In silico structural analysis of secretory clusterin to assess pathogenicity of mutations identified in the evolutionarily conserved regions

Author(s):  
Lipi Das ◽  
Shashank Shekhar ◽  
Pratik Chandrani ◽  
Ashok K. Varma
2021 ◽  
Vol 22 (15) ◽  
pp. 7811
Author(s):  
Olufunmilayo Olukemi Akapo ◽  
Joanna M. Macnar ◽  
Justyna D. Kryś ◽  
Puleng Rosinah Syed ◽  
Khajamohiddin Syed ◽  
...  

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.


2011 ◽  
Vol 32 (4) ◽  
pp. 369-378 ◽  
Author(s):  
Fernando Cardona ◽  
Jose Vicente Sánchez‐Mut ◽  
Hernán Dopazo ◽  
Jordi Pérez‐Tur

Open Biology ◽  
2015 ◽  
Vol 5 (11) ◽  
pp. 150094 ◽  
Author(s):  
Magdalena Machowska ◽  
Katarzyna Piekarowicz ◽  
Ryszard Rzepecki

The main functions of lamins are their mechanical and structural roles as major building blocks of the karyoskeleton. They are also involved in chromatin structure regulation, gene expression, intracellular signalling pathway modulation and development. All essential lamin functions seem to depend on their capacity for assembly or disassembly after the receipt of specific signals, and after specific, selective and precisely regulated interactions through their various domains. Reversible phosphorylation of lamins is crucial for their functions, so it is important to understand how lamin polymerization and interactions are modulated, and which sequences may undergo such modifications. This review combines experimental data with results of our in silico analyses focused on lamin phosphorylation in model organisms to show the presence of evolutionarily conserved sequences and to indicate specific in vivo phosphorylations that affect particular functions.


2017 ◽  
Vol 13 (4) ◽  
pp. 374-380 ◽  
Author(s):  
Souad Ouesleti ◽  
Maria Francisca Coutinho ◽  
Isaura Ribeiro ◽  
Abdehedi Miled ◽  
Dalila Saidane Mosbahi ◽  
...  

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