Surface Structure and Dynamics

Self-Assembly in Membranes and Molecular Dynamics on Surfaces

Collaborative efforts with experimental groups at UVA Chemistry have yielded important findings regarding the organization of proteins in membranes and the dynamics of neurotransmitters on electrode surfaces:
 Bacterial outer membrane proteins are thought to be organized into domains or islands within the membrane. In work with Prof. David Cafiso, the E. coli outer membrane vitamin B12 transporter, BtuB, was spin-labeled, and double electron−electron resonance was used to measure the distances between proteins in intact cells. We designed Monte Carlo simulations to aid in the interpretation of EPR spectra, providing evidence for the presence of specific intermolecular contacts between BtuB monomers that could drive the formation of string-like oligomers. (Nyenhuis, JACS, 2020)
Figure 1: E. Coli Bacterial Outer-Membrane Protein. Double electron–electron resonance was used to measure the distances between E. coli outer membrane vitamin B12 transporters, BtuB, in intact cells. These data alongside Monte Carlo simulations provide evidence for the presence of specific intermolecular contacts between BtuB monomers that could drive the formation of string-like oligomers. Moreover, the EPR data provide evidence for the location of the interacting​ interfaces and indicate that lipopolysaccharide mediates the contacts between BtuB monomers (Nyenhuis, JACS, 2020).
 

Novel carbon microelectrodes enable in vivo detection of neurotransmitters. However, atomistic detail on the diffusion and orientation of neurotransmitters on these surfaces is lacking. In collaboration with Prof. B. Jill Venton, we employed molecular dynamics simulations to investigate the surface structure and diffusion of dopamine (DA) on the pristine basal plane of flat graphene, finding that all DA species rapidly adsorb to the surface and remain adsorbed, even without a holding potential or graphene surface defects. We also found that solvation has a large effect on DA surface dynamics on both flat graphene (Jia, ChemPhysChem, 2022) and curved carbon nanotube surfaces (Jia, Molecules, 2022), which results in diffusivities that depend on adsorbate charge, oxidation state, and surface curvature. Our simulations also show that diffusion differs significantly on H-terminated CNTs and graphene ribbons, and simulations of DA on the edge plane of stacked graphenes are underway.

Figure 1: Simulated Carbon Nanotubes with Adsorbed Dopamine. Dopamine diffuses into and remains in the exterior groove formed by two solvated and parallel (15,15)-carbon nanotubes, enhancing diffusivity along the carbon nanotube axis. The solvating water molecules were omitted for visual clarity (Jia, Molecules, 2022).