Heterogeneous dynamics in partially disordered proteins

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http://hdl.handle.net/10138/330837

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Virtanen , S , Kiirikki , A M , Mikula , K M , Iwai , H & Ollila , O H S 2020 , ' Heterogeneous dynamics in partially disordered proteins ' , Physical Chemistry Chemical Physics , vol. 22 , no. 37 , pp. 21185-21196 . https://doi.org/10.1039/d0cp03473h

Title: Heterogeneous dynamics in partially disordered proteins
Author: Virtanen, Salla; Kiirikki, Anne M.; Mikula, Kornelia M.; Iwai, Hideo; Ollila, O. H. Samuli
Other contributor: University of Helsinki, Biochemistry and Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Biochemistry and Biotechnology
University of Helsinki, Hideo Iwai / Principal Investigator
University of Helsinki, Biophysical chemistry




Date: 2020-10-07
Language: eng
Number of pages: 12
Belongs to series: Physical Chemistry Chemical Physics
ISSN: 1463-9076
DOI: https://doi.org/10.1039/d0cp03473h
URI: http://hdl.handle.net/10138/330837
Abstract: Importance of disordered protein regions is increasingly recognized in biology, but their characterization remains challenging due to the lack of suitable experimental and theoretical methods. NMR experiments can detect multiple timescale dynamics and structural details of disordered protein regions, but their detailed interpretation is often difficult. Here we combine protein backbone(15)N spin relaxation data with molecular dynamics (MD) simulations to detect not only heterogeneous dynamics of large partially disordered proteins but also their conformational ensembles. We observed that the rotational dynamics of folded regions in partially disordered proteins is dominated by similar rigid body rotation as in globular proteins, thereby being largely independent of flexible disordered linkers. Disordered regions, on the other hand, exhibit complex rotational motions with multiple timescales below similar to 30 ns which are difficult to detect from experimental data alone, but can be captured by MD simulations. Combining MD simulations and backbone(15)N spin relaxation data, measured applying segmental isotopic labeling with salt-inducible split intein, we resolved the conformational ensemble and dynamics of partially disordered periplasmic domain of TonB protein fromHelicobacter pyloricontaining 250 residues. To demonstrate the universality of our approach, it was applied also to the partially disordered region of chicken Engrailed 2. Our results pave the way in understanding how TonB transfers energy from inner membrane to the outer membrane receptors in Gram-negative bacteria, as well as the function of other proteins with disordered domains.
Subject: NMR-SPECTROSCOPY
BACKBONE DYNAMICS
ESCHERICHIA-COLI
CONFORMATIONAL DYNAMICS
N-15 RELAXATION
FORCE-FIELD
TONB
DOMAIN
MODEL
PREDICTION
114 Physical sciences
116 Chemical sciences
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