Computational protocol: Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study

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Protocol publication

[…] For all three folding simulations the starting structures (corresponding to the sequences INYWLAHAKAG, INYWLAHAK and INYWLAH) were in the fully extended state as obtained from the program Ribosome (http://www.roselab.jhu.edu/~raj/Manuals/ribosome.html). Missing hydrogen atoms were built with the program PSFGEN through its VMD plugin and assuming an acidic pH (with the histidine residues fully protonated). The choice to use an acidic pH was based on the published conditions reported , for both of the experimentally determined structures of the full length peptide (PDB entries 2DX2 and 1CB3). The peptide termini were unprotected in agreement with the experimental conditions used with the 2DX2 structure. Explicit solvent orthogonal periodic boundary systems were setup using VMD and ions were added to a final equivalent concentration of 100 mM in order to neutralize the total charge of the systems. For the truncated peptide the same system was used throughout the simulation with initial cell dimensions of 40×40×40 Å3, an initial shortest solute-solute distance of 14 Å, and a total of 5897 atoms of which 128 peptide atoms, 5766 water atoms (corresponding to 1922 TIP3 molecules), 1 sodium and 2 chloride ions. For the full length peptide simulation, and as the peptide assumed its persistent compact (helical) conformation, two cycles of reduction of the number of waters were undertaken. The initial system had cell dimensions of 60×60×60 Å3, an initial shortest solute-solute distance of 20 Å, and a total of 20475 atoms of which 177 peptide atoms, 20286 water atoms (corresponding to 6762 TIP3 molecules), 5 sodium and 7 chloride ions. Following the two cycles of water reduction, the final system had cell dimensions of 40×40×40 Å3, an initial shortest solute-solute distance of 22 Å, and a total of 6352 atoms of which 177 peptide atoms, 6171 water atoms (corresponding to 2057 TIP3 molecules), 1 sodium and 3 chloride ions. Finally, for the nonamer peptide the system had cell dimensions of 40×40×40 Å3, an initial shortest solute-solute distance of 12 Å, and a total of 5882 atoms of which 160 peptide atoms, 5718 water atoms (corresponding to 1906 TIP3 molecules), 1 sodium and 3 chloride ions.In addition to these three folding simulations, we have additionally performed a 0.4 µs long simulation of the 11mer (full-length) peptide but starting from the experimentally determined structure and at the lower temperature of 283 K (matching the reported temperature for the experimental work). That system had cell dimensions of 40×40×40 Å3, an initial shortest solute-solute distance of 14 Å, and a total of 5890 atoms of which 177 peptide atoms, 5709 water atoms (corresponding to 1903 TIP3 molecules), 1 sodium and 3 chloride ions.The topology and parameter files used throughout the system preparation were those of the CHARMM22 force field (version c36a2) with the CMAP correction (hereafter referred to as the ‘CHARMM forcefield’). [...] The program CARMA was used for most of the analyses, including removal of overall rotations/translations, calculation of RMSDs from a chosen reference structure, calculation of the radius of gyration, calculation of the average structure (and of the atomic root mean squared fluctuations), production of PDB files from the trajectory, Cartesian space principal component analysis , and corresponding cluster analysis, dihedral space principal component analysis , and cluster analysis, calculation of the frame-to-frame RMSD matrices, etc. Secondary structure assignments were performed with the program STRIDE . All molecular graphics work and preparation of were performed with the program VMD . […]

Pipeline specifications

Software tools VMD, CHARMM, STRIDE
Application Protein structure analysis
Diseases Genetic Diseases, Inborn