Role of Backbone Hydration and Salt-Bridge Formation in Stability of α-Helix in Solution

AbstractWe test molecular level hypotheses for the high thermal stability of α-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to α-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that has three pairs of “i, i+3” glutamic acid(−) and lysine(+) substitutions. Efficient configurational sampling of the EK peptide over a wide temperature range enabled by the replica exchange molecular dynamics technique allows characterization of the stability of α-helix with respect to heat-induced unfolding. We find that near ambient temperatures, the EK peptide predominately samples α-helical configurations with 80% fractional helicity at 300K. The helix melts over a broad range of temperatures with melting temperature, Tm, equal to 350K, that is significantly higher than the Tm of a 21-residue polyalanine peptide, A21. Salt-bridges between oppositely charged Glu− and Lys+ side chains can, in principle, provide thermal stability to α-helical conformers. For the specific EK peptide sequence, we observe infrequent formation of Glu-Lys salt-bridges (with ∼10–20% probability) and therefore we conclude that salt-bridge formation does not contribute significantly to the EK peptide's helical stability. However, lysine side chains are found to shield specific “i, i+4” backbone hydrogen bonds from water, indicating that large side-chain substituents can play an important role in stabilizing α-helical configurations of short peptides in aqueous solution through mediation of water access to backbone hydrogen bonds. These observations have implications on molecular engineering of peptides and biomolecules in the design of their thermostable variants where the shielding mechanism can act in concert with other factors such as salt-bridge formation, thereby increasing thermal stability considerably