Crystal structure of rat haem oxygenase-1 in complex with ferrous verdohaem: presence of a hydrogen-bond network on the distal side

2009 ◽  
Vol 419 (2) ◽  
pp. 339-345 ◽  
Author(s):  
Hideaki Sato ◽  
Masakazu Sugishima ◽  
Hiroshi Sakamoto ◽  
Yuichiro Higashimoto ◽  
Chizu Shimokawa ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Proton Donor ◽  
Water Molecules ◽  
Amino Acid Residues ◽  
Hydrogen Bond Network ◽  
Iron Chelate ◽  
Distal Side ◽  
Haem Oxygenase ◽  
Bond Network

HO (haem oxygenase) catalyses the degradation of haem to biliverdin, CO and ferrous iron via three successive oxygenation reactions, i.e. haem to α-hydroxyhaem, α-hydroxyhaem to α-verdohaem and α-verdohaem to ferric biliverdin–iron chelate. In the present study, we determined the crystal structure of ferrous α-verdohaem–rat HO-1 complex at 2.2 Å (1 Å=0.1 nm) resolution. The overall structure of the verdohaem complex was similar to that of the haem complex. Water or OH− was co-ordinated to the verdohaem iron as a distal ligand. A hydrogen-bond network consisting of water molecules and several amino acid residues was observed at the distal side of verdohaem. Such a hydrogen-bond network was conserved in the structures of rat HO-1 complexes with haem and with the ferric biliverdin–iron chelate. This hydrogen-bond network may act as a proton donor to form an activated oxygen intermediate, probably a ferric hydroperoxide species, in the degradation of α-verdohaem to ferric biliverdin–iron chelate similar to that seen in the first oxygenation step.

(NH4)[B3PO6(OH)3]·0.5H2O

2007 ◽  
Vol 63 (11) ◽  
pp. i185-i185 ◽  
Author(s):  
Wei Liu ◽  
Jingtai Zhao
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Ammonium Ions ◽  
One Dimensional ◽  
Bond Network ◽  
Solvothermal Conditions

The title compound, ammonium catena-[monoboro-monodihydrogendiborate-monohydrogenphosphate] hemihydrate, was obtained under solvothermal conditions using glycol as the solvent. The crystal structure is constructed of one-dimensional infinite borophosphate chains, which are interconnected by ammonium ions and water molecules via a complex hydrogen-bond network to form a three-dimensional structure. The water molecules of crystallization are disordered over inversion centres, and their H atoms were not located.

On the crystal structures and hydrogen bond patterns in proline pseudopolymorphs

2010 ◽  
Vol 25 (3) ◽  
pp. 235-240 ◽  
Author(s):  
Luis E. Seijas ◽  
Gerzon E. Delgado ◽  
Asiloé J. Mora ◽  
Andrew N. Fitch ◽  
Michela Brunelli
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Hydrogen Bond ◽  
Rietveld Method ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Bond Network ◽  
Hydrogen Bond Patterns

Amino acids often cocrystallize with water molecules, which make them pseudopolymorphs of their anhydrous forms. In this work, we discuss in detail the hydrogen bond patterns in anhydrous L-proline and DL-proline and its pseudopolymorphic forms: L-proline monohydrate and DL-proline monohydrate. For this propose, the crystal structure of L-proline anhydrous was determined from synchrotron X-ray powder diffraction data and refined using the Rietveld method. Special emphasis is given to the role played by the water molecule in the hydrogen bond network observed in the crystalline structures.

Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin

2012 ◽  
Vol 177 (2) ◽  
pp. 283-290 ◽  
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Yuko Nabeshima ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals Crystal Structures of the Ferrous Dioxygen Complex of Wild-type Cytochrome P450eryF and Its Mutants, A245S and A245T

2005 ◽  
Vol 280 (23) ◽  
pp. 22102-22107 ◽  
Author(s):  
Shingo Nagano ◽  
Jill R. Cupp-Vickery ◽  
Thomas L. Poulos
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Crystal Structures ◽  
Proton Donor ◽  
Initial Structure ◽  
Hydrogen Bond Network ◽  
Wild Type ◽  
In The Wild ◽  
Site Water ◽  
Bond Network

