Molecular Simulation Of Protein Conformation Transition In Aqueous Solution

The understanding and manipulation of the conformational transition of protein in aqueous solution, which underlies protein refolding, separation and product formulation, is essential to technological development, particularly for recombinant proteins. This dissertation started with an overview of the recent advancement of molecular simulation methods as well as their application in the protein refolding, separation and aggregation. While the major objective of the present study was to explore the way to establish a favorable conformational transition via manipulating the microenviroment by osmolyte, solid surface and polymer, the ultimate goal was to provide a molecular insight for the innovation and application of protein processing techniques.Molecular dynamics simulation of the unfolding of S-peptide as a model protein in urea solution was performed. It was shown that at a low concentration, urea molecules formed hydrogen bonds with the side chains of polar residues and thus restrained the unfolding of the S-peptide and led to an improved stability. In contrast, at a high concentration, urea molecules formed hydrogen bonds with the amino acids served as the backbone of the peptide and thus led to the unfolding of the peptide. The simulation results resembled the experimental observations reported elsewhere. The same mechanism was also valid to those osmolytes including TMAO, betaine, sorbitol, proline and glycerol, indicating that the effect of an osmolyte on the protein stability was determined by both the number and the distribution of hydrogen bonds formed with the protein.Molecular dynamics simulation of a 46 beadsβ-barrel coarse-grained model protein in hydrophobic pore showed that the protein molecules in strong hydrophobic pore likely existed in the single but unfolded states while the aggregation was inhibited by a forced dispersion of protein molecules on the pore surface. Protein conformational transition, including both refolding and aggregating, was triggered simultaneously once the elution started in which the hydrophobic interaction with the pore surface was declined. High yield of native conformation could be obtained when performing the adsorption driven by a moderate intensity of hydrophobic interaction, followed by a fast gradient elution that favored the maximum partition of native protein.Dynamic Monte Carlo simulation was performed to give a molecular insight into the inhibition of protein aggregation with polymer in aqueous solution. Here a lattice HP model was applied for both protein and polymer molecules. It was shown that the native protein aggregated once its native conformation became extended. The protein aggregation was intensified when the solution conditions favored the partially unfolded conformation as opposed to either the native or fully unfolded conformations. Introducing polymers of appropriate hydrophobicity and chain length into the solution was effective to inhibit protein aggregation, in which polymer molecules wrapped around proteins and formed protein-polymer complex thereby segregated the protein molecules. The conformation distribution of protein molecules can be manipulated by polymer compositions.Above simulation results agreed well with experimental results while provided molecular insight of the interaction between the protein undergoing conformational transition with chemical species such as urea, osmolyte, hydrophobic pore and polymer. The feasibility of manipulating protein conformational transition through adjusting solution environment was demonstrated. The results presented above are of fundamental importance to the innovation and application of protein refolding, separation and formulation techniques.