Study On The Changing Of Conformation And Stability Before And After The Combination Of Intrinsically Disordered Proteins CBP And P53

Intrinsically disordered protein P53, which has close relation with tumor, plays a very important role in cell signal transduction network. CBP(CREB binding protein) is a regulation protein of P53, which plays role of scaffolding by its inherent acetylation in cell transcription modification mechanism. There are many binding sites between CBP and P53, especially the binding site between the NCBD(C-terminal domain of CBP protein) and the TAD(N-terminal transcription activation domain of P53 protein). It was found that the TAD monomer is complete disordered, and the monomer NCBD is partly disordered, but their complex is orderly structure. This shows that the binging process is a process of changing their structures. The research not only helps to understand the change of the conformations when they are combined, but also helps to understand the regulatory mechanism of the disordered protein P53.Molecular dynamics(MD) simulation is a powerful tool used to study proteins. In this paper, the MD simulations were used to study interaction of the intrinsically disorderly protein P53 and CBP protein. The MD trajectories were analyzed to provide stability and conformation information by calculating the free energy, the tertiary structure and so on of the monomer TAD, the NCBD and their complex. The main results are as follows:1. TAD monomer which is N-terminal transcription activation domain of P53(consists of 49 residues), NCBD monomer of CBP protein(included 59 residues) and their complex(included 108 residues) are completed for long time molecular dynamics simulations, respectively. Based on the MD simulations, all kinds of the structural parameters are analyzed, which is important to understand the regulation mechanism of P53 and to reveal the interaction mode between the intrinsically disordered protein P53 and CBP at atomic level.2. The research results show that TAD monomer and NCBD monomer is disordered before the combination, which is very flexible and only contains some sparse structure and can't form stable structure. However, when TAD and NCBD are combined with each other, the free energy of the complex is much lower than the free energy of the single monomers TAD with NCBD, showing that the combination complex is more stable, lower flexible and bigger probability forming the secondary structure helix.3. The results further show that the secondary structures change much when the monomers NCBD and TAD combined into the complex. The two new helix structures were found, and the distance between the original two helixes become larger, and the random curls increased too. In the MD simulation of the complex, the distance between helix ?1 and helix of ?3 of NCBD increased, and the distance between helixes ?1 and ?2 become smaller than those in the monomers NCBD and TAD, and the secondary structure helixes and random coil appear bigger probability. The results show that the complex is more stable.The paper is divided into four parts. The first chapter is introduction, introducing the intrinsically disorderly protein and their physiological function, and the CBP protein and P53 protein are disordered, then we introduced the structure domains NCBD, TAD and the relation with human diseases. The second chapter introduced the MD simulation, including the MD simulation, the experience force field, the principle of MD simulation, the analysis method, GROMACS software and the MD developing. In the third chapter, MD simulation was used to study the apo-TAD, apo-NCBD and the complex. The fourth chapter is the conclusion and prospect.