Difference between revisions of "Os10g0505700"
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Lipid transfer proteins (LTPs) are typically present in the majority of prokaryotic and eukaryotic cells [1] such as bacteria, yeasts, plants and animals [2]. Plant nsLTPs are basic (with pI 8–10) disulfide-rich proteins divided into two subfamilies; nsLTP1 (~9 kDa) and nsLTP2 (~7 kDa) [3] and [4]. While both proteins have comparable lipid transfer activity, greater stability of nsLTP2 has been proved [5]. Due to their main biological activity, lipid transportation across bio-membranes in vitro, nsLTPs have received much attention from pharmaceutical viewpoints. Owing to the ability of LTPs in promoting the movement of lipids other than phospholipids, clarification of the underlying mechanisms and specificities would be essential to development of LTP-mediated transport systems and controlled release of low molecular weight drugs. A potential role of LTPs in designing efficient drug delivery systems has been suggested [6] and [7]. Their actual biological roles are diverse, including participating in developmental processes and pathogen resistance [8]. Of the two main isoforms, plant nsLTP1 has been studied more frequently and its structure, function and binding properties are well characterized [9] and [10]. Computational studies on nsLTP1 revealed that the insertion of various lipids into the cavity does not necessarily induce significant structural changes with an exception of a prostaglandin. Proteins from various species also varied in terms of molecular surfaces and electrostatic potentials as well as the ability to bind negatively charged lipids. The lack of specificity of ligand binding is suggested to result from nonspecific character of van der Waals interactions [10]. | Lipid transfer proteins (LTPs) are typically present in the majority of prokaryotic and eukaryotic cells [1] such as bacteria, yeasts, plants and animals [2]. Plant nsLTPs are basic (with pI 8–10) disulfide-rich proteins divided into two subfamilies; nsLTP1 (~9 kDa) and nsLTP2 (~7 kDa) [3] and [4]. While both proteins have comparable lipid transfer activity, greater stability of nsLTP2 has been proved [5]. Due to their main biological activity, lipid transportation across bio-membranes in vitro, nsLTPs have received much attention from pharmaceutical viewpoints. Owing to the ability of LTPs in promoting the movement of lipids other than phospholipids, clarification of the underlying mechanisms and specificities would be essential to development of LTP-mediated transport systems and controlled release of low molecular weight drugs. A potential role of LTPs in designing efficient drug delivery systems has been suggested [6] and [7]. Their actual biological roles are diverse, including participating in developmental processes and pathogen resistance [8]. Of the two main isoforms, plant nsLTP1 has been studied more frequently and its structure, function and binding properties are well characterized [9] and [10]. Computational studies on nsLTP1 revealed that the insertion of various lipids into the cavity does not necessarily induce significant structural changes with an exception of a prostaglandin. Proteins from various species also varied in terms of molecular surfaces and electrostatic potentials as well as the ability to bind negatively charged lipids. The lack of specificity of ligand binding is suggested to result from nonspecific character of van der Waals interactions [10]. | ||
Rice nsLTP2, builds of 69 amino acids and has smaller size, higher structural stability, different disulfide bond pattern and less than 30% sequence similarity with nsLTP1 [11]. Samuel et. al. have performed molecular docking of stearic acid into both LTP1 and LTP2 cavity, demonstrating marked differences between the two isoforms in accommodation of the fatty acid chain in the protein active site. These authors have also reported that there is a tunnel-like hydrophobic cavity running through the whole molecule of rice LTP2 [11]. Despite established beneficial capacities of nsLTP2 to drug delivery [12] and [13] it has not been identified how the plasticity of the protein cavity may help in fitting of diverse molecular shapes and sizes. | Rice nsLTP2, builds of 69 amino acids and has smaller size, higher structural stability, different disulfide bond pattern and less than 30% sequence similarity with nsLTP1 [11]. Samuel et. al. have performed molecular docking of stearic acid into both LTP1 and LTP2 cavity, demonstrating marked differences between the two isoforms in accommodation of the fatty acid chain in the protein active site. These authors have also reported that there is a tunnel-like hydrophobic cavity running through the whole molecule of rice LTP2 [11]. Despite established beneficial capacities of nsLTP2 to drug delivery [12] and [13] it has not been identified how the plasticity of the protein cavity may help in fitting of diverse molecular shapes and sizes. | ||
