Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides

[Image: see text] The intrinsic conformational preferences of small peptides may provide additional insight into the thermodynamics and kinetics of protein folding. In this study, we explore the underlying energy landscapes of two model peptides, namely, Ac-Ala-NH(2) and Ac-Ser-NH(2), using geometry-optimization-based tools developed within the context of energy landscape theory. We analyze not only how side-chain polarity influences the structural preferences of the dipeptides, but also other emergent properties of the landscape, including heat capacity profiles, and kinetics of conformational rearrangements. The contrasting topographies of the free energy landscape agree with recent results from Fourier transform microwave spectroscopy experiments, where Ac-Ala-NH(2) was found to exist as a mixture of two conformers, while Ac-Ser-NH(2) remained structurally locked, despite exhibiting an apparently rich conformational landscape.