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The D2 sequence of the helix differs only at the thermophile valin was replaced for isoleucine in the mesophile. Both models of the mesophilic Doxorubicin Topoisomerase inhibitor and thermophilic D helices of the D1 and D2 proteins were placed in the periodic boundary simulation boxes that were 1 nm larger than the peptides along all three axes. After hydrogen atoms were added to the helices according to basic chemistry rules and the currently selected pH= 8.0, the boxes were filled with TIP3P water, and sodium atoms were iteratively placed at the coordinates with the lowest electrostatic potential until the cell was neutral. Molecular dynamics simulations were run using a multiple time step of 1.25 fs for intra-molecular for Epoxomicin Proteasome inhibitor intermolecular forces. To remove bumps and to correct the covalent geometry, the structures were energy-minimized with the Yamber3 force field using a force cutoff and the Particle Mesh Ewald algorithm to treat long-range electrostatic interactions. After removal of conformational stress by a short steepest descent minimization, the procedure was continued by simulated annealing until convergence was reached, the energy improved by less than 0.012 kcal mol21 during 200 steps.
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