Revision as of 03:38, 7 June 2014
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Contents
Annotated Information
Function
Lipid transfer proteins (LTPs) are typically present in the majority of prokaryotic and eukaryotic cells [1] such as bacteria, yeasts, plants and animals [2]. Plant nsLTPs are basic (with pI 8–10) disulfide-rich proteins divided into two subfamilies; nsLTP1 (~9 kDa) and nsLTP2 (~7 kDa) [3] and [4]. While both proteins have comparable lipid transfer activity, greater stability of nsLTP2 has been proved [5]. Due to their main biological activity, lipid transportation across bio-membranes in vitro, nsLTPs have received much attention from pharmaceutical viewpoints. Owing to the ability of LTPs in promoting the movement of lipids other than phospholipids, clarification of the underlying mechanisms and specificities would be essential to development of LTP-mediated transport systems and controlled release of low molecular weight drugs. A potential role of LTPs in designing efficient drug delivery systems has been suggested [6] and [7]. Their actual biological roles are diverse, including participating in developmental processes and pathogen resistance [8]. Of the two main isoforms, plant nsLTP1 has been studied more frequently and its structure, function and binding properties are well characterized [9] and [10]. Computational studies on nsLTP1 revealed that the insertion of various lipids into the cavity does not necessarily induce significant structural changes with an exception of a prostaglandin. Proteins from various species also varied in terms of molecular surfaces and electrostatic potentials as well as the ability to bind negatively charged lipids. The lack of specificity of ligand binding is suggested to result from nonspecific character of van der Waals interactions [10]. Rice nsLTP2, builds of 69 amino acids and has smaller size, higher structural stability, different disulfide bond pattern and less than 30% sequence similarity with nsLTP1 [11]. Samuel et. al. have performed molecular docking of stearic acid into both LTP1 and LTP2 cavity, demonstrating marked differences between the two isoforms in accommodation of the fatty acid chain in the protein active site. These authors have also reported that there is a tunnel-like hydrophobic cavity running through the whole molecule of rice LTP2 [11]. Despite established beneficial capacities of nsLTP2 to drug delivery [12] and [13] it has not been identified how the plasticity of the protein cavity may help in fitting of diverse molecular shapes and sizes.
Expression
Please input expression information here.
Evolution
Structure of Rice nsLTP2
The rice nsLTP2 is a predominantly α-helical protein consisting of three prominent helices within the N-terminal 40 amino acids. The well conserved cysteine residues form four disulfide bonds to stabilize the three-dimensional fold of the protein. The C-terminal amino acid residues, Lys41–His69, constitute a less structured region of the molecule with a high density of positively charged residues. The r.m.s.d. values for the backbone and all heavy atoms were 1.09 ± 0.20 and 1.54 ± 0.25 Å, respectively. The first 40 amino acids (Ala1–Ala40), constituting the rigid portion of the molecule, have r.m.s.d. values of 0.65 ± 0.1 Å for the backbone and 0.95 ± 0.15 Å for all heavy atoms. Superposition of the 15 NMR structures are shown as a stereo representation in Fig. 3 A. Three helices of rice nsLTP2 positioned at Cys3–Ala16, Thr22–Ala31, and Gln33-Ala40 are colored green,red, and purple, respectively. Helices II and III are connected by a 90° turn to form a very rigid and unique structural motif. The curved helix I accommodates two disulfide bonds (Cys3–Cys35 and Cys11–Cys25). The flexible portion of the polypeptide contains two single-turn helices at positions Tyr45–Tyr48 and Ala54–Val58. A series of hydrophobic residues distributed throughout the nsLTP2 sequence combine to form a hydrophobic cavity. A continuous stretch of hydrophobic residues, Cys61–Ile65, near the C terminus forms a flexible cap over the hydrophobic cavity. The C-terminal region also contains two cysteines bridged to the rigid portion of the molecule (Cys26–Cys61 and Cys37–Cys68). These two disulfide bonds help to maintain the correct orientation of the hydrophobic cap. The final energy-minimized average structure of rice nsLTP2 is shown in Fig.3 B. A ProCheck analysis of the three-dimensional structure revealed that only Ser59 and Ser60 are in the disallowed region, corresponding to 3.6% of the residues in the protein (19). These residues constitute a portion in the flexible C terminus that makes a very sharp turn to cover the hydrophobic cavity.
