scholarly journals Hydrogen Bond Network between Amino Acid Radical Intermediates on the Proton-Coupled Electron Transfer Pathway ofE. coliα2 Ribonucleotide Reductase

2014 ◽  
Vol 137 (1) ◽  
pp. 289-298 ◽  
Author(s):  
Thomas U. Nick ◽  
Wankyu Lee ◽  
Simone Koßmann ◽  
Frank Neese ◽  
JoAnne Stubbe ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Electron Transfer ◽  
Amino Acid ◽  
Ribonucleotide Reductase ◽  
Hydrogen Bond Network ◽  
Electron Transfer Pathway ◽  
Radical Intermediates ◽  
Proton Coupled Electron Transfer ◽  
Acid Radical ◽  
Bond Network

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.

Long-range proton-coupled electron transfer in the Escherichia coli class Ia ribonucleotide reductase

2017 ◽  
Vol 61 (2) ◽  
pp. 281-292 ◽  
Author(s):  
Steven Y. Reece ◽  
Mohammad R. Seyedsayamdost
Keyword(s):  
Escherichia Coli ◽  
Electron Transfer ◽  
Amino Acid ◽  
Long Range ◽  
Ribonucleotide Reductase ◽  
Unnatural Amino Acids ◽  
Radical Mechanism ◽  
Tyrosyl Radical ◽  
Proton Coupled Electron Transfer ◽  
Vis Spectroscopy

Escherichia coli class Ia ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to 2′-deoxynucleotides using a radical mechanism. Each turnover requires radical transfer from an assembled diferric tyrosyl radical (Y•) cofactor to the enzyme active site over 35 Å away. This unprecedented reaction occurs via an amino acid radical hopping pathway spanning two protein subunits. To study the mechanism of radical transport in RNR, a suite of biochemical approaches have been developed, such as site-directed incorporation of unnatural amino acids with altered electronic properties and photochemical generation of radical intermediates. The resulting variant RNRs have been investigated using a variety of time-resolved physical techniques, including transient absorption and stopped-flow UV-Vis spectroscopy, as well as rapid freeze-quench EPR, ENDOR, and PELDOR spectroscopic methods. The data suggest that radical transport occurs via proton-coupled electron transfer (PCET) and that the protein structure has evolved to manage the proton and electron transfer co-ordinates in order to prevent ‘off-pathway’ reactivity and build-up of oxidised intermediates. Thus, precise design and control over the factors that govern PCET is key to enabling reversible and long-range charge transport by amino acid radicals in RNR.

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 High-resolution crystal structures of the solubilized domain of porcine cytochromeb5

2015 ◽  
Vol 71 (7) ◽  
pp. 1572-1581 ◽  
Author(s):  
Yu Hirano ◽  
Shigenobu Kimura ◽  
Taro Tamada
Keyword(s):  
Hydrogen Bond ◽  
Electron Transfer ◽  
High Resolution ◽  
Crystal Structures ◽  
Axial Ligand ◽  
Amino Acid Residues ◽  
Hydrogen Bond Network ◽  
Porcine Liver ◽  
Crystal Forms ◽  
Bond Network

Mammalian microsomal cytochromeb5has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochromeb5from porcine liver were determined at sub-angstrom resolution (0.76–0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.

scholarly journals ENDOR Spectroscopy and DFT Calculations: Evidence for the Hydrogen-Bond Network Within α2 in the PCET of E. coli Ribonucleotide Reductase

2012 ◽  
Vol 134 (42) ◽  
pp. 17661-17670 ◽  
Author(s):  
Tomislav Argirević ◽  
Christoph Riplinger ◽  
JoAnne Stubbe ◽  
Frank Neese ◽  
Marina Bennati
Keyword(s):  
Hydrogen Bond ◽  
Dft Calculations ◽  
Ribonucleotide Reductase ◽  
Hydrogen Bond Network ◽  
E Coli ◽  
Endor Spectroscopy ◽  
Bond Network

scholarly journals Structures of bovine cytochrome oxidase reveal proton active transports

2014 ◽  
Vol 70 (a1) ◽  
pp. C1505-C1505
Author(s):  
Naomine Yano ◽  
Kyoko Shinzawa-Itoh ◽  
Atsuhiro Shimada ◽  
Shuhei Takemutra ◽  
Takako Kawahara ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Electron Transfer ◽  
Cytochrome C ◽  
Water Channel ◽  
Proton Pumping ◽  
Hydrogen Bond Network ◽  
O2 Reduction ◽  
Bond Network ◽  
Full Occupancy ◽  
O2 Binding

Bovine cytochrome c oxidase (CcO) pumps four protons in each catalytic cycle through H-pathway including a hydrogen-bond network and a water channel in tandem. Protons, transferred through the water-channel from the negative side of mitochondrial inner membrane into the hydrogen-bond network, are pumped to the positive side of the membrane electrostatically by net positive charges on a heme (heme a) iron created upon electron transfer to the O2 reduction site. For blockage of backward proton leak from the hydrogen-bond network, which determines the proton-pumping direction, the water channel is closed after O2 binding to initiate proton-pump. Thus, four protons must be collected in the hydrogen-bond network before O2 binding. The X-ray structural analyses of the oxidized/reduced CcO at 1.5/1.6 Å resolution reveal a large cluster composed of ~21 water molecules and a Mg2+ site including Glu198 (Subunit II) bridging CuA and Mg2+. The cluster of the oxidized state have 20 water sites with full occupancy and two sites with partial occupies of water, while that of the reduced state have 19 water sites with full occupancy and 3 sites with partial occupancies. The carboxyl group of Glu198 changes its coordination structure to Mg2+ upon the reduction of the active centers. The cluster is tightly sealed sterically against proton exchanges with the cluster outside except for a short hydrogen-bond network connecting the cluster with H-pathway. Five proton-acceptable groups hydrogen-bonded with the cluster suggest sufficient storage capacity for four proton equivalents. The redox-coupled structural changes in the electron transfer pathway from CuA, the initial electron acceptor from cytochrome c, to heme a suggest redox-driven effective proton donations from the cluster to H-pathway, facilitated by Glu198. These results indicate that the cluster is a crucial element of the proton-pumping system of bovine CcO.

Sign in / Sign up

Export Citation Format

Share Document