scholarly journals A Single Mutation in the Hepta-Peptide Active Site of <i>Aspergillus niger</i> PhyA Phytase Leads to Myriad Biochemical Changes

2012 ◽  
Vol 02 (03) ◽  
pp. 388-394 ◽  
Author(s):  
Abul H. J. Ullah ◽  
Kandan Sethumadhavan ◽  
Stephanie Boone ◽  
Edward J. Mullaney
Keyword(s):  
Aspergillus Niger ◽  
Active Site ◽  
Biochemical Changes ◽  
Single Mutation

scholarly journals PENENTUAN SISI AKTIF SELULASE ASPERGILLUS NIGER DENGAN DOCKING LIGAN

2014 ◽  
Vol 16 (2) ◽  
pp. 94-100 ◽  
Author(s):  
Tigor Nauli
Keyword(s):  
Aspergillus Niger ◽  
Active Site ◽  
Molecular Conformation ◽  
Catalytic Domain ◽  
Binding Free Energy ◽  
Docking Simulation ◽  
Optimization Approach ◽  
Calculation Results ◽  
Substrate Binding Domain ◽  
Specific Metal

Letak dari sisi aktif selulase Aspergillus niger, yang akan menentukan aktivitas katalitiknya, dapat diketahui melalui komputasi. Sebuah ligan selobiosa dimodelkan untuk dapat melakukan simulasi docking pada molekul selulase yang telah diketahui struktur kristalnya. Melalui kalkulasi energi ikatan dan pendekatan optimasi memakai algoritma genetik Lamarckian, dapat dipilih konformasi molekul yang menunjukkan adanya daerah tertentu dengan energi terendah. Struktur yang memiliki daerah semacam ini dianggap mewakili konfigurasi terbaik terikatnya ligan pada sisi aktif yang dicari.Hasil perhitungan memperlihatkan bahwa tekukan protein yang membentuk celah konkaf diantara dua kelompok struktur b-sheet yang saling berlawanan arah pada molekul selulase merupakan sisi aktif dari enzim tersebut. Ligan dapat terikat disana melalui interaksi hidrofilik dengan residu asparagin (Asn20), serin (Ser111), dan glutamin (Gln158). Di salah satu ujung sisi aktif selulase terdapat residu aspartat (Asp99) dan glutamat (Glu116, Glu204) yang akan mempengaruhi aksi katalitik dari enzim selulase apabila residu-residu ini terikat oleh ion-ion divalen.Sisi aktif selulase ini merupakan gabungan dari domain pengikat substrat dan domain katalitik. Penambahan ion logam yang tepat pada sisi aktif enzim selulase Aspergillus niger dapat meningkatkan aktivitas spesifiknya.Kata kunci:docking, ligan, selulase, sisi ikatan, substrat The active site of cellulase from Aspergillus niger that affects the enzyme activity can be searched by computational methods. A ligand of cellobiose is modelled to perform docking simulation to cellulase with known crystal structure. By calculating the binding free energy and optimization approach using Lamarckian's genetic algorithm, a molecular conformation that has a region with the lowest energy value can be selected. The molecule structure with such region represents the best configuration of ligand bound to the active site.The calculation results that the concave cleft formed by protein folding of two anti-parallel b-sheet structures is the active site of the enzyme. A ligand would bind to the site through hydrophilic interactions with asparagine (Asn20), serine (Ser111), and glutamine (Gln158) residues. The aspartic acid (Asp99) and glutamic acid (Glu116, Glu204) residues that reside in one end of the active site determine the catalytic actions of the enzyme when they are binding with some metal ions.It is shown that the active site of this cellulase has substrate-binding domain and catalytic domain together. The introduction of specific metal ions to the active site of Asperillus niger cellulase will increase its specific activity.Keywords: binding site, cellulase, docking, ligand, substrate

scholarly journals Dynamism and Cooperativity Essential for Efficient Catalysis in Aspergillus Niger Monoamine Oxidase

2019 ◽  
Author(s):  
Christian Curado-Carballada ◽  
Ferran Feixas ◽  
Sílvia Osuna
Keyword(s):  
Aspergillus Niger ◽  
Monoamine Oxidase ◽  
Active Site ◽  
Conformational Dynamics ◽  
Catalytic Efficiency ◽  
Building Blocks ◽  
Chiral Amine ◽  
Evolutionary Pathway ◽  
Accelerated Molecular Dynamics ◽  
Open States

