title: Nucleation process in the folding of a domain-swapped dimer.
abstract: Nucleation processes are important for the understanding in protein dynamics. To evaluate the effect of nucleation mechanism in dimerization process, a domain-swapped dimer (Esp8) is simulated with the symmetrized Gō model and the classical Gō model. The pathways of the dimerization are analyzed with computational phi -analysis method. It is found out that some nuclei are observed in the kinetic steps of the dimeric association though the whole pathway is a process with multiple intermediate states. The key residues in the nuclei are rather similar to those observed in the monomeric folding. The differences with the monomeric cases are also discussed. These differences illustrate the effects of dimeric feature on the nucleation process. Besides, manual mutations are carried out to illustrate the importance of the interactions related to the nuclei. It is observed that the mutations in the nuclei-related interactions apparently change the dynamics while other mutations have little effect on the kinetics. All of these results outline a picture that the nucleation processes act as the fundamental steps of high-order organization of protein systems.
authors.affiliation: National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Yan
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Yujie
authors.initials: Y
authors.lastname: Zhang
authors.forename: Meng
authors.initials: M
authors.lastname: Qin
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation; D011336:Probability; D017510:Protein Folding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D011506:Proteins