Effect of electronic polarization on alanine-based peptides' alpha helices.

• Main Author: Tung, Dickson.
• Other Authors: School of Physical and Mathematical Sciences
• Format: Final Year Project
• Language: English
• Published: 2010
• Subjects: DRNTU::Science::Chemistry::Physical chemistry::Electrochemistry
• Online Access: http://hdl.handle.net/10356/39921
• Institution: Nanyang Technological University

It is a general belief that the electrostatic field arising from the electrostatic polarization of an alpha helix is important in protein folding and its stability. In this experiment, polarized protein-specific charges update are employ to introduce this effect into conventional molecular dynamic simulation. Simulation for 3 alanine-based peptides, Ac-AAQAAAAQAAGY-NH2, Ac-AAKAAAAKAAGY-NH2,and Ac-AADAAAADAAGY-NH2 in 40% trifluoroethanol are done. As a comparison, simulation was also done using conventional force fields. Without proper inclusion of electronic polarization effect, the structure generated from the simulation are fairly similar with each other which suggest the system is unable to distinguish the substitution of amino acid. However, helix content calculated and detailed analysis of data produced from PPC update system matches experimental values thus suggesting that PPC update provides a better representation of electronic density on peptide atoms. Hydrogen bonds on alpha helix backbone are also more stable with the implementation of electronic polarization which is critcal to the stability of secondary structures on protein.