Solvation free energies of alanine peptides: The effect of flexibility

The electrostatic (ΔG_el), van der Waals cavity-formation (ΔG_vdw), and total (ΔG) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔG_el, and components ΔG_vdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γ_el, γ_vdw, and γ, respectively. Both γ_el and γ were negative for fixed and flexible peptides, and γ_vdw was negative for fixed peptides. That γ_vdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γ_vdw should be positive. A negative γ_vdw seemingly contradicts the notion that ΔG_vdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔG_vdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γ_vdw was positive. Because most proteins do not assume extended conformations, a ΔG_vdw that increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We find few intramolecular H-bonds but show that the intramolecular van der Waals interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult.