We present a calculation of the amide Iâ² infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for Î²-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide Iâ² IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump.
|Titolo:||Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation|
ZANETTI POLZI, LAURA (Corresponding)
|Data di pubblicazione:||2017|
|Appare nelle tipologie:||1.1 Articolo in rivista|