Study Of The Interaction Between Membrane Protein TAP Molecule And Antigen Peptide By Using Steered Molecular Dynamics

The transporter associated with antigen processing(TAP) plays an essential role in the antigen presentation pathway by translocating cytosolic peptides derived from prot easomal degradation into the endoplasmic reticulum lumen. Recently, more and more s tudies have confirmed that it has a strong relationship with a variety of chronic diseases and autoimmune diseases. In spite of this, due to the lack of experimental data, there are still many problems to be solved, such as the specific conformation of TAP protei n, the mechanism and signal transmission of transport circle.In this paper we use steered molecular dynamics(SMD) to simulate the interaction between antigen peptide and TAP. The antigen peptide transports though TAP’s transporter channel. During this simulation process,due to irregularity of transport channel’s structure and interaction between antigen peptide and TAP molecule, the stationary pull direction can’t be used here. Therefore, we use optimized direction to accomplish this simulation. After 1483ps time of SMD simulation, the antigen peptide transports though TAP molecule successfully, and reaches endoplasmic reticulum region. According to the RMSD(Root Mean Square Deviation), RMSF(Root Mean Square Fluctuation), comparison of the distances between some special residues and our analysis of structural changes during the simulation, we obtain the following conclusion:after SMD simulation, due to the interaction between antigen peptide and TAP molecule, the entrance of transport channel which facing the cytoplasm becomes smaller and the export which facing endoplasmic reticulum becomes larger.