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Computational Analysis of Sterol Ligand Specificity of the Niemann Pick C2 Protein
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Univ Southern Denmark, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark..
Univ Southern Denmark, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark..
Univ Southern Denmark, Dept Biochem & Mol Biol, DK-5230 Odense M, Denmark..
2016 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 55, no 36, 5165-5179 p.Article in journal (Refereed) Published
Abstract [en]

Transport of cholesterol derived from hydrolysis of lipoprotein associated cholesteryl esters out of late endosomes depends critically on the function of the Niemann Pick Cl (NPC1) and C2 (NPC2) proteins. Both proteins bind cholesterol but also various other sterols and both-With strongly varying affinity: The molecular mechanisms under lying this multiligand specificity are not known. On the basis:Of the crystal structure of NPC2, we have here investigated structural details of NPC2 sterol interactions using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA): calculations. We found that an aliphatic side chain in the sterol ligand results in strong binding to NPC2, while side chain oxidized sterols gave weaker binding. Estradiol and the hydrophobic amine U18666A had the lowest affinity of all lested ligands and at the same time showed the highest flexibility within the NPC2 binding pocket. The binding affinity of all ligands correlated highly with their calculated partitioning coefficient (logP) between octanol/water phases and with the potential of sterols to stabilize the protein backbone. prom molecular dynamics simulations, we suggest a general mechanism for NPC2 mediated sterol transfer, in which Phe66, Val96, and Tyr100 act as reversible gate keepers. These residues stabilize the sterol in the binding pose via pi-pi stacking but move transiently. apart during sterol release. A computational mutation analysis revealed that the binding of various ligands depends critically on the same specific amino acid residues within the binding pocket providing shape complementary to sterols, but also on residues in distal regions of the protein.

Place, publisher, year, edition, pages
2016. Vol. 55, no 36, 5165-5179 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-305456DOI: 10.1021/acs.biochem.6b00217ISI: 000383316000018PubMedID: 27533706OAI: oai:DiVA.org:uu-305456DiVA: diva2:1038663
Funder
Novo Nordisk
Available from: 2016-10-19 Created: 2016-10-18 Last updated: 2016-10-19Bibliographically approved

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Poongavanam, Vasanthanathan
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