Poster V11 - Conformational Changes in Bacteriorhodopsin Embedded Within a Purple Membrane on Adsorption to Graphene and PVA Surfaces

Introduction: Microorganisms' purple membrane (PM), containing bacteriorhodopsin (BR)proteins, harnesses solar radiation for energy. This pigment, crucial for light-driven proton pumps, finds applications in bioelectronics, one of which we are focusing on is a memory device. Previous research demonstrated enhanced Q photostate yield through hydrogen bonds and conformational changes when BR monomers bind to graphene sheets. To this end, this study further investigates the Q photostate yield by BR trimers embedded within PM on graphene monolayers and separately over synthetic polyvinyl alcohol (PVA) polymers. Using CHARMM-GUI, the PM was simulated with 70% PG and 30% BPG, GlyC, S-TGD-1, and PGS lipid composition. Trimeric BR structures were inserted into lipid bilayers with six subsequent 250ns simulations using Visual Molecular Dynamics (VMD) and Nanoscale Molecular Dynamics (NAMD), employing CHARMM force fields. Anticipated results include increased hydrogen bonding and electrostatic activity along with Van der Waals forces that enhance electron transfer capabilities.

Materials and

Methods: The PM was developed through the lipid bilayer generation, protein structure insertion, and simulation parameter setup functions of CHARMM-GUI with 70% PG and 30% BPG, GlyC, S-TGD-1, and PGS lipid composition. The trimeric BR structure was retrieved from the OPM database and inserted into the lipid bilayers with Z-axis alignment and 90-degree rotation. Using VMD the two graphene layers are merged with the PM containing BR for the first set of simulations and with two molecules of PVA polymer for the second set of simulations, in each case the graphene and PVA molecules were placed on the extra- and intra-cellular sides of the PM. The modeled structures further underwent NaCl auto-ionization in a water box. NAMD and CHARMM force fields were integrated to independently minimize and equilibrate three independent trials for the control PM and the two experimental models containing graphene and PVA separately. All the simulated trajectories were analyzed for RMSD, center of mass distance analysis, hydrogen bonds, adsorption energies, optimal adsorption distances, and the number and hydrogen bond analysis of the interfacial water molecules for exhaustive analysis.

Results, Conclusions, and Discussions: The control bacteriorhodopsin showed significant variation in Root Mean Square Deviation, peaking at 40Å (Figure 1), whereas trial 1 of the experimental bacteriorhodopsin exhibited less stability, reaching a peak at 50Å (Figure 2). Interaction with graphene stabilized the experimental bacteriorhodopsin around 100ns (Figure 2). Both control and experimental structures displayed consistent hydrogen bond fluctuations in the range of 150-200. Six common strong salt bridges were identified in both control and experimental structures (Table 1), with two broken bridges in the experimental group in the presence of graphene (Table 2). This is ongoing research and an exhaustive analysis to compare the impact of bacteriorhodopsin absorption on graphene and PVA polymer surfaces for enhanced structural stability is currently underway.

Acknowledgements (Optional): We would like to thank Fairfield University INSPIRE (Hardiman) travel grant and for providing computational resources for carrying out molecular simulations.