scholarly journals Structure of a bifunctional alcohol dehydrogenase involved in bioethanol generation inGeobacillus thermoglucosidasius

2013 ◽  
Vol 69 (10) ◽  
pp. 2104-2115 ◽  
Author(s):  
Jonathan Extance ◽  
Susan J. Crennell ◽  
Kirstin Eley ◽  
Roger Cripps ◽  
David W. Hough ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Domain Structure ◽  
Aldehyde Dehydrogenase ◽  
In Silico ◽  
Homology Model ◽  
Structural Mechanism ◽  
Geobacillus Thermoglucosidasius ◽  
Fermentative Metabolism ◽  
Acyl Coenzyme A ◽  
First Time

Bifunctional alcohol/aldehyde dehydrogenase (ADHE) enzymes are found within many fermentative microorganisms. They catalyse the conversion of an acyl-coenzyme A to an alcoholviaan aldehyde intermediate; this is coupled to the oxidation of two NADH molecules to maintain the NAD+pool during fermentative metabolism. The structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from the ethanol-producing thermophileGeobacillus thermoglucosidasiushas been determined to 2.5 Å resolution. This is the first structure to be reported for such a domain.In silicomodelling has been carried out to generate a homology model of the aldehyde dehydrogenase domain, and this was subsequently docked with the ADH-domain structure to model the structure of the complete ADHE protein. This model suggests, for the first time, a structural mechanism for the formation of the large multimeric assemblies or `spirosomes' that are observed for this ADHE protein and which have previously been reported for ADHEs from other organisms.

scholarly journals A novel bifunctional aldehyde/alcohol dehydrogenase catalyzing reduction of acetyl-CoA to ethanol at temperatures up to 95 °C

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiang Wang ◽  
Chong Sha ◽  
Hongcheng Wang ◽  
Kesen Ma ◽  
Juergen Wiegle ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Alcohol Dehydrogenase ◽  
Aldehyde Dehydrogenase ◽  
Half Life ◽  
Cellulosic Ethanol ◽  
Pyrococcus Furiosus ◽  
Biochemical Properties ◽  
Cellulosic Biomass ◽  
Acetyl Coenzyme A ◽  
First Time

AbstractHyperthermophilic Thermotoga spp. are excellent candidates for the biosynthesis of cellulosic ethanol producing strains because they can grow optimally at 80 °C with ability to degrade and utilize cellulosic biomass. In T. neapolitana (Tne), a putative iron-containing alcohol dehydrogenase was, for the first time, revealed to be a bifunctional aldehyde/alcohol dehydrogenase (Fe-AAdh) that catalyzed both reactions from acetyl-coenzyme A (ac-CoA) to acetaldehyde (ac-ald), and from ac-ald to ethanol, while the putative aldehyde dehydrogenase (Aldh) exhibited only CoA-independent activity that oxidizes ac-ald to acetic acid. The biochemical properties of Fe-AAdh were characterized, and bioinformatics were analyzed. Fe-AAdh exhibited the highest activities for the reductions of ac-CoA and acetaldehyde at 80–85 °C, pH 7.54, and had a 1-h half-life at about 92 °C. The Fe-AAdh gene is highly conserved in Thermotoga spp., Pyrococcus furiosus and Thermococcus kodakarensis, indicating the existence of a fermentation pathway from ac-CoA to ethanol via acetaldehyde as the intermediate in hyperthermophiles.

Study on the Substrate Specificity of Xylose Isomerase N91D Mutant from Thermus thermophilus HB8 by Molecular Simulation

2011 ◽  
Vol 236-238 ◽  
pp. 968-973
Author(s):  
Wei Xu ◽  
Rong Shao ◽  
Yan Li ◽  
Ming Yan ◽  
Ping Kai Ouyang
Keyword(s):  
Substrate Specificity ◽  
Catalytic Mechanism ◽  
Molecular Design ◽  
Thermus Thermophilus ◽  
Xylose Isomerase ◽  
Homology Model ◽  
Complex Model ◽  
Structural Mechanism ◽  
Docking Method ◽  
Conserved Residue

