Computational site-directed mutagenesis studies of the role of the hydrophobic triad on substrate binding in cholesterol oxidase

Abstract

Cholesterol oxidase (ChOx) is a flavoenzyme that oxidizes and isomerizes cholesterol (CHL) to form cholest-4-en-3-one. Molecular docking and molecular dynamics simulations were conducted to predict the binding interactions of CHL in the active site. Several key interactions (E361-CHL, N485-FAD, and H447-CHL) were identified and which are likely to determine the correct positioning of CHL relative to flavin-adenine dinucleotide (FAD). Binding of CHL also induced changes in key residues of the active site leading to the closure of the oxygen channel. A group of residues, Y107, F444, and Y446, known as the hydrophobic triad, are believed to affect the binding of CHL in the active site. Computational site-directed mutagenesis of these residues revealed that their mutation affects the conformations of key residues in the active site, leading to non-optimal binding of CHL and to changes in the structure of the oxygen channel, all of which are likely to reduce the catalytic efficiency of ChOx. Proteins 2017; 85:1645-1655. © 2017 Wiley Periodicals, Inc.

Lysozyme and Human Serum Albumin Proteins as Potential Nitric Oxide Cardiovascular Drug Carriers: Theoretical and Experimental Investigation

“…Studying protein–drug interactions, the stability of the formed complexes, investigating the strength of interactions, and the ability to release the drugs from the complexes provides significant information for drug-carrying purposes and answers to important biological questions. − The availability of computerized techniques that allow these investigations to be carried out cost-effectively has revolutionized the area of research concerned with molecular recognition, characterization of proteins, and drug design. − The exploration of the response of biomacromolecules to available drugs through computational techniques is a well-established approach. To find out possible additional use of already approved drugs, these techniques can be employed to screen these drugs against proteins of interest. − …”

Computational insights into binding mechanism of drugs as potential inhibitors against SARS-CoV-2 targets

“…Computational methods are very significant to answer fundamental biologically important questions related to ligand–protein binding affinity, complex stability, and binding mechanisms (Bentel et al 2017 ; Harb et al 2017 ; Iqbal et al 2019 ; Shehadi et al 2020 ; Wang et al 2007 ; Wei et al 2006 ; Arooj et al 2020 ). They have also been used extensively to identify the potential inhibitors of SARS-CoV-2 (Wang et al 2020 ; Ciliberto and Cardone 2020 ; Rahman et al 2020 ).…”