An In-Silico Structural Analysis of the Interactions of SoxY and SoxZ from Moderately Thermophilic Betaproteobacterium, Hydrogenophilus thermoluteolus in the Global Sulfur Oxidation Cycle

2015 ◽  
pp. 1-9 ◽  
Author(s):  
Sujay Ray ◽  
Angshuman Bagchi
Keyword(s):  
Structural Analysis ◽  
In Silico ◽  
Sulfur Oxidation ◽  
Moderately Thermophilic

scholarly journals In Silico Structural Modeling and Analysis of Interactions of Tremellomycetes Cytochrome P450 Monooxygenases CYP51s with Substrates and Azoles

2021 ◽  
Vol 22 (15) ◽  
pp. 7811
Author(s):  
Olufunmilayo Olukemi Akapo ◽  
Joanna M. Macnar ◽  
Justyna D. Kryś ◽  
Puleng Rosinah Syed ◽  
Khajamohiddin Syed ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Structural Analysis ◽  
In Silico ◽  
Web Application ◽  
Cytochrome P450 Monooxygenases ◽  
Agglomerative Clustering ◽  
Ligand Complex ◽  
P450 Monooxygenase ◽  
Study Results

Cytochrome P450 monooxygenase CYP51 (sterol 14α-demethylase) is a well-known target of the azole drug fluconazole for treating cryptococcosis, a life-threatening fungal infection in immune-compromised patients in poor countries. Studies indicate that mutations in CYP51 confer fluconazole resistance on cryptococcal species. Despite the importance of CYP51 in these species, few studies on the structural analysis of CYP51 and its interactions with different azole drugs have been reported. We therefore performed in silico structural analysis of 11 CYP51s from cryptococcal species and other Tremellomycetes. Interactions of 11 CYP51s with nine ligands (three substrates and six azoles) performed by Rosetta docking using 10,000 combinations for each of the CYP51-ligand complex (11 CYP51s × 9 ligands = 99 complexes) and hierarchical agglomerative clustering were used for selecting the complexes. A web application for visualization of CYP51s’ interactions with ligands was developed (http://bioshell.pl/azoledocking/). The study results indicated that Tremellomycetes CYP51s have a high preference for itraconazole, corroborating the in vitro effectiveness of itraconazole compared to fluconazole. Amino acids interacting with different ligands were found to be conserved across CYP51s, indicating that the procedure employed in this study is accurate and can be automated for studying P450-ligand interactions to cater for the growing number of P450s.

scholarly journals Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

2011 ◽  
Vol 32 (4) ◽  
pp. 369-378 ◽  
Author(s):  
Fernando Cardona ◽  
Jose Vicente Sánchez‐Mut ◽  
Hernán Dopazo ◽  
Jordi Pérez‐Tur
Keyword(s):  
Structural Analysis ◽  
Parkinson Disease ◽  
In Silico

Update of the spectrum of mucopolysaccharidoses type III in Tunisia: identification of three novel mutations and in silico structural analysis of the missense mutations

2017 ◽  
Vol 13 (4) ◽  
pp. 374-380 ◽  
Author(s):  
Souad Ouesleti ◽  
Maria Francisca Coutinho ◽  
Isaura Ribeiro ◽  
Abdehedi Miled ◽  
Dalila Saidane Mosbahi ◽  
...  
Keyword(s):  
Structural Analysis ◽  
In Silico ◽  
Missense Mutations ◽  
Novel Mutations ◽  
Type Iii

scholarly journals Structural analysis of the Aβ(15-40) amyloid fibril based on hydrophobicity distribution

2018 ◽  
Author(s):  
Dawid Dułak ◽  
Mateusz Banach ◽  
Malgorzata Gadzała ◽  
Leszek Konieczny ◽  
Irena Roterman
Keyword(s):  
Protein Folding ◽  
Structural Analysis ◽  
Brain Tissue ◽  
In Silico ◽  
Amyloid Fibril ◽  
Causative Factor ◽  
Model Parameters ◽  
Hydrophobic Core

The Aβ42 amyloid is the causative factor behind various neurodegenerative processes. It forms elongated fibrils which cause structural devastation in brain tissue. The structure of an amyloid seems to be a contradiction of protein folding principles. Our work focuses on the Aβ(15-40) amyloid containing the D23N mutation (also known as the “Iowa mutation”), upon which an in silico experiment is based. Models generated using I-Tasser software as well as the fuzzy oil drop model – regarded as alternatives to the amyloid conformation – are compared in terms of their respective distributions of hydrophobicity (i.e. the existence of a hydrophobic core). In this process, fuzzy oil drop model parameters are applied in assessing the propensity of selected fragments for undergoing amyloid transformation.

Identification, Molecular Characterization, and In Silico Structural Analysis of Carboxypeptidase B2 ofAnopheles stephensi

2018 ◽  
Vol 56 (1) ◽  
pp. 72-85 ◽  
Author(s):  
Mahdokht Ilbeigi khamsehnejad ◽  
Navid Dinparast Djadid ◽  
Abbasali Raz
Keyword(s):  
Structural Analysis ◽  
Molecular Characterization ◽  
In Silico
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