Compared withThermus thermophilusHB8 xylose isomerase(TthXI), the increase of the substrate specificity on D-xylose of its N91D mutant (TthXI-N91D) was observed in the previous study. In order to clarify the structural mechanism of TthXI-N91D, the complex model of TthXI with D-xylose was constructed by molecular docking method. The TthXI-N91D homology model was built by WATH IF5.0 based on the above complex. The results indicate that the distance between the conserved residue H53 NE2 and D-xylose O5 has decreased in 0.083 nm in the TthXI-N91D active site. The short distance is propitious to transfer the hydrogen atom during the open ring process of substrate. At the same time, the distance between the conserved residue T89 OG1, involving in combining glucose, and D-xylose C5 has reduced 0.133 nm. The shrunken space has an unfavorable effect on accommodating the larger glucose than xylose, and lead to the enhanced specificity for D-xylose.The above phenomenon maybe the main reason for explaining that TthXI-N91D is easy to combine D-xylose showing enhanced specificity. The results paly an important role in understanding the catalytic mechanism of xylose isomerase and provides the base for its molecular design.

Alcohol and aldehyde dehydrogenase activity in the stomach and small intestine of rats poisoned with methanol

2001 ◽  
Vol 20 (5) ◽  
pp. 255-258
Author(s):  
L Chrostek ◽  
D Szczepura ◽  
M Szmitkowski ◽  
W Jelski ◽  
J Wierzchowski
Keyword(s):  
Small Intestine ◽  
Alcohol Dehydrogenase ◽  
Dehydrogenase Activity ◽  
Aldehyde Dehydrogenase ◽  
Protein Denaturation ◽  
Cell Damage ◽  
Sublethal Dose ◽  
Adh Activity ◽  
Aldehyde Dehydrogenase Activity

The activities of alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) were measured with fluorogenic naphthaldehydes in the stomach and small intestine homogenates of rats dosed with 6 g methanol/kg bw after 6, 12, 24 h and 2, 5, 7 days. After intoxication with a sublethal dose, the ADH activity measured with these naphthaldehydes andALDH activities in the stomach and small intestine were significantly decreased. This inhibition is stronger in the stomach and probably depends on cell damage and protein denaturation. We conclude that the activity measured with 6-methoxy-2-naphthaldehyde (MONAL-62) may be due to the activity of rat ADH-1 isoenzyme, and the activity detected with 4-methoxy-1-naphthaldehyde (MONAL-41) to the activity of rat ADH-2 isoenzyme.

Alcohol Dehydrogenase Isoenzymes and Aldehyde Dehydrogenase Activity in the Serum of Patients with Non-alcoholic Fatty Liver Disease

2018 ◽  
Vol 38 (7) ◽  
pp. 4005-4009 ◽  
Author(s):  
WOJCIECH JELSKI ◽  
BLANKA WOLSZCZAK-BIEDRZYCKA ◽  
ELŻBIETA ZASIMOWICZ-MAJEWSKA ◽  
KAROLINA ORYWAL ◽  
TADEUSZ WOJCIECH LAPINSKI ◽  
...  
Keyword(s):  
Liver Disease ◽  
Alcohol Dehydrogenase ◽  
Fatty Liver ◽  
Dehydrogenase Activity ◽  
Aldehyde Dehydrogenase ◽  
Fatty Liver Disease ◽  
Alcohol Dehydrogenase Isoenzymes ◽  
Alcoholic Fatty Liver ◽  
Alcoholic Fatty Liver Disease ◽  
Aldehyde Dehydrogenase Activity

Identification of Aneuploid Circulating Tumor Cells in Soft-Tissue Sarcoma Patients: A Pilot Study

Oncology ◽  
2020 ◽  
Vol 98 (12) ◽  
pp. 893-896
Author(s):  
Andrea Napolitano ◽  
Alessandro Minelli ◽  
Daniele Santini ◽  
Giuseppe Tonini ◽  
Bruno Vincenzi
Keyword(s):  
Overall Survival ◽  
Pilot Study ◽  
Soft Tissue ◽  
Soft Tissue Sarcoma ◽  
Tumor Cells ◽  
In Silico ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
First Time ◽  
Genome Atlas

