Anusha Kesireddy

• The outer membrane (OM) of Gram-negative bacteria contains various channels which are involved in the uptake of nutrients and antibiotics. However, the structures and functions of many OM channels are yet unknown. The research work reported in this thesis is aimed to understand the structural and functional features of three OM channels using molecular dynamics (MD) simulations in collaboration with single-molecule experiments. In the first part of the thesis, we have proposed a new protocol to study the interactions of lipopolysaccharide (LPS) with OM channels. The current state-of-the-art in the field of membrane simulations is to model the membrane channels in realistic membrane models as lipids influence the functional properties of membrane channels. However, due to the high viscosity of LPS, the interactions of OM channel with LPS and their dynamics is highly biased by the system preparation and placement of LPS molecules around the OM channels in the starting structure. Our protocol provides an improved alternative to reduce this bias and study the lipid interactions and dynamics of OM channels. A further focus of the thesis is on studying the structural and transport features of the VhChiP and OprO channels. Our collaborators have determined the crystal structures of the VhChiP channel in the open as well as in the closed state, however, the molecular details of gating are missing. To this end, we have employed MD simulations to estimate the respective free energy barrier and to predict the key residues involved in the gating of VhChiP channel. Overall, the findings presented in this thesis will improve the functional understanding of the N-terminus gating and the specificity of OM channels as well as the role of lipids in fine-tuning the dynamics of OM channels. Moreover, the protocol presented in this thesis will be helpful in studying the LPS in realistic membrane models.