scholarly journals Structural Basis for the Mechanistic Understanding of Human CD38-controlled Multiple Catalysis

2006 ◽  
Vol 281 (43) ◽  
pp. 32861-32869 ◽  
Author(s):  
Qun Liu ◽  
Irina A. Kriksunov ◽  
Richard Graeff ◽  
Cyrus Munshi ◽  
Hon Cheung Lee ◽  
...  
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Reaction Pathway ◽  
Structural Data ◽  
Product Inhibition ◽  
Structural Basis ◽  
Oh Groups ◽  
Inhibition Effect ◽  
Oxocarbenium Ion ◽  
Polar Interactions ◽  
Covalently Linked

The enzymatic cleavage of the nicotinamide-glycosidic bond on nicotinamide adenine dinucleotide (NAD+) has been proposed to go through an oxocarbenium ion-like transition state. Because of the instability of the ionic intermediate, there has been no structural report on such a transient reactive species. Human CD38 is an ectoenzyme that can use NAD+ to synthesize two calcium-mobilizing molecules. By using NAD+ and a surrogate substrate, NGD+, we captured and determined crystal structures of the enzyme complexed with an intermediate, a substrate, and a product along the reaction pathway. Our results showed that the intermediate is stabilized by polar interactions with the catalytic residue Glu226 rather than by a covalent linkage. The polar interactions between Glu226 and the substrate 2′,3′-OH groups are essential for initiating catalysis. Ser193 was demonstrated to have a regulative role during catalysis and is likely to be involved in intermediate stabilization. In addition, a product inhibition effect by ADP-ribose (through the reorientation of the product) or GDP-ribose (through the formation of a covalently linked GDP-ribose dimer) was observed. These structural data provide insights into the understanding of multiple catalysis and clues for drug design.

scholarly journals Structural insights into the conformational plasticity of the full-length trimeric HIV-1 envelope glycoprotein precursor

2018 ◽  
Author(s):  
Shijian Zhang ◽  
Wei Li Wang ◽  
Shuobing Chen ◽  
Maolin Lu ◽  
Eden P. Go ◽  
...  
Keyword(s):  
Viral Entry ◽  
Envelope Glycoprotein ◽  
Structural Data ◽  
Full Length ◽  
Heptad Repeat ◽  
Structural Basis ◽  
Glycoprotein Precursor ◽  
Helix Bundle ◽  
Conformational Plasticity ◽  
Hiv 1

SummaryThe human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer mediates viral entry into cells and is the major target for the host antibody response. In infected cells, the mature Env [(gp120/gp41)3] is produced by cleavage of a trimeric gp160 precursor. Proteolytic cleavage decreases Env conformational flexibility, allowing the mature Env to resist antibody binding to conserved elements. The conformational plasticity of the Env precursor skews the humoral immune response towards the elicitation of ineffectual antibodies, contributing to HIV-1 persistence in the infected host. The structural basis for the plasticity of the Env precursor remains elusive. Here we use cryo-electron microscopy to visualize two coexisting conformational states of the full-length Env precursor at nominal resolutions of 5.5 and 8.0 Å. The State-P2 conformation features a three-helix bundle of the gp41 heptad repeat region in the core, but has disordered membrane-interactive regions. State-P1 trimers lack the three-helix bundle and instead retain ordered transmembrane and membrane-proximal external regions embracing a central cavity. Our structural data shed light on the unusual plasticity of the Env precursor and provide new clues to Env immunogen discovery.

Crystal structure of hexanoyl-CoA bound to β-ketoacyl reductase FabG4 of Mycobacterium tuberculosis

2013 ◽  
Vol 450 (1) ◽  
pp. 127-139 ◽  
Author(s):  
Debajyoti Dutta ◽  
Sudipta Bhattacharyya ◽  
Amlan Roychowdhury ◽  
Rupam Biswas ◽  
Amit Kumar Das
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Active Site ◽  
Ternary Complex ◽  
Catalytic Mechanism ◽  
Acyl Carrier Protein ◽  
Structural Data ◽  
Acid Synthesis ◽  
Binary Complex ◽  
C Terminus ◽  
Covalently Linked

