Open AccessSide-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides
Author(s) -
Debayan Chakraborty,
Atreyee Banerjee,
David J. Wales
Publication year - 2021
Publication title -
the journal of physical chemistry. b
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.864
H-Index - 392
eISSN - 1520-6106
pISSN - 1520-5207
DOI - 10.1021/acs.jpcb.1c02412
Subject(s) - energy landscape , conformational isomerism , context (archaeology) , polarity (international relations) , folding (dsp implementation) , kinetics , chemistry , chain (unit) , protein folding , side chain , chemical physics , biophysics , physics , molecule , polymer , biology , biochemistry , classical mechanics , paleontology , organic chemistry , astronomy , cell , electrical engineering , engineering
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.