Niraj Hasmukhbhai Modi

• Ion transport through membrane proteins and nanopores is a process of significant importance which has implications ranging from controlling various biological processes to applications in the field of nanoanalytics and stochastic sensing. Therefore it is imperative to probe the behavior and dynamics of ions in nanoscale confinements provided by membrane proteins. The research work reported in this thesis is aimed at understanding ion transport processes, namely ion selectivity and ion conductance, through bacterial outer membrane porins using molecular dynamics simulations. The major focus of this thesis is to probe the phosphate selectivity of the OprP porin from the bacterium Pseudomonas aeruginosa. The protein OprP is induced in the outer membrane of bacteria under conditions of phosphate starvation and is responsible for the high-affinity uptake of phosphate ions under such circumstances. Free-energy molecular dynamics simulations revealed atomic details leading to the phosphate selectivity of the channel. To further understand the phosphate selectivity of OprP and underlying structure-function relationships, several important residues of OprP have been mutated. Such studies on the mutant OprP channels have enabled us to probe the relative contributions of the residues and their properties, namely charge, size, the ability to desolvate the permeating ion etc., in assigning the phosphate selectivity to OprP. Moreover, the findings obtained for the phosphate selectivity of OprP were further extended to probe the diphosphate selectivity of OprO, a homologous porin of OprP with a high sequence and structural similarity. In silico double mutants of OprP and OprO demonstrated a trend to interchange the phosphate selectivity of OprP and the diphosphate selectivity of OprO. The other focus of the thesis is to decipher the ion conductance properties through the OmpF and NanC porins from Escherichia coli. A particular kind of bulky ions, i.e., ionic liquids have been investigated with respect to their temperature-dependent pore conductance properties through OmpF. Such ionic liquids can improve the time-resolution of electrophysiological measurements and may be useful in various biosensing applications. Applied-field simulations revealed the importance of a particular orientation of the permeating ion to be able to pass through the pore. In case of NanC, an asymmetric distribution of charged residues inside the pore was found to be responsible for an asymmetric conductance property and a weak anion selectivity of the porin. In addition, mutants of OmpF and NanC have been generated to modify ion conductance properties of these porins. The findings presented in this thesis enhance the atomistic and functional understanding of ion transport processes through bacterial outer membrane porins in particular and various other membrane proteins in general. Molecular details obtained from such studies can be further exploited to engineer the ion transport properties through nanopores to achieve diverse possible applications, e.g., the design of ion-specific sieves and sensing of biological agents.