Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches.
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.
Chen
Kui
K
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Huang
Xiaohang
X
D020816:Amino Acid Motifs; D000818:Animals; D001483:Base Sequence; D001492:Bass / Q000235:genetics*; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D050600:SNARE Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D055672:Static Electricity; D050825:Synaptosomal-Associated Protein 25 / Q000737:chemistry / Q000235:genetics; D050827:Syntaxin 1 / Q000737:chemistry / Q000235:genetics; D050988:Vesicle-Associated Membrane Protein 2 / Q000737:chemistry / Q000235:genetics
D050600:SNARE Proteins; D050825:Synaptosomal-Associated Protein 25; D050827:Syntaxin 1; D050988:Vesicle-Associated Membrane Protein 2