Abstract
Bacteriorhodopsin (bR) is a photoactive protein that has gained increasing importance as a tool for optical memory storage due to its remarkable photochemical and thermal stability. The two stable photostates (bR and Q) obtained during the bR photocycle are appropriate to designate the binary bit 0 and 1, respectively. Such devices, however, have limited success due to a low quantum yield of the Q state. Many studies have used genetic and chemical modification as optimization strategies to increase the yield of the Q state. Nonetheless, this compromises the overall photochemical stability of bR. This paper introduces a unique way of stabilizing the conformations of bacteriorhodopsin and, thereby, the bR and Q photostates through adsorption onto graphene. All-atom molecular dynamics (MD) simulations with NAMD and CHARMM force fields have been used here to understand the interactive events at the interface of the retinal chromophore within bR and a single-layer graphene sheet. Based on the stable RMSD (~4.5 Å), secondary structure, interactive van der Waals energies (~3000 kcal/mol) and electrostatic energies (~2000 kcal/mol), it is found that the adsorption of bR onto graphene can stabilize its photochemical behavior. Furthermore, the optimal adsorption distance for bR is found to be ~4.25 Å from the surface of graphene, which is regulated by a number of interfacial water molecules and their hydrogen bonds. The conformations of the key amino acids around the retinal chromophore that are responsible for the proton transport are also found to be dependent on the adsorption of bR onto graphene. The quantity and lifetime of the salt bridges also indicate that more salt bridges were formed in the absence of graphene, whereas more were broken in the presence of it due to conformational changes. Finally, the analysis on the retinal dihedrals (C11 = C12-C13 = C14, C12-C13 = C14-C15, C13 = C14-C15 = NZ and C14-C15 = NZ-CE) show that bacteriorhodopsin in the presence of graphene exhibits increased stability and larger dihedral energy values.
Highlights
Bacteriorhodopsin is a widely explored photoactive protein for a variety of biomolecular electronics applications, including optical memory storage [1,2]. bR is a membrane protein found in the salt marsh archaeon, Halobacterium salinarum, and comprises a photoactive moiety called retinal chromophore (C20 H28 O) in the middle of a channel formed by seven transmembrane alpha helices (A–G) [3]
In the case where a protein is adsorbed on a surface, the protein exposes its core hydrophobic residues to strongly interact with the surface. This results in a less solvent-accessible surface area and, a more stable protein. This binding between the protein and the hydrophobic surface is primarily due to the hydrophobic interactions and van der Waals forces, but it is envisaged that such interactions are governed by the number of water molecules at the interface through the electrostatic energies
Higher deviation and less fluctuations in the Root Mean Square Deviation (RMSD) data indicates more conformational changes that occur for bacteriorhodopsin due to its adsorption onto the graphene surface, and based on the graphene and bR interface study, it can be concluded that the optimal distance for these interactions to be maximized is ~4.2 Å
Summary
Bacteriorhodopsin (bR) is a widely explored photoactive protein for a variety of biomolecular electronics applications, including optical memory storage [1,2]. bR is a membrane protein found in the salt marsh archaeon, Halobacterium salinarum, and comprises a photoactive moiety called retinal chromophore (C20 H28 O) in the middle of a channel formed by seven transmembrane alpha helices (A–G) [3]. BR is a membrane protein found in the salt marsh archaeon, Halobacterium salinarum, and comprises a photoactive moiety called retinal chromophore (C20 H28 O) in the middle of a channel formed by seven transmembrane alpha helices (A–G) [3]. It has a primary role of facilitating proton transportation and, generating a proton gradient across the cell membrane through a photochemical cycle [3]. In bR, the ground (bR) state is appropriate to designate bit 0, as it remains stable until a yellow light activates the photocycle. The protein enters the branched photocycle only when the all-trans O intermediate (where Asp is still protonated) is illuminated with red light
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