title: Solvation free energies of alanine peptides: the effect of flexibility.
abstract: The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), 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, ΔGel, and components ΔGvdw, and ΔG, were found to be linear in n, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γel and γ were negative for fixed and flexible peptides, and γvdw was negative for fixed peptides. That γvdw was negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdw should be positive. A negative γvdw seemingly contradicts the notion that ΔGvdw drives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdw for the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdw was positive. Because most proteins do not assume extended conformations, a ΔGvdw 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.
authors: Sealy Center for Structural Biology and Molecular Biophysics, Departments of Biochemistry and Molecular Biology and Pharmacology and Toxicology, University of Texas Medical Branch , 301 University Blvd, Galveston, Texas 77555-0304, United States.
authors: Hironori
authors: H
authors: Kokubo
authors: Robert C
authors: RC
authors: Harris
authors: Dilipkumar
authors: D
authors: Asthagiri
authors: B Montgomery
authors: BM
authors: Pettitt
mesh_terms: D000409:Alanine; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D010455:Peptides; D012997:Solvents; D000409:Alanine