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Author Mustafa, Ghulam ♦ Nandekar, Prajwal P. ♦ Yu, Xiaofeng ♦ Wade, Rebecca C.
Source United States Department of Energy Office of Scientific and Technical Information
Content type Text
Language English
Subject Keyword INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY ♦ ATOMS ♦ COMPARATIVE EVALUATIONS ♦ CRYSTAL STRUCTURE ♦ CYTOCHROMES ♦ GRAIN SIZE ♦ IMPLEMENTATION ♦ INTERACTION RANGE ♦ LAYERS ♦ MEMBRANE PROTEINS ♦ MEMBRANES ♦ MOLECULAR DYNAMICS METHOD ♦ ORIENTATION ♦ PHOSPHOLIPIDS ♦ WATER
Abstract An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions.
ISSN 00219606
Educational Use Research
Learning Resource Type Article
Publisher Date 2015-12-28
Publisher Place United States
Journal Journal of Chemical Physics
Volume Number 143
Issue Number 24


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