scholarly journals Structure of plant PSI-plastocyanin complex reveals strong hydrophobic interactions

2021 ◽  
Author(s):  
Ido Caspy ◽  
Mariia Fadeeva ◽  
Sebastian Kuhlgert ◽  
Anna Borovikova-Sheinker ◽  
Daniel Klaiman ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Genetic Engineering ◽  
Hydrophobic Interactions ◽  
Structural Data ◽  
Oxygenic Photosynthesis ◽  
Water Molecules ◽  
Major Step ◽  
Ferredoxin Oxidoreductase ◽  
Complex Forms ◽  
Oxidized Pc

AbstractPhotosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB / Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared to reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover.One Sentence SummaryGenetic engineering, kinetics and cryo-EM structural data reveal a mechanism in a major step of oxygenic photosynthesis

scholarly journals Structure of plant Photosystem I-plastocyanin complex reveals strong hydrophobic interactions

2021 ◽  
Author(s):  
Ido Caspy ◽  
Mariia Fadeeva ◽  
Sebastian Kuhlgert ◽  
Anna Borovikova-Sheinker ◽  
Daniel Klaiman ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Genetic Engineering ◽  
Photosystem I ◽  
Ternary Complex ◽  
Hydrophobic Interactions ◽  
Structural Data ◽  
Water Molecules ◽  
Ferredoxin Oxidoreductase ◽  
Complex Forms ◽  
Oxidized Pc

Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB / Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared to reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover.

scholarly journals Jumping Ahead with Sleeping Beauty: Mechanistic Insights into Cut-and-Paste Transposition

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 76
Author(s):  
Matthias T. Ochmann ◽  
Zoltán Ivics
Keyword(s):  
Genetic Engineering ◽  
Structural Data ◽  
Sleeping Beauty ◽  
Preclinical Studies ◽  
Gene Vector ◽  
Functional Information ◽  
Vector Systems ◽  
Novel Variants ◽  
Insight Into ◽  
Cellular Genome

Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure–function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.

scholarly journals Mediator-assisted water oxidation by the ruthenium “blue dimer” cis,cis-[(bpy)2(H2O)RuORu(OH2)(bpy)2]4+

2008 ◽  
Vol 105 (46) ◽  
pp. 17632-17635 ◽  
Author(s):  
Javier J. Concepcion ◽  
Jonah W. Jurss ◽  
Joseph L. Templeton ◽  
Thomas J. Meyer
Keyword(s):  
Carbon Dioxide ◽  
Electron Transfer ◽  
Renewable Energy ◽  
Photosystem Ii ◽  
Water Splitting ◽  
Water Oxidation ◽  
Oxygenic Photosynthesis ◽  
Reduced Water ◽  
Insight Into ◽  
Recent Insight

Light-driven water oxidation occurs in oxygenic photosynthesis in photosystem II and provides redox equivalents directed to photosystem I, in which carbon dioxide is reduced. Water oxidation is also essential in artificial photosynthesis and solar fuel-forming reactions, such as water splitting into hydrogen and oxygen (2 H2O + 4 hν → O2 + 2 H2) or water reduction of CO2 to methanol (2 H2O + CO2 + 6 hν → CH3OH + 3/2 O2), or hydrocarbons, which could provide clean, renewable energy. The “blue ruthenium dimer,” cis,cis-[(bpy)2(H2O)RuIIIORuIII(OH2)(bpy)2]4+, was the first well characterized molecule to catalyze water oxidation. On the basis of recent insight into the mechanism, we have devised a strategy for enhancing catalytic rates by using kinetically facile electron-transfer mediators. Rate enhancements by factors of up to ≈30 have been obtained, and preliminary electrochemical experiments have demonstrated that mediator-assisted electrocatalytic water oxidation is also attainable.

scholarly journals Correlating kinetic and structural data on ubiquinone binding and reduction by respiratory complex I

2017 ◽  
Vol 114 (48) ◽  
pp. 12737-12742 ◽  
Author(s):  
Justin G. Fedor ◽  
Andrew J. Y. Jones ◽  
Andrea Di Luca ◽  
Ville R. I. Kaila ◽  
Judy Hirst
Keyword(s):  
Electron Transfer ◽  
Complex I ◽  
Mammalian Cells ◽  
Membrane Surface ◽  
Proton Translocation ◽  
Structural Data ◽  
Nadh:Ubiquinone Oxidoreductase ◽  
Respiratory Complex ◽  
Respiratory Complex I ◽  
Ubiquinone 10

Respiratory complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in mammalian cells, powers ATP synthesis by using the energy from electron transfer from NADH to ubiquinone-10 to drive protons across the energy-transducing mitochondrial inner membrane. Ubiquinone-10 is extremely hydrophobic, but in complex I the binding site for its redox-active quinone headgroup is ∼20 Å above the membrane surface. Structural data suggest it accesses the site by a narrow channel, long enough to accommodate almost all of its ∼50-Å isoprenoid chain. However, how ubiquinone/ubiquinol exchange occurs on catalytically relevant timescales, and whether binding/dissociation events are involved in coupling electron transfer to proton translocation, are unknown. Here, we use proteoliposomes containing complex I, together with a quinol oxidase, to determine the kinetics of complex I catalysis with ubiquinones of varying isoprenoid chain length, from 1 to 10 units. We interpret our results using structural data, which show the hydrophobic channel is interrupted by a highly charged region at isoprenoids 4–7. We demonstrate that ubiquinol-10 dissociation is not rate determining and deduce that ubiquinone-10 has both the highest binding affinity and the fastest binding rate. We propose that the charged region and chain directionality assist product dissociation, and that isoprenoid stepping ensures short transit times. These properties of the channel do not benefit the exhange of short-chain quinones, for which product dissociation may become rate limiting. Thus, we discuss how the long channel does not hinder catalysis under physiological conditions and the possible roles of ubiquinone/ubiquinol binding/dissociation in energy conversion.

