Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol

Marta Murcia,José D Faráldo-Gómez,Frederick R Maxfield,Benoît Roux

doi:10.1194/jlr.m600232-jlr200

Abstract

Steroidogenic acute regulatory protein-related lipid transfer (StART) domains are ubiquitously involved in intracellular lipid transport and metabolism and other cell-signaling events. In this work, we use a flexible docking algorithm, comparative modeling, and molecular dynamics (MD) simulations to generate plausible three-dimensional atomic models of the StART domains of human metastatic lymph node 64 (MLN64) and steroidogenic acute regulatory protein (StAR) proteins in complex with cholesterol. Our results show that cholesterol can adopt a similar conformation in the binding cavity in both cases and that the main contribution to the protein-ligand interaction energy derives from hydrophobic contacts. However, hydrogen-bonding and water-mediated interactions appear to be important in the fine-tuning of the binding affinity and the position of the ligand. To gain insights into the mechanism of binding, we carried out steered MD simulations in which cholesterol was gradually extracted from within the StAR model. These simulations indicate that a transient opening of loop Omega1 may be sufficient for uptake and release, and they also reveal a pathway of intermediate states involving residues known to be crucial for StAR activity. Based on these observations, we suggest specific mutagenesis targets for binding studies of cholesterol and its derivatives that could improve our understanding of the structural determinants for ligand binding by sterol carrier proteins.

Highlights

Steroidogenic acute regulatory protein-related lipid transfer (StART) domains are ubiquitously involved in intracellular lipid transport and metabolism and other cell-signaling events
The StART domain of the steroidogenic acute regulatory protein (StAR) protein is the prototype of a larger, only partially characterized family of lipid binding domains found in other eukaryotic proteins, which are essential in a variety of important processes such as lipid transport and metabolism and cell signaling [3]
Of the 2,000 best-scored solutions obtained from the docking protocol, a total of 1,357 were found inside the metastatic lymph node 64 (MLN64)-StART cavity

Summary

Introduction

Steroidogenic acute regulatory protein-related lipid transfer (StART) domains are ubiquitously involved in intracellular lipid transport and metabolism and other cell-signaling events. To gain insights into the mechanism of binding, we carried out steered MD simulations in which cholesterol was gradually extracted from within the StAR model These simulations indicate that a transient opening of loop 61 may be sufficient for uptake and release, and they reveal a pathway of intermediate states involving residues known to be crucial for StAR activity. Based on these observations, we suggest specific mutagenesis targets for binding studies of cholesterol and its derivatives that could improve our understanding of the structural determinants for ligand binding by sterol carrier proteins.—Murcia, M., J. StART domains are distinct from other known lipidtransfer proteins and are believed to be highly specific for their ligands, which include cholesterol, phosphatidylcholine (PC), carotenoid, and ceramide [23, 24], a common ligand binding mechanism is thought to be characteristic of the entire StART superfamily [25]

Methods

Results

Conclusion