Format

Send to

Choose Destination
FEBS Lett. 2017 Oct;591(20):3265-3275. doi: 10.1002/1873-3468.12836. Epub 2017 Sep 21.

Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation.

Author information

1
Department of Physical and Chemical Sciences, University of L'Aquila, Italy.
2
Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA.
3
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL, USA.
4
Department of Chemistry, Emory University, Atlanta, GA, USA.
5
Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Italy.

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-jump.

KEYWORDS:

fast-folding peptides; molecular dynamics simulations; β-hairpin

PMID:
28881468
PMCID:
PMC5658256
DOI:
10.1002/1873-3468.12836
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Wiley Icon for PubMed Central
Loading ...
Support Center