Lattice And All-atom Simulation Of The Nascent Peptide Folding

Variable natural phenomena are decided by the diversity of the proteins, which have most close relations with their configurations. The configurations of the proteins are extremely complicated and, when they changed a little, their biological functions will deviate from its natural one and even lose all. It is well known that DNA uses the triple coding method to determine the amino acid sequences of proteins. We also call this code as "the first genetic code". In 1950s', Anfinsen presumed that the high-level construction of the protein are decided by the order of amino acids in the protein. This presumption is well proved by lots of corresponding experiments so that it was already accepted generally. Then we call the relation between the configuration and the order of the amino acids as "the second genetic code". The problem of "the first genetic code" has been answered successfully. But so far, we haven't found a efficient key to the lock of "the second genetic code". Variable models and methods have been advanced by the experimental researches or by the theoretical ones. Though they can explain parts of the protein folding mechanism, the essential theory of the protein folding is still out of the sight of the human.Anfinsen used a pancreatic ribonuclease to study the mechanism of the protein folding. He found that, after that the pancreatic ribonuclease lose all its disulfide bonds to form a denatured state, it can spontaneously refold into its native state in a appropriate condition. The experiment gave a huge impact in the protein folding field. Since 1960's, the research of the nascent peptide mostly use the denatured protein which have already lose its high-level configuration as the model to study the process of its refolding when the denatured elements are removed in order to resolve "the second genetic code". Including the results of the researches of the protein folding in vitro, Mr. Chenglu Zou pointed out that nascent peptide folding is different from the refolding in vitro and is a simultaneously- happening process of synthesis, folding, the adjustment of the configuration.The researches of the protein refolding in vitro have provided plenty of the information about the protein folding. Though the actual process of the protein folding is more complex and intricate than that of the protein refolding in vitro, the protein refolding model can provide us some useful methods and results. The research of the nascent peptide folding is the key to resolve the problems of the protein folding.The main work in the paper is to use the lattice model and all-atom model to simulate the co-translational process of the nascent peptide. The results indicate that the folding of the nascent peptide prefers to the refolding of the stretched peptide and is consistent with the experimental phenomena. This model can give us some hints how to overcome the energy potential obstacle to find an efficient way of the protein folding into its native state.