Factors That Affect the Degree of Twist in β-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-β Filament of the GNNQQNY Peptide

摘要

By exploiting the recent availability of the crystal structure of a cross-β filament of the GNNQQNY peptide fragment of the yeast prion protein Sup35, possible factors affecting the twisting of β-sheets structures have been analyzed. The advantage of this system is that it is composed entirely of β-sheet and thus free of potential ambiguities present in systems studied previously. In the crystal the cross-β filament consists of antiparallel β-sheets formed by parallel and in register peptides lying perpendicular to the long axis of the filament. The results of a series of molecular dynamics simulations performed under different conditions indicate that in the absence of crystal packing interactions there is no free energy barrier against twisting for the cross-β filament found planar in the crystal. More specifically, we find that there is only a small change in enthalpy (<3 kJ mol~(-1) per residue) for twists in the range 0—12 degrees with the planar form (in the crystal environment) being enthalpically stabilized. In contrast, entropic contributions, in particular those associated with an increase in backbone dynamics upon twisting, stabilize the twisted form. The degree of twist was found to vary depending on the environmental conditions as the result from an apparent subtle interplay of multiple small contributions. These observations are consistent with the different degrees of twist observed in β-sheets both in native protein structures and amyloid fibrils.