Computational Advances in Structural Biology

Abstract:

We have performed molecular dynamics (MD), replica-exchange (REMD) simulations and kinetic modeling to study folding pathways of model peptides forming helices and a hairpin. The simulation results are in good agreement with available experimental data on structure content and folding timescales, while providing novel microscopic insights into the fundamental processes of secondary structure formation.  For helix-forming peptides, we investigated effects of sequence, length and pH on folding.  In alanine homopeptides (ALA)n of length n=5, 8, 15, and 21 residues we find helix populations and relaxation times increasing from about 6% and ~2 ns for ALA5 to about 60% and ~500 ns for ALA21, and folding free energies decreasing linearly with the increasing number of residues.  For the 21-residue WH21 peptide, we found a marked increase in helix content and relaxation time upon pH increase, which changes the protonation state of its single His. This effect may be explained by changes in solvation. Kinetic coarse-graining showed a heterogenous ‘helix’ state. Helices tended to fold along multiple pathways, through various intermediates. Statistically the helices were most stable in the central region. However, the individual folding transitions tended to follow a random-walk path, with local dynamics involving correlated transitions of blocks of several consecutive hydrogen bonds. For the 16-residue GB1 hairpin peptide a folded fraction of 40% and global relaxation time of 1.8 μs  were calculated at 320 K. Folding followed the zipper model with nucleation at the central turn followed by consecutive hydrogen bond formation. The transitions were highly cooperative, with all backbone hydrogen bonds and sidechain hydrophobic interactions forming essentially at the same time. Coarse grained kinetic modeling showed transitions to off-path intermediates and identified the transition state for hairpin formation, involving the formation of the central turn and first hairpin hydrogen bond. The ‘hairpin’ state was also found to be heterogenous, including the fully folded and partially folded in-register hairpins along the zipper pathway.