Molecular dynamics simulation and essential dynamic analysis of vigna raddiate plant defensin 1

• Main Authors: Chan Lan Shang, 沈群嵐
• Other Authors: Ping-Chiang Lyu
• Format: Others
• Language: en_US
• Published: 2007
• Online Access: http://ndltd.ncl.edu.tw/handle/66489298813097269306

碩士 === 國立清華大學 === 生物資訊與結構生物研究所 === 95 === Vigna radiata plant defensin 1 (VrD1) is one kind of plant defensins, which is the first report to exhibit the insecticidal activity against bruchid. In our previous studies, this insecticidal activity may be through its inhibitory effect on α-amylase activity. Although VrD1 structure has been determined in our laboratory, the detailed mechanism of this inhibition remains unclear. According to our studies, 310 helix in VrD1 which is not observed in other plant defensins probably plays an important role in this inhibition. Arg26 and Trp10 in VrD1 may be critical for the formation of 310 helix. Therefore, we employed molecular dynamic simulation to investigate the relationship between these two residues. In addition, we also built the models of R26K, R26E and W10A mutants and docked these models to α-amylase to elucidate their binding mode. Our simulation results showed that loop L1 has higher correlation with loop L3, which implied there was interaction between Loop L1 and L3. On the other hand, Trp10 was on loop L1 in VrD1 structure. The simulation results also showed the correlation coefficient between Arg26 and Trp10 was higher. Thus, according our results, when replacing Arg26 to Lys (R26K) or Glu (R26E), the orientation of Trp10 would be changed and this change would effect the flexibility of loop L1, and further influence the fluctuation of loop L3.