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The hydration thermodynamics of the GXG tripeptide relative to the referenceGGG is often used to define the conditional hydration contribution of X. Thisquantity or the hydration thermodynamics of a small molecule analog of theside-chain or some combination of such estimates, have anchored theinterpretation of seminal experiments on protein stability and folding. We showthat such procedures to model protein hydration have significant limitations.We study the conditional hydration thermodynamics of the isoleucine side-chainin an extended pentapeptide and in helical deca-peptides, using as appropriatean extended penta-glycine or appropriate helical deca-peptides as reference.Hydration of butane in the gauche conformation provides a small moleculereference for the side-chain. We use the quasichemical theory to parse thehydration thermodynamics into chemical, packing, and long-range interactioncontributions. The chemical contribution reflects the contribution of solventclustering within the defined inner-shell of the solute; the chemicalcontribution of g-butane is substantially more negative than the conditionalchemical contribution of isoleucine. The packing contribution gives the workrequired to create a cavity in the solvent, a quantity of interest inunderstanding hydrophobic hydration. The packing contribution for g-butanesubstantially overestimates the conditional packing of isoleucine. The net ofsuch compensating contributions still disagrees with the conditional freeenergy of isoleucine but by a lesser magnitude. The excess enthalpy and entropyof hydration of g-butane model are also more negative than the correspondingconditional quantities for the side-chain. The conditional solvation ofisoleucine in GGIGG also proves unsatisfactory in describing the conditionalsolvation of isoleucine in the helical peptides.

Conditional solvation of isoleucine in model extended and helical  peptides: context dependence of hydrophobic hydration and the failure of the  group-transfer model