Homology modelling of human DHCR24 (seladin-1) and analysis of its binding properties through molecular docking and dynamics simulations.
Recent biochemical and clinical evidences unveiled that DHCR24 enzyme (3-beta-hydoxysterol-Delta(24)-reductase, also named seladin-1), which catalyzes the last step of the cholesterol biosynthesis, is implicated in relevant neuroprotective processes by modulating the level of cholesterol in membrane. The present study was undertaken with a view to model the DHCR24 enzyme and its catalytic site, analyzing the substrate recognition at an atomic level. A homology model of the enzyme was obtained based on plant Cytokinin Dehydrogenase, and its active site was found to bind the desmosterol plus a set of post-squalenic intermediates of the cholesterol biosynthesis in a binding mode conducive to catalysis, even if the docking results suggested that the enzyme has a clear preference for the last intermediates of such biosynthetic pathway. Since DHCR24 possesses a putative transmembrane segment, the enzyme was, then, inserted in a suitable membrane model and the membrane-anchored structure in complex with desmosterol and cholesterol underwent 10ns MD simulations. Such simulations evidenced a clearly different behavior between substrate and product since the product only completely leaves the catalytic cavity whereas desmosterol firmly conserves its pivotal interactions during all simulation time. This is one of the first reports documenting the enzymatic product egress using simple MD simulations in which all atoms are free to move.
Pedretti
Alessandro
A
Istituto di Chimica Farmaceutica e Tossicologica Pietro Pratesi, Facoltà di Farmacia, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy.
Bocci
Elisabetta
E
Maggi
Roberto
R
Vistoli
Giulio
G
D020134:Catalytic Domain; D002784:Cholesterol / Q000096:biosynthesis; D019295:Computational Biology; D003198:Computer Simulation; D003897:Desmosterol / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism*; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation
D008024:Ligands; D009419:Nerve Tissue Proteins; D003897:Desmosterol; D002784:Cholesterol; D044925:Oxidoreductases Acting on CH-CH Group Donors; C499055:DHCR24 protein, human