Unravelling the role of active-site isolation in reactivity and reaction pathway control for acetylene hydrogenation

2020 ◽  
Vol 56 (47) ◽  
pp. 6372-6375
Author(s):  
Siyang Liu ◽  
Yiming Niu ◽  
Yongzhao Wang ◽  
Junnan Chen ◽  
Xueping Quan ◽  
...  
Keyword(s):  
Active Site ◽  
Bimetallic Catalysts ◽  
Reaction Pathway ◽  
Isolation Effect ◽  
Site Isolation ◽  
Acetylene Hydrogenation ◽  
Supported Pd

Supported PdxCuy bimetallic catalysts were prepared and characterized to illustrate the active-site isolation effect on controlling the reactivity and reaction pathway of acetylene hydrogenation.

Atomistic Insights into Cl–-Triggered Highly Selective Ethylene Electrochemical Oxidation to Epoxide on RuO2: Unexpected Role of the In Situ Generated Intermediate to Achieve Active Site Isolation

ACS Catalysis ◽  
2021 ◽  
pp. 13660-13669
Author(s):  
Jia-Cheng Hong ◽  
Tung-Chun Kuo ◽  
Guo-Lin Yang ◽  
Chi-Tien Hsieh ◽  
Min-Hsiu Shen ◽  
...  
Keyword(s):  
Electrochemical Oxidation ◽  
Active Site ◽  
Site Isolation

scholarly journals Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hengjun Cui ◽  
Andreas U. Müller ◽  
Marc Leibundgut ◽  
Jiawen Tian ◽  
Nenad Ban ◽  
...  
Keyword(s):  
High Resolution ◽  
Sequence Homology ◽  
Active Site ◽  
Bound States ◽  
Biochemical Analysis ◽  
Atp Hydrolysis ◽  
Reaction Pathway ◽  
Post Translational Modification ◽  
Functional States

AbstractPupylation is the post-translational modification of lysine side chains with prokaryotic ubiquitin-like protein (Pup) that targets proteins for proteasomal degradation in mycobacteria and other members of Actinobacteria. Pup ligase PafA and depupylase Dop are the two enzymes acting in this pathway. Although they share close structural and sequence homology indicative of a common evolutionary origin, they catalyze opposing reactions. Here, we report a series of high-resolution crystal structures of Dop in different functional states along the reaction pathway, including Pup-bound states in distinct conformations. In combination with biochemical analysis, the structures explain the role of the C-terminal residue of Pup in ATP hydrolysis, the process that generates the catalytic phosphate in the active site, and suggest a role for the Dop-loop as an allosteric sensor for Pup-binding and ATP cleavage.

scholarly journals Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site

2021 ◽  
Vol 14 ◽  
pp. 117864692110529
Author(s):  
Manon Mirgaux ◽  
Laurence Leherte ◽  
Johan Wouters
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Crystal Structures ◽  
Protein Dynamics ◽  
Active Site ◽  
Reaction Pathway ◽  
Small Unit ◽  
Indoleamine 2,3 Dioxygenase ◽  
Dynamics Simulations

Protein dynamics governs most of the fundamental processes in the human body. Particularly, the dynamics of loops located near an active site can be involved in the positioning of the substrate and the reaction mechanism. The understanding of the functioning of dynamic loops is therefore a challenge, and often requires the use of a multi-disciplinary approach mixing, for example, crystallographic experiments and molecular dynamics simulations. In the present work, the dynamic behavior of the JK-loop of the human indoleamine 2,3-dioxygenase 1 hemoprotein, a target for immunotherapy, is investigated. To overcome the lack of knowledge on this dynamism, the study reported here is based on 3 crystal structures presenting different conformations of the loop, completed with molecular dynamics trajectories and MM-GBSA analyses, in order to trace the reaction pathway of the enzyme. In addition, the crystal structures identify an exo site in the small unit of the enzyme, that is populated redundantly by the substrate or the product of the reaction. The role of this newer reported exo site still needs to be investigated.

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.

Ethanol conversion over Ga2O3-ZrO2 solid solution: empirical evidences of the reaction pathway, the surface acid–base property, and role of isolated gallium ion

2021 ◽  
Author(s):  
Takashi Yamamoto ◽  
Akihito Kurimoto ◽  
Riona Sato ◽  
Shoki Katada ◽  
Hirotaka Mine ◽  
...  
Keyword(s):  
Solid Solution ◽  
Reaction Pathway ◽  
Ethanol Conversion ◽  
Acid Base ◽  
Base Property ◽  
Temperature Range ◽  
Acid Base Property

Ethanol conversion by Ga2O3-ZrO2 solid solution was examined in the temperature range 573–773 K, and acetone/isobutene formation was confirmed under cofeeding of H2O vapor. The reaction pathway was empirically investigated...

Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13C Labeling and ENDOR Spectroscopy

2021 ◽  
Author(s):  
Ana Pérez-González ◽  
Zhi-Yong Yang ◽  
Dmitriy A. Lukoyanov ◽  
Dennis R. Dean ◽  
Lance C. Seefeldt ◽  
...  
Keyword(s):  
Active Site ◽  
13C Labeling ◽  
Endor Spectroscopy ◽  
Femo Cofactor

scholarly journals The Role of Active Site Arginines of Sorghum NADP-Malate Dehydrogenase in Thioredoxin-dependent Activation and Activity

2000 ◽  
Vol 275 (46) ◽  
pp. 35792-35798 ◽  
Author(s):  
Isabelle Schepens ◽  
Eric Ruelland ◽  
Myroslawa Miginiac-Maslow ◽  
Pierre Le Maréchal ◽  
Paulette Decottignies
Keyword(s):  
Malate Dehydrogenase ◽  
Active Site
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