Structural modeling of LAG-3 protein and immunoglobulin domains

• Main Author: Lai, Marcel Chang Long
• Other Authors: Kwoh Chee Keong
• Format: Final Year Project
• Language: English
• Published: 2014
• Subjects: DRNTU::Engineering::Computer science and engineering
• Online Access: http://hdl.handle.net/10356/59087
• Institution: Nanyang Technological University

Lymphocyte-activation gene 3 (LAG3) is a protein that limits the activity of T-cells, which down regulates the immune system. The protein functions can be determined from its structure. However, there is currently no available structure of LAG3 in any database. In order to fully understand its functions, there is a need to model the structure of LAG3. With the rapid growth of computational development, there are various tools available for modeling protein structure. In this project, three current popular tools, I-TASSER, MODELLER and SWISS-MODEL will be employed to predict and evaluate the LAG3 structure. LAG3 structural modeling by I-TASSER and SWISS-MODEL was done using the online interface and modeling in MODELLER was done using a standalone package. After the LAG3 models were initially constructed, PyMOL was used to align those models and the RMSD values were estimated. RMSD helps to compare how much the model deviate from one another. Finally, energy minimization was performed using Swiss-Pdb Viewer to optimize the structures, and comparisons were done among the optimal structures. It is evident from the findings that the I-TASSER model shows the most favorable prediction of the LAG3 structure among the three tools. With the model of LAG3 structure formed, further research can be done on molecular dynamics simulations of the LAG3 protein. Furthermore, different types of antibodies can be researched on to find out which antibodies are able to respond to the LAG3 protein.