[Bioinformatics analysis for the structure and function of lactate dehydrogenase from Schistosoma japonicum].
OBJECTIVE
To predict the structure and function of SjLDH using bioinformatics method.


METHODS
By online analysis at bioinformatics websites such as NCBI (http://www.ncbi.nlm.nih.gov/) and Expasy (http://cn.expasy. org/), and employing software packages such as Vector NTI suite and PCgene to do multi-sequence homological alignment, phylogenetic analysis, secondary structure and topological prediction, homology modeling of tertiary structure, antigenic epitope analysis, etc.


RESULTS
Same conservative sites and key catalytic sites existed among SjLDH and LDHs from other species. Similarity of SjLDH compared to CsLDH, TvLDH and HsLDH was 75%, 17%, 58%-60% respectively. Phylogenetic analysis demonstrated that the evolution relation between SjLDH and DmLDH was closer than the relation between SjLDH and CeLDH, the relationship between SjLDH and HsLDH-B, -C was closer than HsLDH-A. Three transmembrane regions were found, the region of 98aa-106aa in three hydrophilic regions located outside of membrane was inferred as the major antigen epitope. This antigen epitope had significant difference with LDHs from protozoon (Pf., Tg., Tv.) and had 1-3 amino acid residue difference with MmLDH, HsLDH-A, -B, -C, and was the same with CsLDH. One of the key catalytic residues and substrate (pyruvate) binding loop were located in this region. Tertiary structure demonstrated that 98aa-106aa was on the surface of the protein and formed a substrate binding loop, other two key catalytic sites were at the position near the loop.


CONCLUSIONS
The prediction implied that LDH was an ideal molecule for phylogenetic analysis; SjLDH might be a potential molecular target for immunodiagnosis, anti-schistosome drug and vaccine development.
Department of Parasitology, Hainan Medical College, Haikou 571101, China.
Gang
G
Lu
Xin-bing
XB
Yu
Can
C
Huang
Jing
J
Xu
Zhong-dao
ZD
Wu
Shou-yi
SY
Chen
Xu-chu
XC
Hu
D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D015801:Helminth Proteins / Q000737:chemistry / Q000235:genetics*; D007770:L-Lactate Dehydrogenase / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D012549:Schistosoma japonicum / Q000201:enzymology*; D016415:Sequence Alignment / Q000379:methods
D015801:Helminth Proteins; D007770:L-Lactate Dehydrogenase