Improvement On A Simplified Model For Protein Folding Simulation

The research on the protein folding is pioneering and interdisciplinary in the area of life science. The protein is a kind of biological macromolecules constructed by 20 types of amino acid with peptide bond. Protein can achieve a specific three-dimensional structure in which they can perform their biological function related to various life activities. So it has been a research highlight to explore the 3D structure of protein and understand how to achieve the specific structure, that is the so-called "protein folding problem". Since the famous Anfinsen's experiment on enzyme ribonuclease, it is widely accepted that the correct three-dimensional conformation of a protein is contained in its primary amino acid sequence. However how to predict its three-dimensional conformation from its primary sequence and so to predict its function is a challenging work. Because of the limitation of experiment method on protein structures, the information about protein sequence increase faster than the information about protein structure. And the theory research by protein folding simulation becomes an important research technique. When we simulate the protein folding with computers the main problem arising is the incapability of computing power compared to the enormous conformation space of protein. In order to achieve the balance between them, people have proposed various simplified models. In our job we adopted an appropriate simplified model and made some improvement on them, so as to reveal more characteristics and rules about protein folding. Our work can be divided into two main parts: (1) We made improvement on Ramachandran model which can be successfully used on the simulation of 3-helices protein folding. The investigating target of the original Ramachandran model is a de novo designed sequence. Our goal is to make it available for sequences of native proteins. (2) With the improved Ramachandran model, we can explore the thermodynamic and kinetic characteristic of protein folding, folding pathway and the symmetries of protein sequences and structures.