Chen Kui, Huang Xiaohang
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Comput Biol Chem. 2007 Oct;31(5-6):378-83. doi: 10.1016/j.compbiolchem.2007.08.002. Epub 2007 Aug 17.
Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches.
从海鲈中克隆出了编码四个SNARE（N-乙基马来酰亚胺敏感融合蛋白附着蛋白受体）基序的三条cDNA序列，并使用14种不同的网络服务器和软件对推导的肽序列进行了结构预测分析。利用生物信息学方法，分别将SNARE 7S核心复合物的“离子层”结构、三维延伸和构象特征与哺乳动物X射线晶体学研究的结果进行了比较。结果表明，鱼类SNARE核心复合物的形成和稳定可能是由疏水缔合、核心氨基酸R基团之间的氢键以及分子水平的静电吸引驱动的。这表明鱼类的SNARE蛋白相互作用可能与哺乳动物具有相同的分子机制，这表明了SNARE核心复合物理论的普遍性和可靠性。这项工作也是一次尝试，即仅通过计算机化方法来获取似乎与通过X射线晶体学获得的蛋白质三维结构信息相似的信息。
