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

Wang NJ, Lee CC, Cheng CS, Lo WC, Yang YF, Chen MN, Lyu PC - BMC Genomics (2012)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.

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 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.

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.

Show MeSH
The structural and functional analyses of rice nsLTP2. (A) A structure of a rice nsLTP1 myristate complex. (B) Competitive experiment between ANS and LysoPC14. (C) CD spectra of wild-type rice nsLTP2 and its mutants. (B) and (C) were reprinted from our previous data [51].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3303721&req=5

Figure 3: The structural and functional analyses of rice nsLTP2. (A) A structure of a rice nsLTP1 myristate complex. (B) Competitive experiment between ANS and LysoPC14. (C) CD spectra of wild-type rice nsLTP2 and its mutants. (B) and (C) were reprinted from our previous data [51].

Mentions: We have used the protein-protein docking model (Autodock) [49] to investigate the importance of the conserved hydrophobic residues, e.g., Leu8, Phe36, Phe39, Tyr45, Tyr48 and Val49, around the binding cavity of rice nsLTP2 (Figure 3A) [50]. The results indicated that changing a single residue of Leu8, Phe36, or Val49 to alanine was sufficient to destroy the integrity of the cavity. Other mutant proteins (i.e., F39A, Y45A, and Y48A) typically had native-like structure but were less stabilized compared with the wild type nsLTP2 (Figure 3B and 3C). According to our Prosite-styled pattern for the Type II nsLTPs, to which the rice LTP2 belongs, the sequence of these structurally important residues are highly conserved. The occurrence frequencies for Leu at the position 8, [Phe or Leu] at the position 36, [Phe or Tyr] at the position 39 position, [Tyr or Phe] at position 48, and [Val or Ile] at the position 49 are all ≥92%. The occurrence of [Phe or Leu] at position 45 is also high (75%). Thus, residues with higher conservation may play an important role in structural stability or lipid binding ability.


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

Wang NJ, Lee CC, Cheng CS, Lo WC, Yang YF, Chen MN, Lyu PC - BMC Genomics (2012)

The structural and functional analyses of rice nsLTP2. (A) A structure of a rice nsLTP1 myristate complex. (B) Competitive experiment between ANS and LysoPC14. (C) CD spectra of wild-type rice nsLTP2 and its mutants. (B) and (C) were reprinted from our previous data [51].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3303721&req=5

Figure 3: The structural and functional analyses of rice nsLTP2. (A) A structure of a rice nsLTP1 myristate complex. (B) Competitive experiment between ANS and LysoPC14. (C) CD spectra of wild-type rice nsLTP2 and its mutants. (B) and (C) were reprinted from our previous data [51].
Mentions: We have used the protein-protein docking model (Autodock) [49] to investigate the importance of the conserved hydrophobic residues, e.g., Leu8, Phe36, Phe39, Tyr45, Tyr48 and Val49, around the binding cavity of rice nsLTP2 (Figure 3A) [50]. The results indicated that changing a single residue of Leu8, Phe36, or Val49 to alanine was sufficient to destroy the integrity of the cavity. Other mutant proteins (i.e., F39A, Y45A, and Y48A) typically had native-like structure but were less stabilized compared with the wild type nsLTP2 (Figure 3B and 3C). According to our Prosite-styled pattern for the Type II nsLTPs, to which the rice LTP2 belongs, the sequence of these structurally important residues are highly conserved. The occurrence frequencies for Leu at the position 8, [Phe or Leu] at the position 36, [Phe or Tyr] at the position 39 position, [Tyr or Phe] at position 48, and [Val or Ile] at the position 49 are all ≥92%. The occurrence of [Phe or Leu] at position 45 is also high (75%). Thus, residues with higher conservation may play an important role in structural stability or lipid binding ability.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.

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 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.

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.

Show MeSH