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- W4242640524 abstract "Conformationally dynamic peptides and proteins display both important biochemical properties and present a challenge for computational modeling. Characterizing the accessible structural landscape represents one route to understand their function with molecular level detail. We characterize a self-labeling 29-residue peptide, MP01-Gen4, that undergoes structural alterations in the presence of a perfluoroaromatic reaction partner. Replica exchange molecular dynamics (REMD) shows MP01 to access a broad set of states, that microsecond-long explicit solvent simulations only minimally sample. REMD and structural network analysis find an altered and reduced conformational landscape when MP01 interacts non-covalently or is covalently attached to the perfluoroaromatic small molecule. Residues throughout the peptide, notably at the C-terminus, interact with the small molecule in conformational state-dependent manners. The results help explain and generate hypotheses for experimental observations including the importance of flexibility and the role of the N- and C-terminal regions, both of which are distant from the active cysteine. The simulations highlight the importance of substantial sampling in minimally stabilized, conformationally dynamic systems and supplies a case study for small molecule-mediated, peptide conformational changes.<br>" @default.
- W4242640524 created "2022-05-12" @default.
- W4242640524 creator A5004173902 @default.
- W4242640524 date "2020-07-22" @default.
- W4242640524 modified "2023-09-26" @default.
- W4242640524 title "Conformational Landscape Reduction of a Dynamic 29-Residue Peptide by a Perfluoroaromatic Small Molecule" @default.
- W4242640524 doi "https://doi.org/10.26434/chemrxiv.12679226" @default.
- W4242640524 hasPublicationYear "2020" @default.
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