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Binding and release of cholesterol in the Osh4 protein of yeast
Author(s) -
Singh Rishi P.,
Brooks Bernard R.,
Klauda Jeffery B.
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22263
Subject(s) - antiparallel (mathematics) , binding energy , molecular dynamics , chemistry , saccharomyces cerevisiae , crystallography , yeast , binding protein , binding site , cholesterol , biochemistry , stereochemistry , biophysics , biology , computational chemistry , gene , physics , quantum mechanics , magnetic field , nuclear physics
Sterols have been shown experimentally to bind to the Osh4 protein (a homolog of the oxysterol binding proteins) of Saccharomyces cerevisiae within a binding tunnel, which consists of antiparallel β‐sheets that resemble a β‐barrel and three α‐helices of the N‐terminus. This and other Osh proteins are essential for intracellular transport of sterols and ultimately cell life. Molecular dynamics (MD) simulations are used to study the binding of cholesterol to Osh4 at the atomic level. The structure of the protein is stable during the course of all MD simulations and has little deviation from the experimental crystal structure. The conformational stability of cholesterol within the binding tunnel is aided in part by direct or water‐mediated interactions between the 3‐hydroxyl (3‐OH) group of cholesterol and Trp 46 , Gln 96 , Tyr 97 , Asn 165 , and/or Gln 181 as well as dispersive interactions with Phe 42 , Leu 24 , Leu 39 , Ile 167 , and Ile 203 . These residues along with other nonpolar residues in the binding tunnel and lid contribute nearly 75% to the total binding energy. The strongest and most populated interaction is between Gln 96 and 3‐OH with a cholesterol/Gln 96 interaction energy of −4.5 ± 1.0 kcal/mol. Phe 42 has a similar level of attraction to cholesterol with −4.1 ± 0.3 kcal/mol. A MD simulation without the N‐terminus lid that covers the binding tunnel resulted in similar binding conformations and binding energies when compared with simulations with the full‐length protein. Steered MD was used to determine details of the mechanism used by Osh4 to release cholesterol to the cytoplasm. Phe 42 , Gln 96 , Asn 165 , Gln 181 , Pro 211 , and Ile 206 are found to direct the cholesterol as it exits the binding tunnel as well as Lys 109 . The mechanism of sterol release is conceptualized as a molecular ladder with the rungs being amino acids or water‐mediated amino acids that interact with 3‐OH. Proteins 2009. Published 2008 Wiley‐Liss, Inc.