scholarly journals Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases

2016 ◽  
Vol 44 (1) ◽  
pp. 315-328 ◽  
Author(s):  
Lindsey A. Flanagan ◽  
Alison Parkin
Keyword(s):  
Active Site ◽  
Precious Metal ◽  
Active Sites ◽  
Review Paper ◽  
Spectroscopic Studies ◽  
Electrochemical Studies ◽  
Control Centre ◽  
Catalytic Active Sites ◽  
Membrane Bound ◽  
Insight Into

Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H2, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O2 tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH.

Spectroscopic studies on two-iron ferredoxins

1974 ◽  
Vol 7 (4) ◽  
pp. 443-504 ◽  
Author(s):  
R. H. Sands ◽  
W. R. Dunham
Keyword(s):  
High Spin ◽  
Active Site ◽  
Active Sites ◽  
Spectroscopic Studies ◽  
Transport Proteins ◽  
Distorted Tetrahedron ◽  
X Ray ◽  
Iron Proteins ◽  
Electron Transport Proteins ◽  
Reduced State

The application of magnetic resonance techniques to biological systems has permitted a detailed study of the nature of the active sites of many proteins that had not been possible previously. Among these is the whole class of iron—sulphur proteins which have been implicated as electron transport proteins in a variety of fundamental processes: photosynthesis, hydroxylation and nitrogen fixation to name but a few.The single-iron proteins in this class, the rubredoxins, have been studied extensively by chemical, spectroscopic and X-ray crystallographic techniques (Lovenberg, 1973), and the active site is composed of a single iron atom bound in a distorted tetrahedron of cysteine sulphur ligands. The iron is high-spin ferric in the oxidized state and high-spin ferrous in the reduced state. This structure is shown in Fig. I (α).

scholarly journals Stoichiometric active site modification observed by alkali ion titrations of Sn-Beta

2019 ◽  
Vol 9 (16) ◽  
pp. 4339-4346 ◽  
Author(s):  
Samuel G. Elliot ◽  
Irene Tosi ◽  
Sebastian Meier ◽  
Juan S. Martinez-Espin ◽  
Søren Tolborg ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Catalytic Properties ◽  
Alkali Ions ◽  
Functional Assays ◽  
Insight Into ◽  
Alkali Ion

Titrations and functional assays are combined to gain insight into the stoichiometric correlations for alkali ions and the tin active sites in Sn-Beta, and show that three different states with distinct catalytic properties exist.

scholarly journals Revealing the Active Site of Gold Nanoparticles for the Peroxidase-Like Activity: The Determination of Surface Accessibility

Catalysts ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 517 ◽  
Author(s):  
Ching-Ping Liu ◽  
Kuan-Chung Chen ◽  
Ching-Feng Su ◽  
Po-Yen Yu ◽  
Po-Wei Lee
Keyword(s):  
Gold Nanoparticles ◽  
Active Site ◽  
Photoelectron Spectroscopy ◽  
Active Sites ◽  
Inhibition Mechanism ◽  
Surface Accessibility ◽  
Peroxidase Mimics ◽  
Catalytic Active Sites ◽  
Surface Modified ◽  
First Time

Despite the fact that the enzyme-like activities of nanozymes (i.e., nanomaterial-based artificial enzymes) are highly associated with their surface properties, little is known about the catalytic active sites. Here, we used the sulfide ion (S2−)-induced inhibition of peroxidase-like activity to explore active sites of gold nanoparticles (AuNPs). The inhibition mechanism was based on the interaction with Au(I) to form Au2S, implying that the Au(I) might be the active site of AuNPs for the peroxidase-like activity. X-ray photoelectron spectroscopy (XPS) analysis showed that the content of Au(I) on the surface of AuNPs significantly decreased after the addition of S2−, which might be contributed to the more covalent Au–S bond in the formation of Au2S. Importantly, the variations of Au(I) with and without the addition of S2− for different surface-capped AuNPs were in good accordance with their corresponding peroxidase-like activities. These results confirmed that the accessible Au(I) on the surface was the main requisite for the peroxidase-like activity of AuNPs for the first time. In addition, the use of S2− could assist to determine available active sites for different surface modified AuNPs. This work not only provides a new method to evaluate the surface accessibility of colloidal AuNPs but also gains insight on the design of efficient AuNP-based peroxidase mimics.

