Atomistic Simulations of Protein Conformational Changes: Biological and Engineering Applications

S M Yead Murshed Jewel

Proteins are large bio-molecules exist in all living organisms consist of amino acids. Molecular interactions result in a hierarchy of protein structures essential to biological functionalities. In this thesis, through simulations we investigate several important biological processes and engineering applications directly related to conformational changes of different proteins. First, we implemented a hybrid force field (PACE) to investigate the conformational changes of lactose permease during the sugar transport process. A new coarse-grained force field for sugar molecule has been developed and implemented. Our simulation results showed important structural changes on LacY and dynamic interactions during lactose/H+ symport. In addition, we implemented the PACE force field to study the drug transport and the associated conformational changes of multidrug transport proteins. Our results indicated the structural changes from both the extrusion (E) and the binding (B) state to the access (A) state, which strongly support the existing postulation that in substrate-free situation the AcrB should adopt the symmetric AAA resting state. Secondly, we have performed all-atom molecular simulations to investigate the denaturation process of a soy-protein and two potential engineering applications. The first application is the use of denatured soy-protein for graphite nanoplatelet dispersion. Our results demonstrated that, TFE is able to effectively denature the soy protein, especially at high temperature leading to much smaller agglomeration sizes and therefore significantly improved dispersion. The second application is the use of denatured soy-protein for making solid ion conductors. Our results showed that, ion transport in the protein ion conductor is facilitated by the anions “locked” by specific functional groups in the protein structure. A decoupled transport mechanism, similar to the conduction in ceramic conductors is also proposed. Finally, we have investigate the potential application of self-assembled synthetic peptides as the coating materials on sulfur nanoparticles through all-atom simulations. Three different types of electrically conductive synthetic peptides were evaluated in our study. Results indicated that both poly-proline and poly (leucine-lysine) peptides can effectively cover the sulfur surface in both pyrrolidinone and DOL/DME solvents while only poly (leucine-lysine) peptide can slow down the loss of active sulfur materials at the cathode side of a Li-S cell.

Atomistic Simulations of Protein Conformational Changes: Biological and Engineering Applications

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