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Computing the stability diagram of the Trp-cage miniprotein.

ABSTRACT: We report molecular dynamics simulations of the equilibrium folding/unfolding thermodynamics of an all-atom model of the Trp-cage miniprotein in explicit solvent. Simulations are used to sample the folding/unfolding free energy difference and its derivatives along 2 isochores. We model the DeltaG(u)(P,T) landscape using the simulation data and propose a stability diagram model for Trp-cage. We find the proposed diagram to exhibit features similar to globular proteins with increasing hydrostatic pressure destabilizing the native fold. The observed energy differences DeltaE(u) are roughly linearly temperature-dependent and approach DeltaE(u) = 0 with decreasing temperature, suggesting that the system approached the region of cold denaturation. In the low-temperature denatured state, the native helical secondary structure elements are largely preserved, whereas the protein conformation changes to an "open-clamp" configuration. A tighter packing of water around nonpolar sites, accompanied by an increasing solvent-accessible surface area of the unfolded ensemble, seems to stabilize the unfolded state at elevated pressures.

SUBMITTER: Paschek D

PROVIDER: S-EPMC2582582 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The Trp-cage: optimizing the stability of a globular miniprotein.

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Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

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