<b><i>Background:</i></b> Circulating tumor cells (CTCs) have been identified and shown to have prognostic and predictive roles in several types of carcinoma. More recently, aneuploid CTCs have become subject of a growing interest, as aneuploidy is considered a hallmark of cancer often associated with poor prognosis. Here, we aimed to identify for the first time aneuploid CTCs in soft-tissue sarcoma (STS) patients and show supportive in silico evidence on the prognostic role of aneuploidy in mesenchymal cancers. <b><i>Methods:</i></b> In our pilot study, we collected blood from 4 metastatic STS patients and 4 age- and sex-matched healthy controls. After sample processing, cells were cyto-centrifuged onto glass slides and FISH was performed using 5 probes. The in silico analysis was performed using data from The Cancer Genome Atlas cohort of STS patients, using the validated Aneuploidy Score. We divided the patients in two populations (aneuploidy-high, Ane-Hi, and aneuploidy-low, Ane-Lo) using the median value of the Aneuploidy Score as a cutoff. Kaplan-Meier curves associated with log-rank test were used to compare progression-free and overall survival between groups. GraphPad Prism 8.0 (La Jolla, CA, USA) was used for statistical analyses. <b><i>Results:</i></b> Aneuploid CTCs were identified in all 4 STS patients and in none of the controls, with a median value of 4 (range 3–6) per 7 mL of blood. Ane-Hi patients showed a significantly worse progression-free and overall survival compared to Ane-Lo patients. The same trend was maintained when analyzing the data based on the different histologies. <b><i>Conclusions:</i></b> We identified for the first time aneuploid CTCs in STS patients using fluorescence in situ hybridization in a surface marker-independent way. We also showed that the Aneuploidy Score has a prognostic value both in terms of progression-free survival and overall survival in STS patients using The Cancer Genome Atlas data, regardless of the histology.

P144 IN SILICO IDENTIFICATION OF PUTATITVE CLAUDIN CHANNEL BLOCKERS

2020 ◽  
Vol 26 (Supplement_1) ◽  
pp. S30-S30
Author(s):  
Emma Wu ◽  
Priyanka Samanta ◽  
Ye Li ◽  
Le Shen ◽  
Fatemeh Khalili ◽  
...  
Keyword(s):  
In Silico ◽  
Homology Model ◽  
Docking Studies ◽  
Channel Blockers ◽  
Barrier Dysfunction ◽  
Dynamic Simulations ◽  
Epithelial Barrier Function ◽  
In Vitro Measurements ◽  
Potential Ligand

Abstract Compromised epithelial barrier function is known to be associated with inflammatory bowel disease (IBD) and may contribute to disease development. One mechanism of barrier dysfunction is increased expression of paracellular tight junction ion and water channels formed by claudins. Claudin-2 and -15 are two such channels. We hypothesize that blocking these channels could be a viable therapeutic approach to treat diarrhea in IBD. In an effort to develop blockers of these channels, we turn to our previously developed and validated in silico models of claudin-15 (Samanta et al. 2018). We reasoned that molecules that can bind with the interior of claudin pores can limit paracellular water and ion flux. Thus, we used docking algorithms to search for putative drugs that bind in the claudin-15 pore. AutoDock Vina (Scripps Research Institute) was initially used to assess rigid docking using small molecule ligand databases. The ligands were analyzed based on binding affinity to the pore and visualized using VMD (University of Illinois at Urbana-Champaign) for their potential blockage of the channel. Overall, a total of eight candidate ligands from the databases were identified: three from the UICentre database of 10000 ligands, one chemically similar structure identified in another online database (Chemspider), and four which are modifications on the chemical structure generated using ChemDraw. The analysis revealed that the eight ligands were docked in two predominant positions. In the first position, the ligands with more rings docked in an almost linear fashion and interacted with both D55 and D64 pore residues. In the second position of binding, the ligands were more flexible and could hence fold to interact only with D55 residues, thus biding predominantly in the center of the pores. To further evaluate these ligands, we will now turn to 1) flexible claudin-15 docking studies, 2) molecular dynamic simulations and, 3) in vitro measurements using monolayers induced to express claudin -15 and claudin-15 mutants. We also developed a claudin-2 homology model on which we will perform docking studies and in vitro measurements, which we expect will result in similar candidate ligands for blocking claudin-2. Finally, other databases will be analyzed for potential ligand blockers of claudin-2 and -15.

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