Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Felipe Cardoso Ramos, Stefano Caprasecca, Lorenzo Cupellini and Benedetta Mennucci
Universita di Pisa, Italy
Posters & Accepted Abstracts: J Proteomics Bioinform
Statement of the Problem: The light harvesting apparatus of typical purple photosynthetic bacteria is composed by the LH1 and LH2 complexes, which act together in the absorption and transfer of light energy to the photosynthetic reaction center (RC). The LH2 complexes are circular membrane proteins formed by nine dimeric apoproteins, the α and β chains, bound to one carotenoid (Car) molecule and three bacteriochlorophyll a (Bchl) molecules (B800, B850α and B850β). Purple bacteria express LH2 complexes with different αβ apo-proteins depending on the light intensity, which allows them to adapt to the luminosity conditions. The species Rhodopseudomonas acidophila (Rps. acidophila), for example, produces LH2 complexes with absorption at 800 and 850 nm (B800-850) when in high light (HL) conditions, but when in low light (LL) conditions they are replaced by complexes that absorb at 800 and 820 nm (B800-820). Methodology & Theoretical Orientation: Here, we performed classical molecular dynamics (MD) simulations of LH2 complexes from purple bacteria in lipid membranes, aimed to generate atomistic models for these light harvesting complexes, focusing on the genus Rhodopseudomonas. Findings: Analysing the trajectories obtained, we verified that the size and the circular shape of complexes were well preserved along the simulations. In addition, our simulations were able to reproduce the main protein pigments interactions described in the crystallographic structures. Conclusion & Significance: Through the simulation protocol applied it was possible to produce equilibrated models for entire HL and LL LH2 complexes in membranes. These models are currently been employing in hybrid quantum mechanics/ molecular mechanics (QM/MM) calculations which will allow us to simulate the absorption spectra of the complexes. At the end of this study, we hope to provide detailed structural explanations about the occurrence of different spectra and contribute to the understanding of the molecular mechanisms that govern the purple bacteria adaptation to dark environments.