<p><b> </b><i>Aspergillus niger </i>Monoamine Oxidase (MAO-N) is a homodimeric enzyme responsible for the oxidation of amines into the corresponding imine. Laboratory evolved variants of MAO-N in combination with a non-selective chemical reductant represents a powerful strategy for the deracemisation of chiral amine mixtures and, thus, is of interest for obtaining chiral amine building blocks. MAO-N presents a rich conformational dynamics with a flexible ß-hairpin region that can adopt closed, partially closed and open states. Despite the ß-hairpin conformational dynamics is altered along the laboratory evolutionary pathway of MAO-N, the connection between the ß-hairpin conformational dynamics and active site catalysis still remains unclear. In this work, we use accelerated molecular dynamics to elucidate the potential interplay between the ß-hairpin conformational dynamics and catalytic activity in MAO-N wild type and its evolved D5 variant. Our study reveals a delicate communication between both MAO-N subunits that impacts the active site architecture, and thus its catalytic efficiency. In both MAO-N WT and the laboratory evolved D5 variant, the ß-hairpin conformation in one of the monomers affects the productive binding of the substrate in the active site of the other subunit. However, both MAO-N WT and D5 variants show a quite different behaviour due to the distal mutations introduced experimentally with Directed Evolution. </p>

Invertase from Hyper Producer Strain of Aspergillus niger: Physiochemical Properties, Thermodynamics and Active Site Residues Heat of Ionization

2009 ◽  
Vol 16 (9) ◽  
pp. 1098-1105 ◽  
Author(s):  
Habibullah Nadeem ◽  
Muhammad Rashid ◽  
Muhammad Riaz ◽  
Bibi Asma ◽  
Muhammad Javed ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Active Site ◽  
Active Site Residues ◽  
Producer Strain ◽  
Physiochemical Properties

Synthesis of New Bis-pyrazolines Endowed with Potent Antifungal Activity against Candida albicans and Aspergillus niger

2020 ◽  
Vol 17 ◽  
Author(s):  
Belgin Sever ◽  
Mehlika Dilek Altıntop ◽  
Ahmet Özdemir
Keyword(s):  
Candida Albicans ◽  
Molecular Docking ◽  
Antifungal Activity ◽  
Aspergillus Niger ◽  
Mtt Assay ◽  
Active Site ◽  
Antifungal Agents ◽  
Docking Studies ◽  
Antifungal Effects ◽  
Nih 3T3

Background: Due to the increasing number of cases of invasive fungal infections (IFIs), there is an urgent need to identify potent antifungal agents capable of combating IFIs. Pyrazolines are one such class of therapeutically active agents that could be considered to fulfil this need. Objective: In this context, this paper aims to identify two new series of bis-pyrazolines endowed with potent antifungal activity against Candida albicans and Aspergillus niger. Methods: Two new series of bis-pyrazolines (4a-i, 5a-e) were synthesized through an efficient and and versatile synthetic procedure. The compounds were screened for their antifungal effects on C. albicans and A. niger using a broth microdilution method. Their cytotoxic effects on NIH/3T3 mouse embryonic fibroblast cell line were determined using MTT assay. Molecular docking studies were performed in the active site of lanosterol 14α-demethylase (CYP51) to shed light on their antifungal effects using Schrödinger’s Maestro molecular modeling package. Results And Discussion: 5,5'-(1,4-Phenylene)bis[1-(2-(5-phenyl-1,3,4-oxadiazol-2-yl)thio)acetyl)-3-(2-thienyl)-4,5- dihydro-1H-pyrazole] (4a) and 5,5'-(1,4-phenylene)bis[1-(2-(4-(2-hydroxyethyl)-1-piperazinylthiocarbamoyl)thio)acetyl)-3- (2-thienyl)-4,5-dihydro-1H-pyrazole] (5a) were found as the most promising antifungal agents in this series. Compounds 4a and 5a showed pronounced antifungal activity against C. albicans (MIC= 0.016 mg/mL) and A. niger (MIC= 0.008 mg/mL). Based on MTT assay, their antifungal effects were selective (IC50 > 0.500 mg/mL for NIH/3T3 cell line). Molecular docking studies suggested that compounds 5a-e might show their anticandidal effects via CYP51 inhibition in regard to their stronger interactions in the active site of CYP51. Conclusion: Compounds 4a and 5a stand out as potential antifungal agents for the management of IFIs caused by C. albicans and A. niger.

THE ALLOSTERIC NATURE OF NAD-SPECIFIC ISOCITRIC DEHYDROGENASE FROM ASPERGILLI

1965 ◽  
Vol 43 (1) ◽  
pp. 111-118 ◽  
Author(s):  
Marianne F. Chan ◽  
C. S. Stachow ◽  
B. D. Sanwal
Keyword(s):  
Aspergillus Niger ◽  
Environmental Factors ◽  
Kinetic Study ◽  
Active Site ◽  
Initial Velocity ◽  
Velocity Data ◽  
Allosteric Site ◽  
Isocitric Dehydrogenase ◽  
Citrate Accumulation

A kinetic study of the NAD-dependent isocitric dehydrogenase from Aspergillus niger (citrate excretor) and A. flavus (nonexcretor) has been made. The enzyme from both sources is markedly and specifically activated by citrate. Analysis of initial velocity data shows that the enzyme possibly has a distinct allosteric site that can bind both isocitrate and citrate, and an active site that is specific for isocitrate. It is conjectured that citrate accumulation by A. niger may be due to a 'desensitization' of the allosteric site of the enzyme by environmental factors.

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