1. Phys. Dept., Fudan Univ., Shanghai, People’s Republic of China
A Graphine-Induced Transformation of Peptide Secondary Structure
Student: Luchun Ou, Professor: Guanghong Wei
Phys. Dept., Fudan Univ., Shanghai, People’s Republic of China
Recent experimental data show that the polypeptide (DELERRIRELEARIK) undergoes a structural transtion from α-helical to β -sheet-like secondary structure upon the addition of graphite particles to the peptide solution [1].
I. Introduction
The pathogenesis of some diseases featuring amyloids is associated with an α-β conformational transitions of part of the proteins.
Experimental results [1]
However, it is difficult to investigate the detailed process of peptide conformational transition by experiments. By molecular dynamic simulations, we can study the peptide conformational transition mechanism induced by graphine.
II. Model and method:
Molecular Dynamic Simulation (Software: GROMACS; All-atom model; OPLS force field). MD simulations solve Newton’s equations of motion for a system of N interacting atoms:
The forces are the negative derivatives of a potential function V:
III. Results and Discussion
IV. Problems and Directions
A trimer is stable in solution with or without graphine during the simulation time.
Two peptide chains are stable in helical structure in solution in the absence of graphine. A dimeric structure is obtained in our MD run in the presence of graphine.
The peptide may need much longer time to undergo the secondary structural transitions. The time scale for structural transition is minutes in experiments, while simulations can only reach to hundreds of nanoseconds.
The peptide is dimeric under physiological buffer conditions [2]. It may be interesting to see what will happen when a dimer is adsorbed at the interface.
Other strategies will be used to study the peptide conformational transition mechanism induced by graphine.
References
Xiaobo Mao, Yibing, Wang, Lei Liu, Lin Niu, Yanlian Yang, and Chen Wang, Langmuir, 2009, 25(16),
Burkhard, P., Meier, M., and Lusig, A., Protein Sci., 2000, 9,