Structural and Thermodynamic Properties Analysis of the Escherichia coli FIS-DNA Complex Using Molecular Dynamics Simulation

• Main Authors: Ching-Fong Lin, 林慶豐
• Other Authors: Sheh‐Yi Sheu
• Format: Others
• Language: zh-TW
• Published: 2008
• Online Access: http://ndltd.ncl.edu.tw/handle/98430211074143642887

碩士 === 國立陽明大學 === 生物醫學資訊研究所 === 96 === The regulation of gene expression is to have relations to the assembly of the DNA binding proteins which bind to DNA to initiate the transcription. Some of these proteins have the ability to promote bending or looping of DNA. The FIS protein regulates gene expression in Escherichia coli by this property of bending DNA. There are many researches to discover the mechanism of FIS protein binds to DNA. However the experiment data only show the supposititious results and figure out the model of FIS-DNA complex structure. This research uses molecular dynamics simulation to compute the detail of the interaction between FIS and DNA. We observed FIS prominently affects the DNA bending by the type of local bending. Analyzing the DNA structure properties, roll and slide, also demonstrates the local bending type and region. The hydrogen bonds between FIS and DNA are analyzed to compare with the experiment data. Finally we compute the binding free energy between FIS and DNA to estimate the result of simulation and compare with the value of λ-repressor-DNA complex.