FabGs, or β-oxoacyl reductases, are involved in fatty acid synthesis. The reaction entails NADPH/NADH-mediated conversion of β-oxoacyl-ACP (acyl-carrier protein) into β-hydroxyacyl-ACP. HMwFabGs (high-molecular-weight FabG) form a phylogenetically separate group of FabG enzymes. FabG4, an HMwFabG from Mycobacterium tuberculosis, contains two distinct domains, an N-terminal ‘flavodoxintype’ domain and a C-terminal oxoreductase domain. The catalytically active C-terminal domain utilizes NADH to reduce β-oxoacyl-CoA to β-hydroxyacyl-CoA. In the present study the crystal structures of the FabG4–NADH binary complex and the FabG4–NAD+–hexanoyl-CoA ternary complex have been determined to understand the substrate specificity and catalytic mechanism of FabG4. This is the first report to demonstrate how FabG4 interacts with its coenzyme NADH and hexanoyl-CoA that mimics an elongating fattyacyl chain covalently linked with CoA. Structural analysis shows that the binding of hexanoyl-CoA within the active site cavity of FabG significantly differs from that of the C16 fattyacyl substrate bound to mycobacterial FabI [InhA (enoyl-ACP reductase)]. The ternary complex reveals that both loop I and loop II interact with the phosphopantetheine moiety of CoA or ACP to align the covalently linked fattyacyl substrate near the active site. Structural data ACP inhibition studies indicate that FabG4 can accept both CoA- and ACP-based fattyacyl substrates. We have also shown that in the FabG4 dimer Arg146 and Arg445 of one monomer interact with the C-terminus of the second monomer to play pivotal role in substrate association and catalysis.

Decolorization of azo dye C.I. Reactive Black 5 by ozonation in aqueous solution: influencing factors, degradation products, reaction pathway and toxicity assessment

2015 ◽  
Vol 73 (7) ◽  
pp. 1500-1510 ◽  
Author(s):  
Qing Zheng ◽  
Yong Dai ◽  
Xiangyun Han
Keyword(s):  
Aqueous Solution ◽  
Degradation Products ◽  
Reaction Pathway ◽  
Degradation Mechanism ◽  
Exchange Chromatography ◽  
Computational Method ◽  
Photobacterium Phosphoreum ◽  
Toxicity Tests ◽  
Reactive Black 5 ◽  
Oh Groups

In this study, ozonation treatment of C.I. Reactive Black 5 (RB5) was investigated at various operating parameters. The results showed that the aqueous solution initially containing 200 mg/L RB5 was quickly decolorized at pH 8.0 with an ozone dose of 3.2 g/h. Reaction intermediates with m/z 281, 546, 201, 350, 286 and 222 were elucidated using liquid chromatography-mass spectrometry, while sulfate ion, nitrate ion and three carboxylic acids (i.e., oxalic acid, formic acid, and acetic acid) were identified by ion exchange chromatography. Thus, the cleavage of the azo bond and the introduction of OH groups in the corresponding positions were proposed as the predominant reaction pathway. The detachment of sulfonic groups was also commonly observed during the ozonation treatment. The proposed degradation mechanism was confirmed by frontier electron density calculations, suggesting the feasibility of predicting the major events in the whole ozonation process with the computational method. Compared with RB5 degradation, the reduction of total organic carbon (TOC) proceeded much more slowly, and approximately 54% TOC was removed after 4 h of ozonation. Acute toxicity tests with Photobacterium phosphoreum showed that the toxicity of reaction solution was firstly increased and then decreased to a negligible level after 160 min.

scholarly journals How Na+ activates thrombin – a review of the functional and structural data

2008 ◽  
Vol 389 (8) ◽  
Author(s):  
James A. Huntington
Keyword(s):  
Crystal Structures ◽  
Blood Coagulation ◽  
Protein C ◽  
Coagulation Factor ◽  
Structural Data ◽  
Monovalent Cation ◽  
Coagulation Cascade ◽  
Structural Basis ◽  
Thrombin Activity ◽  
Great Relevance

Abstract Thrombin is the ultimate coagulation factor; it is the final protease generated in the blood coagulation cascade and is the effector of clot formation. Regulation of thrombin activity is thus of great relevance to determining the correct haemostatic balance, with dysregulation leading to bleeding or thrombosis. One of the most enigmatic and controversial regulators of thrombin activity is the monovalent cation Na+. When bound to Na+, thrombin adopts a ‘fast’ conformation which cleaves all procoagulant substrates more rapidly, and when free of Na+, thrombin reverts to a ‘slow’ state which preferentially activates the protein C anticoagulant pathway. Thus, Na+-binding allosterically modulates the activity of thrombin and helps determine the haemostatic balance. Over the last 30 years, there has been much research investigating the structural basis of thrombin allostery. Biochemical and mutagenesis studies established which regions and residues are involved in the slow→fast conformational change, and recently several crystal structures of the putative slow form have been solved. In this article, the biochemical and crystallographic data are reviewed to see if we are any closer to understanding the conformational basis of the Na+ activation of thrombin.