Figure
1
A, stereo representation of the 15 best superimposed NMR structures of rice nsLTP2 (only the backbone atoms are shown for clarity). B, solution structure of rice nsLTP2. Disulfide bonds involved in the three-dimensional structure are shown in ball-and-stick representation. Helix I (green) and helix II (red) are connected through a loop (Gly17–Pro21). Helix II and helix III (purple) are joined by a sharp 90° turn. The region containing two single turn helices and the C terminus are shown inorange and brown, respectively.
Labs working on this gene
Please input related labs here.
References
Please input cited references here. Mojtaba Tousheha, Mehran Miroliaeia Computational evaluation on the binding affinity of non-specific lipid-transfer protein-2 with fatty acids.Comput Biol Med. 2013 Nov;43(11):1732-8.
Structured Information
| Gene Name |
Os10g0505700 |
|---|---|
| Description |
Similar to Nonspecific lipid-transfer protein 2 (nsLTP2) (7 kDa lipid transfer protein) |
| Version |
NM_001071543.1 GI:115482829 GeneID:4349061 |
| Length |
523 bp |
| Definition |
Oryza sativa Japonica Group Os10g0505700, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 10:19790378..19790900 |
| Sequence Coding Region |
19790543..19790818 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008403:19790378..19790900 source=RiceChromosome10 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008403:19790378..19790900 source=RiceChromosome10 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcgaagtgggcggcgatcatggcggtgctgctgctggcggcggcgtgggcgccggcgccggcgacggcgcagtgcaacgccgggcagctggcgatctgcgcgggcgcgatcatcggcgggtcgacgccgtcggcgtcgtgctgctccaacctgcgcgcgcagagggggtgcttctgccagtacgcgcgcaacccggcgtacgcctcctacatcaacagcgccaacgcccgcaagaccctcacctcctgcggcatcgccatcccccgctgctag</cdnaseq> |
| Protein Sequence |
<aaseq>MAKWAAIMAVLLLAAAWAPAPATAQCNAGQLAICAGAIIGGSTP SASCCSNLRAQRGCFCQYARNPAYASYINSANARKTLTSCGIAIPRC</aaseq> |
| Gene Sequence |
<dnaseqindica>83..358#agcagccagcagccaactgcatcgatatcgatcgatcactcgaccgaccatctcacaagcaaagcaaaagctcgtggcaacaatggcgaagtgggcggcgatcatggcggtgctgctgctggcggcggcgtgggcgccggcgccggcgacggcgcagtgcaacgccgggcagctggcgatctgcgcgggcgcgatcatcggcgggtcgacgccgtcggcgtcgtgctgctccaacctgcgcgcgcagagggggtgcttctgccagtacgcgcgcaacccggcgtacgcctcctacatcaacagcgccaacgcccgcaagaccctcacctcctgcggcatcgccatcccccgctgctaggcacgctcgatctcccgccgccgcgcgccgccgctcgccggcgccggcgccggccatggtgcgtggcaaatatatatatatatatatatatatatatatatatatatatatatactgtgtgtacgtgcgcttgaataaaggacgtgagttaatttgatcggtgtc</dnaseqindica> |
| External Link(s) |
