A study on protein secondary structure phase transition based on an effective hydrogen bonding potential
Leong, Hon Wai
Date of Issue2013
School of Physical and Mathematical Sciences
In this thesis, we define the single unit of a polypeptide as crank. Using this convention, we formulate the Hamiltonian of polypeptide. In our canonical formalism, the dihedral angles of polypeptide chain are treated as generalized coordinates, and we take the assumption that the effective potential of a polypeptide chain is contributed by hydrogen bonding alone. We have employed such formalism to analyze the normal modes distribution of polypeptide secondary structures, such as the α-helix and the β-sheet. Interestingly, our results are in agreement with literature. Following this success, assuming that the dihedral angles of each crank only folds into five distinct states, we derive the grand partition function of polypeptide chain. We study the phase transition of polypeptide secondary structures and its statistical properties. Our theory has successfully demonstrated the α-β-coil phase transition of polypeptide secondary structure in a single plot. Our results emphasize the role of hydrogen bonding network in polypeptide secondary structure phase transition. At the conclusion of this thesis, we discuss the potential of our research and the obstacles to be overcome in order to refine the results obtained so far.