Modeling Motivation

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In our 2016 iGEM project, immune and protein information searching is inevitably required. Therefore, McHug is a software platform that is created to arrange your data and search the protein infomation from several databases. We will output your data with a user-friendly interface and you can easily browse the results by submitting in a requested form. The concept of McHug software is originated from 2016 CGU iGEM group. We aim to test the potential of Leishmania to be a new vaccine adjuvant by carrying antigens directly into immune cells. The antigen peptides will be presented on MHCI or II molecules to activate T cells. Therefore, McHug is created to predict the peptides on MHC molecules and help to optimize the peptide presentation and T cell activation. Also, cloning efficiency is considered to be an important step of the experiment. We then expect that this platform and help us shorten the antigen sequence so that it can be more effective to subclone the shuttle vector. The major functions of McHug can be sorted into 3 parts:
1. Protein Structure
Protein structure can affect the possibility of being epitope. Peptides in strong structural sequences like alpha-helix have small chance to be antigenic determinant. On the other hand, sequences in loop structure tend to be recognized by the immune system, specifically by antibodies, B cells, or T cells. Here, McHug shows you the 3D structure of your protein and you can select the peptide sequence to be colored. In case you want to design an epitope sequence to generate antibodies, you can choose sequences on the protein surface in a visible way.
2. MHC Affinity Graphs
Pathogenic proteins will be chopped into peptides and presented by MHC molecules to activate T cells. Therefore, the prediction of MHC affinity in your protein sequence can help you design your experiment. McHug is generated to arrange your numerical data into an easy understanding graph. We can show your IEDB prediction result in a trend chart. Also, users can enter the affinity threshold to curtail the signal in low-affinity position. Each affinity of amino acid in the chart stands for the nonamer starting from the specific amino acid position. Users can easily choose the high-affinity sequence and optimize their experiment.
3. Modification Sites
McHug will provide you the basic information of protein modifications. Moreover, the modification sites will be shown correspondingly to the amino acid position of MHC affinity chart. With the information, users can twig the profile of the protein.
4. Conservation Level
Protein conservation level will be given after BLASTing and multiple sequence aligning the submitted protein sequence. The outcome indicates the protein sequence conservation level between homologous protein sequences in different species. The conservation data will also be shown correspondingly to the amino acid position of MHC affinity chart. Users can choose the highly conserved peptide sequence to perform their experiment. In the project of CGU iGEM 2016, highly conserved region of pathogenic antigens sequence indicates a higher common share of pathogens. This can ensure the high coverage of the vaccine. (Future Work)

Demo

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This demo clip was filmed to showcase how to use McHug software and explan the function of result page. The protein ID we used in this clip was OVA protein so that you can see the result of our targeting antigen. The ultimate goal of McHug platform is to integrate several protein databases and provide the users with easy-understanding illustrations.
So far, we are able to show you protein 3D structure on the top of the interface. You can easily zoom in and zoom out to peek every part of your protein. And even select a partial peptide sequence. The peptide sequence in the protein will light up and reveal its position in the 3D structure. Moreover, MHC binding affinity and protein annotations are shown below. Amino acid positions are arranged correspondingly so that you can check all the information side by side. McHug 2016 also features the visualized interface which can transform loads of numerical data into legible charts and all basic protein information are integrated into a canvas penal at the buttom of the page.

Results

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Notebook

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