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. 1999 Nov;77(5):2470–2478. doi: 10.1016/S0006-3495(99)77083-9

Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute

San Biagio PL 1, V Martorana V 1, D Bulone 1, MB Palma-Vittorelli 1, MU Palma 1
PMCID: PMC1300523  PMID: 20540927

Abstract

Molecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the system and hydration reconfiguration is also elicited. Switching is seen to occur on a time scale two orders of magnitude longer than that of the reconfiguration time of the solute taken alone, or that of the unperturbed solvent. Qualitatively, these results are unaffected by a different choice of the water-water interaction potential. They show that already at an elementary level, solvent-induced interactions alone, when fully accounted for, can be responsible for configurational and dynamical features essential to protein folding and function.

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Selected References

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