Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues

One of the most common fundamental secondary-structure elements of proteins is the ˇ-sheet. Folding of ˇ-sheets into various structures, e.g., ˇ-hairpins, ˇ-barrels, and amyloids, is believed to provide the energy required to drive various processes, including membrane-protein insertion into and translocation across the outer membrane of Gram-negative bacteria. The folding of the ˇ-hairpin has also been proposed to function as a conformational switch in some systems. In this chapter, we review the contributions of molecular dynamics simulations to resolving the energetics of ˇ-hairpin folding, the mechanics of ˇ-barrel insertion into the membrane by the BAM complex, the dynamics of ˇ-hairpin conformational switching, and the structures of disease-causing amyloids.