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Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method.

Messaoudi A, Belguith H, Ben Hamida J - Evol. Bioinform. Online (2011)

Bottom Line: By contrast, very little is known about plant lipases.In this investigation, a homology model of Arabidopsis thaliana lipase (NP_179126) was constructed using a human gastric lipase (PDB ID: 1HLG), as a template for model building.Natural substrates: tributyrin, trioctanoin and triolen were docked into the model to investigate ligand-substrate interaction.

View Article: PubMed Central - PubMed

Affiliation: Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, Tunisie.

ABSTRACT
Triacylglycerol lipases have been thoroughly characterized in mammals and microorganisms. By contrast, very little is known about plant lipases. In this investigation, a homology model of Arabidopsis thaliana lipase (NP_179126) was constructed using a human gastric lipase (PDB ID: 1HLG), as a template for model building. This model was then assessed for stereochemical quality and side chain environment. Natural substrates: tributyrin, trioctanoin and triolen were docked into the model to investigate ligand-substrate interaction.

No MeSH data available.


Ramachandran plot values showing number of residues in favoured, allowed and outlier region.
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f2-ebo-7-2011-099: Ramachandran plot values showing number of residues in favoured, allowed and outlier region.

Mentions: Studies of Yang et al27 demonstrated that a sequence identity higher than 25% between two proteins is indicative of similar three-dimensional structures. In our case, target and template protein share 32% of sequence identity. Based on this alignment, a model of Arabidopsis thaliana lipase was built using a human gastric lipase (PDB ID: 1HLG) as a template for the model building (Fig. 1). The modeled enzyme is a monomer folded into α/β domain. It consists of eight central stranded β sheet flanked by twenty two α helices. The same structure is shared by other lipase enzymes from mammalian and bacterial origin, the number of α helices and β sheet differ from a species to another. The Ramachandran plot in Figure 2 indicated the region of possible angle formations by w (phi) and c (psi) angles. The conventional terms represent the torsion angles on either side of alpha carbon in peptides. The plot was divided into three regions: favored (91.5%), allowed (6%) and outlier (2.5%). This result is significant since the high percentage of residues in favored region (>90%). This indicates that the built model is of good quality. Errat plot assesses the arrangement of different types of atoms with respect to each other in protein models (Fig. 3). Errat is a sensitive technique, which is good for identifying incorrectly-folded regions in preliminary protein models. ERRAT is a so-called “overall quality factor” for non-bonded atomic interactions, and higher scores mean higher quality. The normally-accepted range is >50 for a high quality model.22 In the current case, the ERRAT score for the model is 58.989. The Verify 3D method assesses protein structures using three-dimensional profiles. This program analyzes the compatibility of an atomic model (3D) with its own amino acid sequence (1D). The scores range from −1 (bad score) to +1 (good score).29 The verify score diagram presented in Figure 4 validate the Arabidopsis thaliana lipase model.


Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method.

Messaoudi A, Belguith H, Ben Hamida J - Evol. Bioinform. Online (2011)

Ramachandran plot values showing number of residues in favoured, allowed and outlier region.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140413&req=5

f2-ebo-7-2011-099: Ramachandran plot values showing number of residues in favoured, allowed and outlier region.
Mentions: Studies of Yang et al27 demonstrated that a sequence identity higher than 25% between two proteins is indicative of similar three-dimensional structures. In our case, target and template protein share 32% of sequence identity. Based on this alignment, a model of Arabidopsis thaliana lipase was built using a human gastric lipase (PDB ID: 1HLG) as a template for the model building (Fig. 1). The modeled enzyme is a monomer folded into α/β domain. It consists of eight central stranded β sheet flanked by twenty two α helices. The same structure is shared by other lipase enzymes from mammalian and bacterial origin, the number of α helices and β sheet differ from a species to another. The Ramachandran plot in Figure 2 indicated the region of possible angle formations by w (phi) and c (psi) angles. The conventional terms represent the torsion angles on either side of alpha carbon in peptides. The plot was divided into three regions: favored (91.5%), allowed (6%) and outlier (2.5%). This result is significant since the high percentage of residues in favored region (>90%). This indicates that the built model is of good quality. Errat plot assesses the arrangement of different types of atoms with respect to each other in protein models (Fig. 3). Errat is a sensitive technique, which is good for identifying incorrectly-folded regions in preliminary protein models. ERRAT is a so-called “overall quality factor” for non-bonded atomic interactions, and higher scores mean higher quality. The normally-accepted range is >50 for a high quality model.22 In the current case, the ERRAT score for the model is 58.989. The Verify 3D method assesses protein structures using three-dimensional profiles. This program analyzes the compatibility of an atomic model (3D) with its own amino acid sequence (1D). The scores range from −1 (bad score) to +1 (good score).29 The verify score diagram presented in Figure 4 validate the Arabidopsis thaliana lipase model.

Bottom Line: By contrast, very little is known about plant lipases.In this investigation, a homology model of Arabidopsis thaliana lipase (NP_179126) was constructed using a human gastric lipase (PDB ID: 1HLG), as a template for model building.Natural substrates: tributyrin, trioctanoin and triolen were docked into the model to investigate ligand-substrate interaction.

View Article: PubMed Central - PubMed

Affiliation: Unité de Protéomie Fonctionnelle and Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El Manar, Tunisie.

ABSTRACT
Triacylglycerol lipases have been thoroughly characterized in mammals and microorganisms. By contrast, very little is known about plant lipases. In this investigation, a homology model of Arabidopsis thaliana lipase (NP_179126) was constructed using a human gastric lipase (PDB ID: 1HLG), as a template for model building. This model was then assessed for stereochemical quality and side chain environment. Natural substrates: tributyrin, trioctanoin and triolen were docked into the model to investigate ligand-substrate interaction.

No MeSH data available.