scholarly journals Structural and functional insight into pan-endopeptidase inhibition by α2-macroglobulins

2017 ◽  
Vol 398 (9) ◽  
pp. 975-994 ◽  
Author(s):  
Theodoros Goulas ◽  
Irene Garcia-Ferrer ◽  
Aniebrys Marrero ◽  
Laura Marino-Puertas ◽  
Stephane Duquerroy ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Large Cage ◽  
Covalent Linkage ◽  
Conformational Rearrangement ◽  
Bait Region ◽  
Active Site Cleft ◽  
Structural Details ◽  
Physical Entrapment ◽  
Insight Into

Abstract Peptidases must be exquisitely regulated to prevent erroneous cleavage and one control is provided by protein inhibitors. These are usually specific for particular peptidases or families and sterically block the active-site cleft of target enzymes using lock-and-key mechanisms. In contrast, members of the +1400-residue multi-domain α2-macroglobulin inhibitor family (α2Ms) are directed against a broad spectrum of endopeptidases of disparate specificities and catalytic types, and they inhibit their targets without disturbing their active sites. This is achieved by irreversible trap mechanisms resulting from large conformational rearrangement upon cleavage in a promiscuous bait region through the prey endopeptidase. After decades of research, high-resolution structural details of these mechanisms have begun to emerge for tetrameric and monomeric α2Ms, which use ‘Venus-flytrap’ and ‘snap-trap’ mechanisms, respectively. In the former, represented by archetypal human α2M, inhibition is exerted through physical entrapment in a large cage, in which preys are still active against small substrates and inhibitors that can enter the cage through several apertures. In the latter, represented by a bacterial α2M from Escherichia coli, covalent linkage and steric hindrance of the prey inhibit activity, but only against very large substrates.

scholarly journals A pyridinic Fe-N4 macrocycle models the active sites in Fe/N-doped carbon electrocatalysts

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Travis Marshall-Roth ◽  
Nicole J. Libretto ◽  
Alexandra T. Wrobel ◽  
Kevin J. Anderton ◽  
Michael L. Pegis ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Catalytic Properties ◽  
Molecular Model ◽  
Reduction Reaction ◽  
Electrochemical Studies ◽  
Onset Potential ◽  
Nitrogen Doped ◽  
Nitrogen Doped Carbon ◽  
Excellent Selectivity

Abstract Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum catalysts for the oxygen reduction reaction (ORR) in fuel cells; however, their active site structures remain poorly understood. A leading postulate is that the iron-containing active sites exist primarily in a pyridinic Fe-N4 ligation environment, yet, molecular model catalysts generally feature pyrrolic coordination. Herein, we report a molecular pyridinic hexaazacyclophane macrocycle, (phen2N2)Fe, and compare its spectroscopic, electrochemical, and catalytic properties for ORR to a typical Fe-N-C material and prototypical pyrrolic iron macrocycles. N 1s XPS and XAS signatures for (phen2N2)Fe are remarkably similar to those of Fe-N-C. Electrochemical studies reveal that (phen2N2)Fe has a relatively high Fe(III/II) potential with a correlated ORR onset potential within 150 mV of Fe-N-C. Unlike the pyrrolic macrocycles, (phen2N2)Fe displays excellent selectivity for four-electron ORR, comparable to Fe-N-C materials. The aggregate spectroscopic and electrochemical data demonstrate that (phen2N2)Fe is a more effective model of Fe-N-C active sites relative to the pyrrolic iron macrocycles, thereby establishing a new molecular platform that can aid understanding of this important class of catalytic materials.