Reactions of ZnR2 Compounds with Dibenzoyl: Characterisation of the Alkyl-Transfer Products and a Striking Product-Inhibition Effect

2011 ◽  
Vol 17 (45) ◽  
pp. 12713-12721 ◽  
Author(s):  
Izabela Dranka ◽  
Marcin Kubisiak ◽  
Iwona Justyniak ◽  
Michał Lesiuk ◽  
Dominik Kubicki ◽  
...  
Keyword(s):  
Product Inhibition ◽  
Inhibition Effect ◽  
Alkyl Transfer

scholarly journals Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 β-1,4-xylosidase from Geobacillus thermoleovorans IT-08

PLoS ONE ◽  
2018 ◽  
Vol 13 (4) ◽  
pp. e0196358 ◽  
Author(s):  
Ali Rohman ◽  
Niels van Oosterwijk ◽  
Ni Nyoman Tri Puspaningsih ◽  
Bauke W. Dijkstra
Keyword(s):  
Product Inhibition ◽  
Structural Basis ◽  
Geobacillus Thermoleovorans

scholarly journals Green synthesis via electrolysis in microemulsions

2001 ◽  
Vol 73 (12) ◽  
pp. 1895-1905 ◽  
Author(s):  
James F. Rusling
Keyword(s):  
Turnover Rate ◽  
Recent Progress ◽  
Reaction Pathway ◽  
Reaction Rates ◽  
Synthetic Methods ◽  
Reaction Pathways ◽  
Lower Toxicity ◽  
Reduction Potentials ◽  
Covalently Linked ◽  
High Yields

Electrolysis in microemulsions is a promising approach for environmentally friendly chemical synthetic methods of the future. Employing microemulsions instead of organic solvents for electrosynthesis has the advantages of lower toxicity and cost, high dissolving power for reactants and mediators of unlike solubility, enhancement of reaction rates by controlling the reduction potentials of mediators, possible reaction pathway control, and recycling of microemulsion components. This paper reviews recent progress in using microemulsions for direct and mediated electrosynthesis, including formation of carbon­carbon bonds. Rates of mediated reactions can be controlled by manipulating microemulsion composition. Examples are presented, in which reaction pathways of direct and mediated electrolyses can be controlled with microemulsions to give desired products in high yields. Such control has been demonstrated with dissolved and surface-bound mediators. For a covalently linked scaffold of poly(l-lysine) and cobalt corrin vitamin B12 hexacarboxylate attached to graphite, catalytic turnover rate for reduction of 1,2-dibromocylcohexane was optimized by optimizing microemulsion composition.

scholarly journals Kinetic studies of oxidized nicotinamide–adenine dinucleotide-facilitated reactions of d-glyceraldehyde 3-phosphate dehydrogenase

1974 ◽  
Vol 143 (2) ◽  
pp. 353-363 ◽  
Author(s):  
Patricia J. Harrigan ◽  
David R. Trentham
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Temperature Jump ◽  
Reaction Pathway ◽  
Kinetic Studies ◽  
Rate Equations ◽  
First Order ◽  
Diffusion Controlled ◽  
Relaxation Temperature ◽  
Pig Muscle ◽  
Kinetics Of

The kinetics of the acylation of d-glyceraldehyde 3-phosphate dehydrogenase from pig muscle by 1,3-diphosphoglycerate in the presence of NAD+ has been analysed by using the relaxation temperature-jump method. At pH7.2 and 8°C the rate of acylation of the NAD+-bound (or holo-) enzyme was 3.3×105m−1·s−1 and the rate of phosphorolysis, the reverse reaction, was 7.5×103m−1·s−1. After a temperature-jump perturbation the equilibrium of NAD+ binding to the acyl-enzyme was re-established more rapidly than that of the acylation. The rate of phosphorolysis of the apoacylenzyme from sturgeon muscle and of aldehyde release from the d-glyceraldehyde 3-phosphate–apoenzyme complex were ≤40m−1·s−1 and ≤12s−1 respectively at pH8.0 and 22°C, which means that both processes are too slow to contribute significantly to the reaction pathway of the reversible NAD+-linked oxidative phosphorylation of d-glyceraldehyde 3-phosphate. Phosphorolysis of both acyl-apoenzyme and acyl-holoenzyme was first-order in Pi up to 100mm-Pi and more. PO43− could be the reactive species of the phosphorolysis of the acyl-holoenzyme, in which case phosphorolysis is a diffusion-controlled reaction, although other kinetically indistinguishable rate equations for the reaction are possible.

scholarly journals Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

2020 ◽  
Author(s):  
Timur Gimadiev ◽  
Ramil Nugmanov ◽  
Dinar Batyrshin ◽  
Timur Madzhidov ◽  
Satoshi Maeda ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Chemical Reaction ◽  
Relational Database ◽  
Quantum Chemical ◽  
Reaction Pathway ◽  
Transition States ◽  
Structural Data ◽  
Database Management System ◽  
Pathway Data ◽  
Machine Learning Applications

Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

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