. The coordination numbers around the Pr3+ cations are seven (1×) and eight (2×) while all four [MoO4]2− anions are again surrounded by five Pr3+ cations each. Six of the latter represent the coordination environment around the [Mo2O7]2− entities. Besides the thorough comparison of the crystal structures single crystal Raman spectra were recorded for both Pr6Mo10O39 phases.

scholarly journals Crystal structure of a nickel compound comprising two nickel(II) complexes with different ligand environments: [Ni(tren)(H2O)2][Ni(H2O)6](SO4)2

2020 ◽  
Vol 76 (3) ◽  
pp. 314-317
Author(s):  
Karilys González Nieves ◽  
Dalice M. Piñero Cruz
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
Molar Ratio ◽  
Water Molecules ◽  
Nickel Compound ◽  
Counter Anion ◽  
Cationic Complex ◽  
Coordinated Water ◽  
Co Precipitation ◽  
Metal Ligand

The title compound, diaqua[tris(2-aminoethyl)amine]nickel(II) hexaaquanickel(II) bis(sulfate), [Ni(C6H18N4)(H2O)2][Ni(H2O)6](SO4)2 or [Ni(tren)(H2O)2][Ni(H2O)6](SO4)2, consists of two octahedral nickel complexes within the same unit cell. These metal complexes are formed from the reaction of [Ni(H2O)6](SO4) and the ligand tris(2-aminoethyl)amine (tren). The crystals of the title compound are purple, different from those of the starting complex [Ni(H2O)6](SO4), which are turquoise. The reaction was performed both in a 1:1 and 1:2 metal–ligand molar ratio, always yielding the co-precipitation of the two types of crystals. The asymmetric unit of the title compound, which crystallizes in the space group Pnma, consists of two half NiII complexes and a sulfate counter-anion. The mononuclear cationic complex [Ni(tren)(H2O)2]2+ comprises an Ni ion, the tren ligand and two water molecules, while the mononuclear complex [Ni(H2O)6]2+ consists of another Ni ion surrounded by six coordinated water molecules. The [Ni(tren)(H2O)2] and [Ni(H2O)6] subunits are connected to the SO4 2− counter-anions through hydrogen bonding, thus consolidating the crystal structure.

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