Properties of DNA- and Protein-Scaffolded Lipid Nanodiscs

Abstract

The properties of natural lipid bilayers are vital to the regulation of many membrane proteins. Scaffolded nanodiscs provide an in vitro lipid bilayer platform to host membrane proteins in an environment that approximates native lipid bilayers. However, the properties of scaffold-enclosed bilayers may depart significantly from those of bulk cellular membranes. Therefore, to improve the usefulness of nanodiscs it is essential to understand the properties of lipids restricted by scaffolds. We used computational molecular dynamics and modeling approaches to understand the effects of nanodisc size, scaffold type (DNA or protein), and hydrophobic modification of DNA scaffolds on bilayer stability and degree to which the properties of enclosed bilayers approximate bulk bilayers. With respect to achieving bulk bilayer behavior, we found that charge neutralization of DNA scaffolds was more important than the total hydrophobic content of their modifications: bilayer properties were better for scaffolds having a large number of short alkyl chains than those having fewer long alkyl chains. Further, complete charge neutralization of DNA scaffolds enabled better lipid binding, and more stable bilayers, as shown by steered molecular dynamics simulations that measured the force required to dislodge scaffolds from lipid bilayer patches. Considered together, our simulations provide a guide to the design of DNA-scaffolded nanodiscs suitable for studying membrane proteins.

Structural and Biophysical Properties of Supercharged and Circularized Nanodiscs

“…Using eq , we determined the width of such a boundary layer to be ≈20 Å, which corresponds to a corona of ≈2.5 DMPC lipids wide. This provides experimental verification of MD simulations, reporting that the lipid packing is high in the center of nanodiscs and gradually drops the closer the lipids are to the surrounding MSP. , Ideally, the choice of the MSP for nanodisc preparation should be made by making sure to use a MSP large enough that the membrane protein is unlikely to be located in the region of the lipid bilayer corresponding to the boundary lipid layer. In this regard, it is interesting to note that the Escherichia coli lipid transporter MsbA has up to a 100-fold tighter binding to ATP but a slower hydrolysis rate in large nanodiscs (MSP1E3D1) compared to that in smaller nanodiscs (MSP1D1) .…”

Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes

“…Coarse-grained MD simulations found that the number of charge-neutralized DNA nucleotides can be as important as the length of the hydrophobic alkyl chains in stabilizing a patch of a lipid bilayer encircled by a DNA origami nanodisc. 36 Another all-atom MD study of membrane-spanning nanopores 37 found the density of the charges along the DNA backbone to affect the transmembrane transport of water and ions. While computational exploration of larger DNA−lipid constructs is currently possible using the allatom MD approach, 38 multiresolution simulation approaches 39 are expected to bring out the best combination of computational efficiency and molecular realism.…”

“…In addition to the hydrophobicity of individual charge-neutralized nucleotides, their density within a DNA duplex can also influence the binding and insertion of DNA into a lipid bilayer membrane. Coarse-grained MD simulations found that the number of charge-neutralized DNA nucleotides can be as important as the length of the hydrophobic alkyl chains in stabilizing a patch of a lipid bilayer encircled by a DNA origami nanodisc . Another all-atom MD study of membrane-spanning nanopores found the density of the charges along the DNA backbone to affect the transmembrane transport of water and ions.…”

General Protocol for Constructing Molecular Models of Nanodiscs

“…Several molecular dynamics (MD) studies have been performed on NDs and related lipid particles, analyzing their self-assembly and structural properties. ,− However, setting up simulation systems of NDs is not a trivial task. In 2015, Siuda and Tieleman published a potential protocol for constructing NDs in silico , based on the crystal structure with PDB ID 1AV1 .…”