The Forced Unfolding Of Cold Shock Protein By Steered Molecular Dynamics Simulation

The mechanisms of protein folding and unfolding, is the important field of protein research. The proteins must fold into their correct three-dimensional conformation in order to attain their biological function. Protein folding is the most fundamental and universal example of biological self-assembly. How a polypeptide chain folds into a stable, native structure in vivo is dependent on amino acid sequence and native solution environment. Generally, the polypeptide chain with given amino acid sequence can spontaneously fold into a certain three-dimensional structure with unique biological function. But structual transition could take place when the environment of protein is changed, that is to say, the three-dimensional strunture of protein is determined by not only its thermodynamic stability, but also the micro-environment of protein and kinetic process.Structual transition of protein is common phenomena in organism. The research found that the structural transition and misfolding of protein could lead to serious diseases. On the other hand, the overexpression of recombinant proteins in Escherichia coli often results in the accumulation of the protein, producing inactive insoluble deposits inside the cells, called inclusion bodies. Therefore, the study on the mechanism of protein folding and the development of more efficient folding methods is very important in theory and practice.Besides a series of experimental techniques(AFM, optical tweezers etc.), the molecular dynamics simulation posses irreplaceable effect for such research.Molecular dynamics, one of the most populars simulation methods, has been proved to be a p powerful tool in simulating dynamic properties of protein. Molecular dynamics simulations can provide a atomical realistic view of the folding and unfolding process from picosecond to millisecond. even though MD simulation about biomacromolecule is in a short time, MD simulations have succeed in these field, and it need further development to overcome its disadvantage.Thermophilic and mesophilic cold shock protein,which have been employed to model forced unfolding of cold shock protein. We study the unfolding process and mechanism of the proteins by external force with dynamics software package NAMD. The completely unfolding of the proteins were thought as end of dynamics simulation.We chiefly study the unfolding mechanism of the proteins under the interaction of hydrogen bond; electrostatic and hydrophobe, come to the conclusion as follow:1. We not only introduced the basic principle of molecular dynamics simulation, concept of steered molecular dynamics simulation, and basic principle of protein.2. Using steered molecular dynamics simulation, we explored the unfolding process of mesophilic cold shock protein by constant velocity and constant force. The results indicate thatβsheet of C terminal of mesophilic cold shock protein is reptured, susequentlyβsheet of N terminal. Then we explored the interior force that determine the unfolding process.3. Using steered molecular dynamics in constant velocity and constant force, we explored the Similarities and Differences in the Forced Unfolding of Thermophilic and Mesophilic Cold Shock Proteins. The results indicate that the proteins follow same unfolding process, in the course of constant velocity unfolding, the C terminal is reptured at first, susequently N terminal. But the mestphilic cold shock protein need a bigger force in the beginning.With continuing advances in both computers and algorithms, computer simulations will play an even more important role for understanding of protein folding/unfolding and functional motions in the future.