Protein folding in cellular environments is still an open question even after decades of scientific scrutiny. In vivo, proteins perform their biological functions by folding into their native states within confining cellular environments that include  lipid membranes and chaperons, and within cavities, among others. Here, we address this problem by using all-atom molecular dynamics simulations in explicit water to study formation of secondary structure in an intrinsically disordered protein, the decapeptide fragment of the full-length amyloid �-protein, the A�(21-30) decapeptide, under confinement. Metastable �-hairpin structures found in this decapeptide, and characterized by a lifetime in bulk water, are shown to become more stable or unstable when confined inside small pores with either polar or non-polar surfaces. For progressively smaller pores the stability of these �-hairpin structures is shown to depend on the nature of this surface rather than on the effects of confinement on the solvent water.

Confinement effects on protein dynamics in polar and non-polar pores: A molecular-dynamics study

243rd National Meeting (2012)

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