Dinucleotides docking to scorpion polypeptide toxins: a molecular modeling method for protein functional site recognition.
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 (LqhIT2, PDB ID:2I61) 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 docking is a suitable molecular modeling method that could be developed for protein functional site recognition.
Zhu
Jun
J
School of Life Science and Bio-pharmaceutics, Shenyang Pharmaceutical University, P.O. Box 17, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning Province 110016, PR China.
Wang
Jian
J
Cheng
Mao-Sheng
MS
Zhang
Jing-Hai
JH
D000595:Amino Acid Sequence; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry / Q000235:genetics; D008722:Methods; D008958:Models, Molecular; D016296:Mutagenesis; D009711:Nucleotides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012604:Scorpion Venoms / Q000737:chemistry* / Q000235:genetics
C076349:LqhIT2 insect toxin; D009711:Nucleotides; D010455:Peptides; D012604:Scorpion Venoms; C058792:anti-epilepsy peptide, Buthrus martensii; D003545:Cysteine