Bioinformatics and molecular modelling - Essay Example

Plant lipases are often considered to be involved in regulating certain plant growths and developments (Bos and Laxminarayan, 2011; 42). They are mainly found in seeds where triglycerides are stored in the form of intracellular structures or the oil bodies. Lipases usually hydrolyze triglycerides to fatty acids and glycerol that produces energy needed for seed germination. The plant lapses are usually classified into three main groups with the first group consisting of the triacylglycerol hydrolases that are mainly found in seeds.

Their study is vital since they are responsible for seed alteration especially during storage. The second group is the acylhydrolases that are found in various plant tissues. They often exhibit limited specificity for their substrates; therefore, they are unable to hydrolyze triglycerides. However, they are cable to catalyze some esterification processes or reactions (Appel and Feytmans, 2009; p. 68). The profound acylhydrolases include phospholipases A and B, sulfolipases, glycolipases, and monoglyceride lipases.

The last group in this category is the phosphorlipases that involve plant metabolism, degradation, and rearrangement. Other than the above classification, the recent studies have led to different classification of lipases based on comparison of the sequences of their amino acid among other fundamental biological and physicochemical properties (Gupta, 2007; 34). This modern classification led to eleven subfamilies. Despite being a member of many protein families, the lipases often have similar architecture that is described by the ?

-hydrolase fold. The activities of all lipases often rely on the catalytic triad that is usually fromed by the Asp, Ser, and His residues. In the sequence of the amino acid especially involving ?/? hydrolases, these three residues often follow the user-Asp-His order. Additionally, lipases often share the consensus sequence defined by the Gly-Xaa-Ser-Xaa-Gly where X may be a residue of an amino acid (Bos and Laxminarayan, 2011; p. 33). The three dimensional structure of any protein molecule often provides valuable insight into the molecular function, organization, docking stimulation, and the effective designing of drug experiments.

The lack of an experimentally determined crystal structure, the homology modeling may be used to provide an opportunity in obtaining a reasonable 3D model. Currently, the 3D models often provide a perfect means of predicting the structure of biomolecules since it yields models that are suitable for a wide application spectrum that are structurally based thereby providing molecular design for mechanism investigation. The 3D approach is capable of providing a reasonable structure model that is often related to template that shares more than 25 percent sequence identity.

An Arabidopsis thaliana lipase model is greatly proposed to investigate the model organism mainly in the plant biology since it is relatively small and and it is genetically tractable genome. Methods The Target and Template Proteins The model is perfect in determining adequate template for the homology modeling for the Arabidopsis thaliana. This sequence allows the alignment of amino acid sequence against the protein data bank (PDB) and this is performed by means of BLAST algorithm. According to the sequence algorithm, both the template (1HLG) and the target share 31 percent of the sequence identity.