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Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation
Ist Teil von
FEBS letters, 2017-10, Vol.591 (20), p.3265-3275
Ort / Verlag
England
Erscheinungsjahr
2017
Quelle
Free E-Journal (出版社公開部分のみ)
Beschreibungen/Notizen
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.