Energetics was analyzed for the aggregation of an 11-residue peptide. An all-atom molecular dynamics simulation was conducted with explicit solvent, and the energy-representation theory of solution was employed to compute the solvation free energies of the peptide and its aggregates. The aggregation in the pure-water solvent was observed to be inhibited by the solvation. The driving force of aggregate formation is the interactions among the peptide molecules, and the sum of the intra-aggregate and solvation terms per monomer is more favorable for larger aggregates. The effect of the cosolvent was then examined by focusing on the mixtures of water with urea and dimethyl sulfoxide (DMSO). It was actually shown that the derivative of the excess chemical potential of a flexible solute species with respect to the cosolvent concentration is determined exactly by the corresponding derivative of the free energy of solvation. The cosolvent effect on the equilibrium of aggregate formation can thus be addressed by comparing the solvation free energies with and without the cosolvent, and both the urea and DMSO cosolvents were found to inhibit the aggregation. The cosolvent-induced change in the solvation free energy was further decomposed into the contributions from the cosolvent and water. Their dependencies on the degree of aggregation were seen to be weak for large aggregates, and the roles of the electrostatic, van der Waals, and excluded-volume components in the solvation energetics were discussed.

The cosolvent effect on the equilibrium of peptide aggregation is reviewed from the energetic perspective. It is shown that the excess chemical potential is stationary against the variation of the distribution function for the configuration of a flexible solute species and that the derivative of the excess chemical potential with respect to the cosolvent concentration is determined by the corresponding derivative of the solvation free energy averaged over the solute configurations. The effect of a cosolvent at low concentrations on a chemical equilibrium can then be addressed in terms of the difference in the solvation free energy between pure-water solvent and the mixed solvent with the cosolvent, and illustrative analyses with all-atom model are presented for the aggregation of an 11-residue peptide by employing the energy-representation method to compute the solvation free energy. The solvation becomes more favorable with addition of the urea or DMSO cosolvent, and the extent of stabilization is smaller for larger aggregate. This implies that these cosolvents inhibit the formation of an aggregate, and the roles of such interaction components as the electrostatic, van der Waals, and excluded-volume are discussed.Protein or peptide can be harmful upon formation of aggregate [1][2][3][4]. It is considered that such amyloidoses as Alzheimer's, Parkinson's, and prion diseases are caused by the amyloid aggregation, and the formation of inclusion body is an impeding factor for massive expression in the field of protein engineering. The extent of aggregate formation of a peptide is determined by the interactions among the peptides forming the aggregate and those between the peptides and the surrounding solvent. In fact, the potential function is fixed for the interactions within the peptide aggregate when the peptide species is identified, whereas it can be tuned for the interactions with the surrounding environment. A common scheme for treating a peptide aggregate is thus to control the solvent environment with cosolvent [5-10], and since the cosolvent interacts with the peptide in a different manner from water, the interactions among the peptide, cosolvent, and water needs to be elucidated at the molecular level toward rational design of a cosolvent.The aggregation mechanism of peptide has been investigated both theoretically and experimentally . Molecular dynamics (MD) simulation has proven to be useful to address atomic-level processes, in particular, and the peptidepeptide and peptide-solvent interactions were analyzed to reveal the driving force of aggregate formation [12,14,16,[18][19][20][21][22][23][24]30]. In the context of statistical thermodynamics, the extent of peptide aggregation is described by the equilibrium constant of aggregation. It is determined by the balance of the The cosolvent effect on peptide aggregation is addressed with all-atom molecular dynamics simulation and freeenergy calculation. It is shown from the variational principle that the stability of a flexible solute species is modulated ...