We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-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 I' 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
Zanetti-Polzi, L., Davis, C.m., Gruebele, M., Dyer, R.b., Amadei, A., Daidone, I. (2017). Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS LETTERS, 591(20), 3265-3275 [10.1002/1873-3468.12836].
Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation
A. AmadeiMembro del Collaboration Group
;
2017-01-01
Abstract
We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-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 I' 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-jumpI documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.