Modeling mis-folded lysozyme aggregates
© Chotikasemsri and Rinehart; licensee BioMed Central Ltd. 2008
Published: 8 July 2008
Rosetta++ is freely distributed software used to predict all possible protein conformations by calculating the folding energy of the protein sequences. An included docking function is used to simulate a protein binding as homo- and hetero-dimers or trimers structures. This program is used to explore the possible conformations of one protein, which may not be easily found in the traditional approaches, such as NMR and crystallography. From these computer models, we can predict denatured and aggregate forms of proteins.
Materials and methods
Import native lysozyme sequence (gi:45384212) from NCBI and structure (PDB 1E8L) from PDB websites
Run lysozyme in Ab initio mode to start folding independently from the original protein sequence.
Docking each fold as homodimers to define the lowest energy to form lysozyme fibril structures.
Analyze the results.
Conclusions and discussions
Most of lowest radius of gyration come from the same Ab Initio fold (Figure 4b), but all the six lowest energy scores have many different and diverse form of structures (Figure 5b). Therefore, if we want to group or cluster all this potential fibril homodimers, we should sort by radius of gyration to maintain the structure within groups.
For future study, we hope that the model of the fibrilar forms of denatured lysozyme will help us understand how to block fibril formation and model interactions with heat shock proteins or other chaperones during the dis-aggregation process (refolding mechanism) .
We would like to acknowledge use of the BISC (Bioinformatics and Information Science Center) and Biotechnology Center of Western Kentucky University.
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