Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study

• Published in: Biochimica et biophysica acta 2013-02, Vol.1828 (2), p.284-293
• Main Authors: Piggot, Thomas J., Holdbrook, Daniel A., Khalid, Syma
• Format: Article
• Language: English
• Subjects: Biological Transport; Biological Transport, Active; Cell Membrane - metabolism; Computer Simulation; Diffusion; E. coli; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Hydrogen Bonding; Ligands; Lipid Bilayers - chemistry; Lipopolysaccharide; Lipopolysaccharides - chemistry; Membrane protein; Models, Molecular; Molecular Conformation; Molecular dynamics; Molecular Dynamics Simulation; Phosphatidylcholines - chemistry; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Proteins - chemistry; Receptors, Cell Surface - chemistry; Receptors, Cell Surface - metabolism; Simulation; TonB
• ISSN: 0005-2736; 0006-3002; 1879-2642
• DOI: 10.1016/j.bbamem.2012.08.021

The TonB-dependent transporters mediate high-affinity binding and active transport of a variety of substrates across the outer membrane of Escherichia coli. The substrates transported by these proteins are large, scarce nutrients that are unable to gain entry into the cell by passive diffusion across the complex, asymmetric bilayer that constitutes the outer membrane. Experimental studies have identified loop regions that are essential for the correct functioning of these proteins. A number of these loops have been implicated in ligand binding. We report the first simulations of an E. coli outer membrane protein in an asymmetric model membrane that incorporates lipopolysaccharide (LPS) molecules. Comparative simulations of the apo and holo forms of the TonB-dependent transporter FecA in different membrane models enable us to identify the nature of the LPS–protein interactions and determine how these interactions impact upon the conformational dynamics of this protein. In particular, our simulations provide molecular-level insights into the influence of the environment and ligand on the dynamics of the functionally important loops of FecA. In addition, we provide insights into the nature of the protein–ligand interactions and ligand induced conformational change in FecA. [Display omitted] ► Molecular dynamics simulations of the TonB dependent transporter, FecA ► A complex model of the E. coli outer membrane is used. ► Simulations show that LPS–FecA interactions affect the dynamics of the protein. ► Simulations reveal conformational rearrangements of the protein interior. ► The dynamic response of the loops to the presence of ligands is shown.