These projects simulate protein folding inside the exit tunnel of the ribosome.
The ribosome is a large protein/RNA molecule that is used to translate mRNA into a protein. It does this by successively adding amino acids which correspond to codons in the mRNA sequence. Once these amino acids have been added to the chain, the peptide is extruded through a tunnel inside the ribosome, which is about ten nanometers long.
In an extended conformation (i.e. the peptide is completely stretched out) it would take ~30 amino acids to span the tunnel's length. This means that for the first part of the protein's life it is folding inside a tunnel!
Most modern protein folding experiments and simulations do not directly attack this phenomenon. We intend to explore the protein folding process within the ribosome tunnel in an attempt to look at protein folding as it happens in the cell.
This project simulates a 39 residue peptide within the exit tunnel.
List of Contributors
This project is managed by Christian Schwantes at lab of Vijay Pande at Stanford University.
Christian Schwantes is a Graduate Student in Vijay Pande's group at Stanford University. He is interested in understanding how biomolecular reactions work at the atomic level. In addition, he has worked recently on developing the methodology for turning a simulation into something that is scientifically useful.
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