scholarly journals Structural Basis for Autoinhibition of CTP:Phosphocholine Cytidylyltransferase (CCT), the Regulatory Enzyme in Phosphatidylcholine Synthesis, by Its Membrane-binding Amphipathic Helix

2013 ◽  
Vol 289 (3) ◽  
pp. 1742-1755 ◽  
Author(s):  
Jaeyong Lee ◽  
Svetla G. Taneva ◽  
Bryan W. Holland ◽  
D. Peter Tieleman ◽  
Rosemary B. Cornell
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Membrane Lipid ◽  
Structural Basis ◽  
Soluble Form ◽  
Amphipathic Helix ◽  
Inhibitory Interaction ◽  
Ctp:Phosphocholine Cytidylyltransferase ◽  
Membrane Bound ◽  
Dynamics Simulations

CTP:phosphocholine cytidylyltransferase (CCT) interconverts between an inactive soluble and active membrane-bound form in response to changes in membrane lipid composition. Activation involves disruption of an inhibitory interaction between the αE helices at the base of the active site and an autoinhibitory (AI) segment in the regulatory M domain and membrane insertion of the M domain as an amphipathic helix. We show that in the CCT soluble form the AI segment functions to suppress kcat and elevate the Km for CTP. The crystal structure of a CCT dimer composed of the catalytic and AI segments reveals an AI-αE interaction as a cluster of four amphipathic helices (two αE and two AI helices) at the base of the active sites. This interaction corroborates mutagenesis implicating multiple hydrophobic residues within the AI segment that contribute to its silencing function. The AI-αE interaction directs the turn at the C-terminal end of the AI helix into backbone-to-backbone contact with a loop (L2) at the opening to the active site, which houses the key catalytic residue, lysine 122. Molecular dynamics simulations suggest that lysine 122 side-chain orientations are constrained by contacts with the AI helix-turn, which could obstruct its engagement with substrates. This work deciphers how the CCT regulatory amphipathic helix functions as a silencing device.

scholarly journals Insight into the active site nature of zeolite H-BEA for liquid phase etherification of isobutylene with ethanol

RSC Advances ◽  
2019 ◽  
Vol 9 (62) ◽  
pp. 35957-35968 ◽  
Author(s):  
Nina V. Vlasenko ◽  
Yuri N. Kochkin ◽  
German M. Telbiz ◽  
Oleksiy V. Shvets ◽  
Peter E. Strizhak
Keyword(s):  
Liquid Phase ◽  
Active Site ◽  
Active Sites ◽  
Acid Sites ◽  
Bronsted Acid ◽  
Brønsted Acid Sites ◽  
Silanol Groups ◽  
Etbe Synthesis ◽  
Brönsted Acid ◽  
Insight Into

The active sites of H-BEA zeolites for ETBE synthesis are the weak Brønsted acid sites representing internal silanol groups.

A Pyridinic Fe-N4 Macrocycle Effectively Models the Active Sites in Fe/N-Doped Carbon Electrocatalysts

2020 ◽  
Author(s):  
Travis Marshall-Roth ◽  
Nicole J. Libretto ◽  
Alexandra T. Wrobel ◽  
Kevin Anderton ◽  
Nathan D. Ricke ◽  
...  
Keyword(s):  
Oxygen Reduction ◽  
Active Sites ◽  
Catalytic Properties ◽  
Reduction Reaction ◽  
Iron Phthalocyanine ◽  
Electrochemical Studies ◽  
Onset Potential ◽  
Nitrogen Doped Carbon ◽  
Iron Active Sites

Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum in fuel cells, but their active site structures are poorly understood. A leading postulate is that iron active sites in this class of materials exist in an Fe-N<sub>4</sub> pyridinic ligation environment. Yet, molecular Fe-based catalysts for the oxygen reduction reaction (ORR) generally feature pyrrolic coordination and pyridinic Fe-N<sub>4</sub> catalysts are, to the best of our knowledge, non-existent. We report the synthesis and characterization of a molecular pyridinic hexaazacyclophane macrocycle, (phen<sub>2</sub>N<sub>2</sub>)Fe, and compare its spectroscopic, electrochemical, and catalytic properties for oxygen reduction to a prototypical Fe-N-C material, as well as iron phthalocyanine, (Pc)Fe, and iron octaethylporphyrin, (OEP)Fe, prototypical pyrrolic iron macrocycles. N 1s XPS signatures for coordinated N atoms in (phen<sub>2</sub>N<sub>2</sub>)Fe are positively shifted relative to (Pc)Fe and (OEP)Fe, and overlay with those of Fe-N-C. Likewise, spectroscopic XAS signatures of (phen<sub>2</sub>N<sub>2</sub>)Fe are distinct from those of both (Pc)Fe and (OEP)Fe, and are remarkably similar to those of Fe-N-C with compressed Fe–N bond lengths of 1.97 Å in (phen<sub>2</sub>N<sub>2</sub>)Fe that are close to the average 1.94 Å length in Fe-N-C. Electrochemical studies establish that both (Pc)Fe and (phen<sub>2</sub>N<sub>2</sub>)Fe have relatively high Fe(III/II) potentials at ~0.6 V, ~300 mV positive of (OEP)Fe. The ORR onset potential is found to directly correlate with the Fe(III/II) potential leading to a ~300 mV positive shift in the onset of ORR for (Pc)Fe and (phen<sub>2</sub>N<sub>2</sub>)Fe relative to (OEP)Fe. Consequently, the ORR onset for (phen<sub>2</sub>N<sub>2</sub>)Fe and (Pc)Fe is within 150 mV of Fe-N-C. Unlike (OEP)Fe and (Pc)Fe, (phen<sub>2</sub>N<sub>2</sub>)Fe displays excellent selectivity for 4-electron ORR with <4% maximum H<sub>2</sub>O<sub>2</sub> production, comparable to Fe-N-C materials. The aggregate spectroscopic and electrochemical data establish (phen<sub>2</sub>N<sub>2</sub>)Fe as a pyridinic iron macrocycle that effectively models Fe-N-C active sites, thereby providing a rich molecular platform for understanding this important class of catalytic materials.<p><b></b></p>

Catalytic Resonance Theory: Parallel Reaction Pathway Control

2019 ◽  
Author(s):  
M. Alexander Ardagh ◽  
Manish Shetty ◽  
Anatoliy Kuznetsov ◽  
Qi Zhang ◽  
Phillip Christopher ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Active Site ◽  
Active Sites ◽  
Reaction Pathway ◽  
Control Strategies ◽  
Oscillation Amplitude ◽  
Catalytic Performance ◽  
Parallel Reaction ◽  
Resonance Theory ◽  
Static Conditions

Catalytic enhancement of chemical reactions via heterogeneous materials occurs through stabilization of transition states at designed active sites, but dramatically greater rate acceleration on that same active site is achieved when the surface intermediates oscillate in binding energy. The applied oscillation amplitude and frequency can accelerate reactions orders of magnitude above the catalytic rates of static systems, provided the active site dynamics are tuned to the natural frequencies of the surface chemistry. In this work, differences in the characteristics of parallel reactions are exploited via selective application of active site dynamics (0 < ΔU < 1.0 eV amplitude, 10<sup>-6</sup> < f < 10<sup>4</sup> Hz frequency) to control the extent of competing reactions occurring on the shared catalytic surface. Simulation of multiple parallel reaction systems with broad range of variation in chemical parameters revealed that parallel chemistries are highly tunable in selectivity between either pure product, even when specific products are not selectively produced under static conditions. Two mechanisms leading to dynamic selectivity control were identified: (i) surface thermodynamic control of one product species under strong binding conditions, or (ii) catalytic resonance of the kinetics of one reaction over the other. These dynamic parallel pathway control strategies applied to a host of chemical conditions indicate significant potential for improving the catalytic performance of many important industrial chemical reactions beyond their existing static performance.

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