The study of conformational transitions in proteins via molecular dynamics simulations

Molecular dynamics simulations of small, yet biologically relevant, proteins were performed to gather detailed information about the conformational transitions involved for each protein. In preparation, a recently developed implicit solvent model (GBSW), was applied to chemotaxis Y (CheY) to investigate its usefulness in mechanistic studies of conformational transitions. The results were compared to explicit solvent simulations and many properties were well reproduced. However, the GBSW model appears to overestimate hydrogen-bonding interactions, leading to overstabilization of certain secondary structural motifs and, more importantly, qualitatively different behaviors for the active site groups. This highlighted the value of using both explicit and implicit solvent simulations for complementary mechanistic insights in the analysis of conformational transitions.; To explore the coupling between conformational transition and phosphorylation, CheY was used as a simple but representative example of protein allostery. Results support an activation mechanism in which the beta4 - alpha4 loop gates the isomerization of Tyr 106. The role of phosphorylation and Thr 87 is deemed indirect because they stabilize the active configuration of the beta4 - alpha4 loop. This role of stabilizing, rather than causing, specific conformational transition is likely a feature in many signaling systems. The current analysis of CheY also helps to make clear that neither the "old" (induced-fit) nor the "new" (population-shift) views for protein allostery is complete because they emphasize the kinetic (mechanistic) and thermodynamic aspects of allosteric transitions, respectively.; The effects of temperature and salt concentration on structural stability were studied with human Lymphotactin (hLtn). Ion distribution and stability exhibited a dependence on the local sequence and structure. Whereas chloride association to the protein is enhanced overall as the temperature increases, the chloride and sodium distributions in the C-terminal helical region were strikingly higher at lower temperature. The C-terminal helix partially melted while a short beta strand formed at the higher temperature with little salt dependence. The N-terminal region was observed to develop partial helical structure with a higher salt concentration. These observed behaviors are consistent with solvent and salt screening stabilizing hLtn, and suggest that electrostatic interactions are likely involved in facilitating the dramatic transition of hLtn to the non-chemokine fold.