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Structure. 2019 Feb 5;27(2):359-370.e12. doi: 10.1016/j.str.2018.10.013. Epub 2018 Dec 6.

Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements.

Author information

1
Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA. Electronic address: fabrizio.marinelli@nih.gov.
2
Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA.

Abstract

Double electron-electron resonance (DEER) is a popular technique that exploits attached spin labels to probe the collective dynamics of biomolecules in a native environment. Like most spectroscopic approaches, DEER detects an ensemble of states accounting for biomolecular dynamics as well as the labels' intrinsic flexibility. Hence, the DEER data alone do not provide high-resolution structural information. To disentangle this variability, we introduce a minimally biased simulation method to sample a structural ensemble that reproduces multiple experimental signals within the uncertainty. In contrast to previous approaches, our method targets the raw data themselves, and thereby it brings forth an unbiased molecular interpretation of the experiments. After validation on the T4 lysozyme, we apply this technique to interpret recent DEER experiments on a membrane transporter binding protein (VcSiaP). The results highlight the large-scale conformational movement that occurs upon substrate binding and reveal that the unbound VcSiaP is more open in solution than the X-ray structure.

KEYWORDS:

T4 lysozyme; VcSiaP; adaptive biasing approach; coupling simulations and experiments; double electron-electron resonance; maximum entropy principle; molecular dynamics; restrained-average dynamics; substrate-binding protein; tripartite ATP-independent periplasmic transporter

PMID:
30528595
DOI:
10.1016/j.str.2018.10.013

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