This article is part of the supplement: Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012)
Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)
- Equal contributors
1 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
2 Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
3 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
4 Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
5 Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
BMC Genomics 2012, 13(Suppl 1):S9 doi:10.1186/1471-2164-13-S1-S9Published: 17 January 2012
In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database -- nsLTPDB -- which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/ webcite.
Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC × G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L, F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs.
Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.