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.

The Conductance of Tetraalkylammonium Iodides in Aqueous Proline and Hydroxyproline Solutions

1979 ◽  
Vol 34 (10) ◽  
pp. 1225-1229
Author(s):  
B. Sesta ◽  
C. La Mesa ◽  
C. Cantale ◽  
M. Vincenzini
Keyword(s):  
Dielectric Constant ◽  
Electrostatic Interactions ◽  
Hydrophobic Interactions ◽  
Molecular Water ◽  
Water Molecules ◽  
Destructive Effect ◽  
Iodide Ions ◽  
Tetraalkylammonium Ions ◽  
Equivalent Conductance ◽  
Tetrabutylammonium Iodide

Abstract The density, viscosity and dielectric constant of aqueous proline and hydroxyproline solutions have been determined at 25 °C. The results appear to indicate that the two aminoacids have a destructive effect on the molecular water aggregates. The equivalent conductance of tetramethylammonium iodide and tetrabutylammonium iodide in aqueous proline and hydroxyproline solutions has been measured at 25°C. The aminoacids increase the viscosity of the solutions and decrease the limiting equivalent conductance of the two electrolytes. Electrostatic interactions of the iodide ions with the water molecules and hydrophobic interactions of the tetraalkylammonium ions with the aminoacids also seem to affect the conductometric behaviour of the electrolytes.

scholarly journals Thermodynamics of semi-specific ligand recognition: the binding of dipeptides to the E.coli dipeptide binding protein DppA

2021 ◽  
Author(s):  
Mohamad K. M. Zainol ◽  
Robert J. C. Linforth ◽  
Donald J. Winzor ◽  
David J. Scott
Keyword(s):  
Hydrophobic Interactions ◽  
Chemical Reactivity ◽  
Water Structure ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
Water Molecules ◽  
Aqueous Environment ◽  
Arginine Residues ◽  
Structure Flexibility

AbstractThis investigation of the temperature dependence of DppA interactions with a subset of three dipeptides (AA. AF and FA) by isothermal titration calorimetry has revealed the negative heat capacity ($$\Delta {C}_{p}^{o}$$ Δ C p o ) that is a characteristic of hydrophobic interactions. The observation of enthalpy–entropy compensation is interpreted in terms of the increased structuring of water molecules trapped in a hydrophobic environment, the enthalpic energy gain from which is automatically countered by the entropy decrease associated with consequent loss of water structure flexibility. Specificity for dipeptides stems from appropriate spacing of designated DppA aspartate and arginine residues for electrostatic interaction with the terminal amino and carboxyl groups of a dipeptide, after which the binding pocket closes to become completely isolated from the aqueous environment. Any differences in chemical reactivity of the dipeptide sidechains are thereby modulated by their occurrence in a hydrophobic environment where changes in the structural state of entrapped water molecules give rise to the phenomenon of enthalpy–entropy compensation. The consequent minimization of differences in the value of ΔG0 for all DppA–dipeptide interactions thus provides thermodynamic insight into the biological role of DppA as a transporter of all dipeptides across the periplasmic membrane.

scholarly journals Robust recognition and exploratory analysis of crystal structures via Bayesian deep learning

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Andreas Leitherer ◽  
Angelo Ziletti ◽  
Luca M. Ghiringhelli
Keyword(s):  
Deep Learning ◽  
Crystal Structures ◽  
Metallic Nanoparticles ◽  
Materials Science ◽  
Structural Data ◽  
Structure Identification ◽  
Science Data ◽  
Major Step ◽  
Geometrical Properties ◽  
Uncertainty Estimates

AbstractDue to their ability to recognize complex patterns, neural networks can drive a paradigm shift in the analysis of materials science data. Here, we introduce ARISE, a crystal-structure identification method based on Bayesian deep learning. As a major step forward, ARISE is robust to structural noise and can treat more than 100 crystal structures, a number that can be extended on demand. While being trained on ideal structures only, ARISE correctly characterizes strongly perturbed single- and polycrystalline systems, from both synthetic and experimental resources. The probabilistic nature of the Bayesian-deep-learning model allows to obtain principled uncertainty estimates, which are found to be correlated with crystalline order of metallic nanoparticles in electron tomography experiments. Applying unsupervised learning to the internal neural-network representations reveals grain boundaries and (unapparent) structural regions sharing easily interpretable geometrical properties. This work enables the hitherto hindered analysis of noisy atomic structural data from computations or experiments.

scholarly journals X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein

2019 ◽  
Vol 75 (9) ◽  
pp. 841-851 ◽  
Author(s):  
Hiromi Yoshida ◽  
Katsuhiro Kojima ◽  
Masaki Shiota ◽  
Keiichi Yoshimatsu ◽  
Tomohiko Yamazaki ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Disulfide Bonds ◽  
Hydrophobic Interactions ◽  
Direct Electron Transfer ◽  
Glucose Dehydrogenase ◽  
Catalytic Subunit ◽  
Effective Electron ◽  
Α Subunit ◽  
X Ray ◽  
Membrane Bound

The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe–4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.

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