Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

Nai Jyuan Wang, Chi Ching Lee, Chao Sheng Cheng, Wei-Cheng Lo, Ya Fen Yang, Ming Nan Chen, Ping Chiang Lyu*

*Corresponding author for this work

Research output: Contribution to journalConference articlepeer-review

28 Scopus citations

Abstract

Background: Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain.

Methods: 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/.

Results: 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 Prositestyled 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.

Conclusions: 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.

Original languageEnglish
Article numberS9
JournalSeries on Advances in Bioinformatics and Computational Biology
Volume13
DOIs
StatePublished - 1 Jan 2012
Event10th Asia Pacific Bioinformatics Conference, APBC 2012 - Melbourne, Australia
Duration: 17 Jan 201219 Jan 2012

Fingerprint Dive into the research topics of 'Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)'. Together they form a unique fingerprint.

Cite this