Prediction of solvent dependent beta-roll formation of a self-assembling silk-like protein domain

Triblock copolymers consisting of a middle silk-like [(Gly - Ala)(3) - Gly - Glu](n) block flanked by two hydrophilic end blocks that assume a random conformation in aqueous solution at all pH spontaneously assemble into micrometre long fibers at low pH. As elucidating the molecular structure of the stacked middle blocks, by various experimental methods, has thus far proved to be elusive, we complement the experimental approach by performing extensive replica exchange molecular dynamics (REMD) simulations. We predict the thermodynamically stable conformation of the middle block to be a beta-roll. This structure differs from flat, antiparallel silk beta-sheets, such as 1SLK (PDB protein data bank), by a smaller water-accessible surface and by increased possibilities for internal hydrogen bonding. As opposed to the flat sheet, the beta-roll is not inconsistent with the circular dichroism (CD) spectra in water, and directly explains the width of the fibers in water, as deduced from small angle X-ray scattering (SAXS). The flat surfaces of the beta-roll are densely covered with alanine methyl side groups, promoting hydrophobic stacking into a fiber. In agreement with experimental observations on silk crystals and on [(Gly - Ala)(3) - Gly - Glu](n) in water and methanol, we show that the stable structure of [(Gly - Ala)(3) - Gly - Glu](n) is solvent-dependent. The beta-roll is preferred in water, whereas the flat, antiparallel beta-sheet is most stable in methanol. The two structures can interconvert via a transformation resembling that of an accordion pleat. These findings explain the conformational properties of net uncharged [(Gly - Ala)(3) - Gly - Glu](n) in water, and provide a rationale for the solvent-dependency of the molecular conformation of silk-like Gly-Ala repeats in general. They may thus facilitate the design of new self-assembling silk-like materials with novel functionality.