Interaction of Monotopic Membrane Enzymes with a Lipid Bilayer: A Coarse-Grained MD Simulation Study

Abstract

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.

Tryptophan Residues Promote Membrane Association for a Plant Lipid Glycosyltransferase Involved in Phosphate Stress

“…Binding and mutation data indicate that these Trp segments constitute bilayer anchor regions for the enzyme as well as substrate-interacting ones. In atDGD2 (and atC-DGD1), these regions are separated by a multitude of positive charges, likely to interact with stimulatory anionic phospholipids and potentially also promoting bilayer (or interface) penetration (25). Together, this may constitute the mechanism for control, where the amount of anionic phospholipids will determine the frequency of contacts between the catalytic region in atDGD2 and the acceptor lipid substrate GalDAG in the membrane interface.…”

“…It seems that most membrane GTs synthesizing major glycolipids are of the larger GT-B organization type (22)(23)(24). Many of these lack transmembrane segments and are anchored in the membrane interface by charge and hydrophobic interactions, qualifying as monotopic membrane proteins (25). The membrane-associated species seem to be enriched in positively charged residues, especially in their N domains, yielding high calculated pI values (24,26).…”

Massive Formation of Intracellular Membrane Vesicles in Escherichia coli by a Monotopic Membrane-bound Lipid Glycosyltransferase

“…the curvature change that the monotopic prostaglandin synthase COX-2 seems to cause in a bilayer (63,78). In Fig.…”

“…8 schematic for a comparison of surface charges). Intriguingly, it was recently reported from a molecular dynamics comparison of a dozen monotopic membrane proteins that the more Lys and Arg residues and to some extent His, in addition to hydrophobic ones in the binding surfaces, the deeper into the bilayer the proteins seem able to penetrate, potentially even reaching anionic phospholipids in the opposite monolayer (63). His is frequently found interacting with phospholipid headgroups in membrane protein three-dimensional structures, especially in sites for cardiolipin (64).…”

“…In addition, His often contributes a pH dependence for binding (65,66), becoming cationic at a slightly reduced pH. The more deeply penetrating monotopic proteins also caused a local convex change in bilayer curvature, which was absent for less penetrating species (63). Likewise, positively supercharged (soluble) green fluorescent protein can penetrate through mammalian membranes but where correspondingly charged peptides failed (67).…”