Molecular dynamics simulation of microperoxidase in aqueous solution in terms of the ABEEM/MM method

作者：Cui Bao-Qiu; Gong Li-Dong^*; Zhao Dong-Xia

来源：Acta Physico - Chimica Sinica, 2008, 24(6): 1035-1040.

DOI：10.3866/PKU.WHXB20080621

• ABEEM/MM fluctuating charge molecular force field
• microperoxidase
• heme
• conformation
• molecular dynamics simulation

In terms of the atom-bond electronegativity equilization fluctuating charge molecular mechanics(ABEEM/MM), molecular dynamics simulation on aqueous microperoxidases (MP) was performed. The impact of water molecules on the structure of MP, the ruffling conformation of the heme, and the orientation of the axially ligated imidazole were investigated. Results show that, in the aqueous solution, the backbone amino acids of the NIP are stable, while the ruffling conformation of heme turns to be planar, which comes from the interaction between water and MP. The orientation of the axially coordinated imidazole is mainly determined by the histidine bonded with the imidazole, while the electrostatic force between the imidazole and the side-chained propionic acid group of the heme is only a subsidiary factor.

• 出版日期2008-6
• 单位辽宁师范大学