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A Small Protein

The goal of this tutorial is the simulation of a small protein and one of its mutants. The protein, called chignolin, is a designed protein of 10 amino acid residues that, when synthesized, shows a stable 3D structure in aqueous solution (see S. Honda, K. Yamasaki, Y. Sawada and H. Morii. 10 Residue Folded Peptide Designed by Segment Statistics. Structure 12, 1507–1518 (2004) [Link]). The size of the protein means that molecular dynamics simulations of reasonable length can be carried out without using excessive computer resources.

This tutorial is more advanced than some of the others in the pDynamo distribution as a detailed guide of how to perform each of the tasks is not given. Instead readers are encouraged to find their own solutions.

The steps in the tutorial are given below whereas programs implementing possible solutions to each of the tasks may be found in the tutorials/aSmallProtein subdirectory of the pDynamo distribution.

Set up simulation models of chignolin and its mutant. Structures for the proteins determined experimentally by NMR spectroscopy exist in the PDB with entry codes 1UAO and 2E4E, respectively.
Refine the experimental structures by energy minimization in vacuum.
Generate unfolded structures of the proteins that are suitable for simulation.
Solvate the folded and unfolded proteins.
Perform molecular dynamics simulations of the folded and unfolded proteins.
Analyze the trajectories produced by the simulations to see how the conformations of the proteins change.