Difference between revisions of "Team:BostonU/Modeling"

Modeling

One of the main parts of our project was developing a model to help us predict the best places to split a protein. A model was previously developed in Matlab by a graduate student in our lab, Billy Law, and we built off of this model in our project. The overall goal of our model was to find places to split the protein that would create inert halves but still have robust activity when dimerization occurs.

Proteins are comprised of long strings of amino acids. Theoretically, given a protein that is n amino acids long, there are n-1 places to split the protein, since you can split it between each amino acid. This would be unfeasible and too time consuming, so we focused on three major criteria in order to narrow down split site choices.

Our first criteria was to choose to split the protein’s exterior regions. We hypothesized that splitting a protein through its core could potentially interfere with its folding activity and function. We also know that proteins generally have hydrophilic surfaces and hydrophobic cores.

Therefore, we focused on avoiding hydrophobic regions in the protein and targeting hydrophilic regions.

We used the Janin hydrophobicity scale, which assigns each amino acid a number based on how hydrophobic it is (the higher the number is, the more hydrophobic the amino acid is). We took a running average of the hydrophobicity of 11 consecutive amino acids in our model to create a hydrophobicity curve of the entire protein.

Our second criteria was to avoid the secondary structures in the protein: the alpha helices and beta sheets. We hypothesized that splitting through these sheets could also potentially disrupt folding activity and function.

We used an online tool

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