Cytochrome P450eryF (CYP107A) from Saccaropolyspora ertherea catalyzes the hydroxylation of 6-deoxyerythronolide B, one of the early steps in the biosynthesis of erythromycin. P450eryF has an alanine rather than the conserved threonine that participates in the activation of dioxygen (O2) in most other P450s. The initial structure of P450eryF (Cupp-Vickery, J. R., Han, O., Hutchinson, C. R., and Poulos, T. L. (1996) Nat. Struct. Biol. 3, 632–637) suggests that the substrate 5-OH replaces the missing threonine OH group and holds a key active site water molecule in position to donate protons to the iron-linked dioxygen, a critical step for the monooxygenase reaction. To probe the proton delivery system in P450eryF, we have solved crystal structures of ferrous wild-type and mutant (Fe2+) dioxygen-bound complexes. The catalytic water molecule that was postulated to provide protons to dioxygen is absent, although the substrate 5-OH group donates a hydrogen bond to the iron-linked dioxygen. The hydrogen bond network observed in the wild-type ferrous dioxygen complex, water 63-Glu360-Ser246-water 53-Ala241 carbonyl in the I-helix cleft, is proposed as the proton transfer pathway. Consistent with this view, the hydrogen bond network in the O2·A245S and O2 ·A245T mutants, which have decreased or no enzyme activity, was perturbed or disrupted, respectively. The mutant Thr245 side chain also perturbs the hydrogen bond between the substrate 5-OH and dioxygen ligand. Contrary to the previously proposed mechanism, these results support the direct involvement of the substrate in O2 activation but raise questions on the role water plays as a direct proton donor to the iron-linked dioxygen.

scholarly journals Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo Di Rienzo ◽  
Mattia Miotto ◽  
Leonardo Bò ◽  
Giancarlo Ruocco ◽  
Domenico Raimondo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Computational Method ◽  
Side Chain ◽  
Water Molecules ◽  
Amino Acid Side Chain ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Protein Environment

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

Anomalous proton conduction behavior across a nanoporous two-dimensional conjugated aromatic polymer membrane

2020 ◽  
Vol 22 (5) ◽  
pp. 2978-2985
Author(s):  
Le Shi ◽  
Zhixuan Ying ◽  
Ao Xu ◽  
Yonghong Cheng
Keyword(s):  
Hydrogen Bond ◽  
Atomic Structure ◽  
Proton Conduction ◽  
Polymer Membrane ◽  
Water Molecules ◽  
Two Dimensional ◽  
Hydrogen Bond Network ◽  
Aromatic Polymer ◽  
Conduction Behavior ◽  
Bond Network

The unique atomic structure of 2D-CAP can induce the formation of a stable local hydrogen bond network, thus restraining the motion of involved water molecules and impeding proton penetration.

L-2-Aminobutyric acid: two fully ordered polymorphs with Z′ = 4

2010 ◽  
Vol 66 (2) ◽  
pp. 253-259 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Diffraction Data ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Bond Network

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 α-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.

scholarly journals Energetics of the Proton Transfer Pathway for Tyrosine D in Photosystem II

2016 ◽  
Vol 69 (9) ◽  
pp. 991 ◽  
Author(s):  
Keisuke Saito ◽  
Naoki Sakashita ◽  
Hiroshi Ishikita
Keyword(s):  
Hydrogen Bond ◽  
Photosystem Ii ◽  
Proton Transfer ◽  
Electrostatic Interactions ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Redox States ◽  
Redox Active ◽  
Bond Network ◽  
Tyrosine D

The proton transfer pathway for redox active tyrosine D (TyrD) in photosystem II is a hydrogen-bond network that involves D2-Arg180 and a series of water molecules. Using quantum mechanical/molecular mechanical calculations, the detailed properties of the energetics and structural geometries were investigated. The potential-energy profile of all hydrogen bonds along the proton transfer pathway indicates that the overall proton transfer from TyrD is energetically downhill. D2-Arg180 plays a key role in the proton transfer pathway, providing a driving force for proton transfer, maintaining the hydrogen-bond network structure, stabilising P680•+, and thus deprotonating TyrD-OH to TyrD-O•. A hydrophobic environment near TyrD enhances the electrostatic interactions between TyrD and redox active groups, e.g. P680 and the catalytic Mn4CaO5 cluster: the redox states of those groups are linked with the protonation state of TyrD, i.e. release of the proton from TyrD. Thus, the proton transfer pathway from TyrD may ultimately contribute to the conversion of S0 into S1 in the dark in order to stabilise the Mn4CaO5 cluster when the photocycle is interrupted in S0.

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