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Monotopic membrane proteins bind tightly to cell membranes but do not generally span the lipid bilayer. Their interactions with lipid bilayers may be studied via coarse-grained molecular dynamics (CG-MD) simulations. Understanding such interactions is important as monotopic enzymes frequently act on hydrophobic substrates, while X-ray structures rarely provide direct information about their interactions with membranes. CG-MD self-assembly simulations enable prediction of the orientation and depth of insertion into a lipid bilayer of a monotopic protein, and also of the interactions of individual protein residues with lipid molecules. The CG-MD method has been evaluated via comparison with extended (>30 ns) atomistic simulations of monoamine oxidase, revealing good agreement between the results of coarse-grained and atomistic simulations. CG-MD simulations have been applied to a set of 11 monotopic proteins for which three-dimensional structures are available. These proteins may be divided into two groups on the basis of the results of the simulations. One group consists of those proteins which are inserted into the lipid bilayer to a limited extent, interacting mainly at the phospholipid-water interface. The second group consists of those which are inserted more deeply into the bilayer. Those monotopic proteins which are inserted more deeply cause significant local perturbation of bilayer properties such as bilayer thickness. Deeper insertion seems to correlate with a greater number of basic residues in the "foot" whereby a monotopic protein interacts with the membrane.

Original publication

DOI

10.1021/bi8017398

Type

Journal article

Journal

Biochemistry

Publication Date

17/03/2009

Volume

48

Pages

2135 - 2145

Keywords

Animals, Binding Sites, Computer Simulation, Databases, Protein, Enzymes, Humans, Hydrolases, Hydrophobic and Hydrophilic Interactions, Isomerases, Lipid Bilayers, Membrane Proteins, Models, Molecular, Oxidoreductases, Phospholipids, Protein Binding, Protein Conformation, Protein Structure, Secondary, Static Electricity, Transferases