Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study

Abstract

Molecular dynamics simulation techniques have been used to investigate the effect of 2,2,2-trifluoroethanol (TFE) as a cosolvent on the stability of three different secondary structure-forming peptides: the ␣-helix from Melittin, the three-stranded ␤-sheet peptide Betanova, and the ␤-hairpin 41-56 from the B1 domain of protein G. The peptides were studied in pure water and 30% (vol͞vol) TFE͞water mixtures at 300 K. The simulations suggest that the stabilizing effect of TFE is induced by the preferential aggregation of TFE molecules around the peptides. This coating displaces water, thereby removing alternative hydrogen-bonding partners and providing a low dielectric environment that favors the formation of intrapeptide hydrogen bonds. Because TFE interacts only weakly with nonpolar residues, hydrophobic interactions within the peptides are not disrupted. As a consequence, TFE promotes stability rather than inducing denaturation. F or more than three decades, 2,2,2-trifluoroethanol (TFE) has been used as a cosolvent for the study of peptides in solution because NMR and CD studies show that the presence of TFE increases the population of ␣-helix and ␤-sheet content in secondary-structure-forming peptides in TFE͞water mixtures (1-3). Despite the effects of TFE having been known for such a long time, the mechanism by which TFE stabilizes secondary structure in peptides is still not clear. One possible explanation is the preferential solvation of the folded state by TFE (3). According to this hypothesis, TFE acts within the context of a preexisting helix-coil equilibrium, and the preferential interaction of TFE with the folded state shifts the equilibrium toward more structured conformations (3). The molecular nature of the TFE-peptide interaction is not clear, however. Alternative mechanisms have also been proposed to explain the stabilizing effect of TFE. In particular, the effect could result from TFE reinforcing hydrogen bonds between carbonyl and amidic NH groups by the removal of water molecules in the proximity of the solute (4) and͞or the lowering of the dielectric constant (1). Furthermore, small-angle x-ray-scattering studies (2) show that TFE forms clusters in water as the concentration of the organic cosolvent is increased, with a maximum at 30% (vol͞vol) TFE. Reiersen and Rees (5) have proposed that such TFE clusters locally assist the folding of secondary-structure elements by providing a solvent matrix that promotes hydrophobic interactions between amino acid side chains. Recent NMR studies involving small peptides in TFE provide some support for this hypothesis (6-8). Each of these mechanisms could explain the stabilization of ␣-helical peptides in solution (1, 3) but not necessarily the stabilization of ␤-structure (1, 2).In recent years molecular dynamics (MD) simulations have been increasingly used to understand the complex conformational equilibria of polypeptides in solution and to predict structural preferences (9-11). In particular, the importance of side-chain interactions in determining pepti...

Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data

“…A native-like fold in TFE/water at pH 2 (MD_pH2_TFE) seems to prefer protein-TFE interaction over protein-water interaction as indicated by the peak of the first solvation layer of TFE around 0.5 nm. This is in agreement with results from previous MD simulations of peptides in explicit TFE/water solutions which showed an accumulation of TFE molecules at the peptide surface Roccatano et al 2002;Diaz et al 2002;Mehrnejad et al 2007). At high temperature or with distance restraints applied (MD_pH2_TFE_HT and MD_pH2_TFE_DR) both solvents penetrate the protein.…”

“…Solution X-ray scattering studies suggest that an important factor is the clustering of the alcohol molecules in TFE aqueous solution (Hong et al 1999). NMR data, supported by MD simulations of peptides in explicit TFE/water solutions, show that this clustering results in an accumulation of TFE molecules around the peptide surface Roccatano et al 2002;Diaz et al 2002;Mehrnejad et al 2007). By coating the peptide surface they partially exclude water molecules (Starzyk et al 2005).…”

An Immunodominant Epitope of Myelin Basic Protein Is an Amphipathic α-Helix

“…5d) (33). In summary, the explanation for both the EPR and CD observations is that TFE provides a low dielectric environment that favors the formation of intrapeptide hydrogen bonds, thus stabilizing the ␣-helix formed by mMBP (83-92) (34).…”

Solvation in protein (un)folding of melittin tetramer–monomer transition

“…It has been suggested that this propensity for aggregation may act in coordination with their hydrophobic nature to bind with the hydrophobic residues of proteins (10,34). The hydrophobic aggregates reduce the local polarity surrounding the peptide, resulting in an increase in intramolecular hydrogen bonding (16,35,36). There is, however, limited experimental evidence of direct binding of fluorinated alcohols with hydrophobic residues (22,37).…”