Dinucleotides docking to scorpion polypeptide toxins: A molecular modeling method for protein functional site recognition

作者：Zhu Jun; Wang Jian; Cheng Mao Sheng; Zhang Jing Hai^*

来源：Biochemical and Biophysical Research Communications, 2009, 378(2): 157-161.

DOI：10.1016/j.bbrc.2008.10.122

• Molecular modeling
• Dinucleotides
• Predicting functional site
• Automated docking

To understand the principles underlying Protein folding, many Molecular modeling methods are being developed for predicting functional positions. In this work, fully flexible dinucleotides d(pApA), d(pApC) d(pApG), d(pApT), d(pCpA), d(pCpC), d(pCpG), d(pCpT), d(pGpA), d(pGpC), d(pGpG), d(pGpT), d(pTpA), d(pTpC), d(pTpG), and d(pTpT) were first docked onto the surface of scorpion polypeptide toxins (LqhlT2, PDB ID:2161) and homology modeled ANEPIII. Automated docking was able to identify sites on scorpion polypeptide toxins where favorable nucleotide interactions can occur, and those sites were in agreement with the mutation data of this protein published recently [I, Karbat, R. Kahn, L Cohen, N. Ilan, N. Gilles, G. Corzo, O. Froy, M. Gur, G. Albrecht, S.H. Heinemann, D. Gordon, M. Gurevitz. The unique pharmacology of the scorpion alpha-like toxin Lqh3 is associated with its flexible C-tail, Febs J 274 (2007) 1918-1931]. Simulation results suggested that dinucleotides clocking is a suitable molecular modeling method that could be developed for protein functional site recognition.

• 出版日期2009-1-9
• 单位沈阳药科大学