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Molecular Dynamics Simulations of Folding of Saturated Polyalanine Based on the Rigidbody Dynamics Model

Author: ZhangJing
Tutor: XuPeiJun
School: Liaoning Normal University
Course: Particle Physics and Nuclear Physics
Keywords: rigidbody dynamical model saturated polyalanine 2I9M saturated polypeptide chain molecular force field molecular dynamics simulation
CLC: Q51
Type: Master's thesis
Year: 2011
Downloads: 26
Quote: 0
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Abstract


The research of protein folding is a new frontier in life science. In recent years , protein folding simulation with computers has become an important research mean. But many phen omena of interest in biological occur in milliseconds or even more long time. For a larger biol ogical system, it is hard to reach all-atom molecule simulation time. In order to overcome the defects and assure the calculation precision at the same time, we according to different protein molecule structure to establish appropriate rigidbody dynamics models, using the TINKER process packages to simulate protein folding. The main content of this article include :(1)We make molecular dynamics simulation about saturated polyalanine folding. According to molecular structure, saturated polyalanine can be substructured into two different rigidbody dynamics models. We make molecular simulations aboutα-helix of seventeen saturated polyalanine based on the rigidbody dynamical models in five different force fields (AMBER99, CHARMM27, OPLSAA, AMBER99SB and AMOEBAPRO), respectively. Change the number of residues for saturated polyalanine, then we make molecular simulations aboutα-helix of nine and thirteen saturated polyalanine based on the rigidbody dynamical models in the same condition. We compare the results with those of the all-atom simulations, and the results of simulations among rigidbody models. All results show that, within the framework of rigidbody dynamical model, theα-helix not only depends on the definition of rigidbody and the force fields , but on the the number of residues for saturated polyalanine.(2)In order to further expand the rigidbody dynamics model, we make molecular dynamics simulation about saturated 2I9M polypeptide chain folding. According to molecular structure, saturated 2I9M polypeptide chain can be substructured into two different rigidbody models. Within four different force fields (AMBER99, CHARMM27, OPLSAA and AMBER99SB), we make molecular simulations aboutα-helix of saturated polyalanine based on the rigidbody dynamical models. We compare the results with those of the all-atom simulations. All results show that, within the framework of rigidbody dynamical models, saturated 2I9M polypeptide chain don’t formα-helix, the research of simulation still needs further exploration.

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CLC: > Biological Sciences > Biochemistry > Protein
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