Team:Brasil-USP/LcpBioinformatics
Lcp Bioinformatics
Thinking a little more about Lcp (Latex clearing protein), our team applied some bioinformatic tools to try and get more information about this protein’s properties and structure. Unlike RoxA (Rubber oxygenase A), Lcp crystallographic structure has not been solved yet (RoxA PDB: 4B2N). It has been indeed shown that Lcp is able to link itself to a prosthetic heme group in a non-covalent way (b-type), unlike what happens in RoxA (c-type)1.
Using prediction methods, such as Iterative Threading ASSEmbly Refinement (I-TASSER)2, we attempt to predict Lcp structure based on its amino acid sequence but results did not show good structure models using I-TASSER (Figure 1). Although, it is possible to observe that secondary structure prediction reveals that Lcp could consist of many loops and unstructured regions that are also observed in RoxA (32% helical and 7% beta sheet)3, which might suggest some similarity between these two proteins. For RoxA, a complex structure composed by three large loops forming a tower (each loop formed by helices and non-structured regions) was proposed to determine the exo-cleavage rubber polymer (Figure 3).3
The difficulty of finding a model might be due to the protein’s high complexity, distinctly of RoxA because it performs endo-cleavage of the rubber polymer. In fact, I-TASSER was not able to predict even a heme ligand.
We performed a bioinformatics analysis of Lcp predicting its structure, creating an HMM model and comparing RoxA and Lcp secondary structure based on reported data.
Click <a href="https://static.igem.org/mediawiki/2015/0/0b/BrasilUSP_lcpbioinformatics.pdf">here</a> to see our analysis.