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Conformational ensemble of a multidomain protein explored by Gd3+ electron paramagnetic resonance

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Title: Conformational ensemble of a multidomain protein explored by Gd3+ electron paramagnetic resonance
Authors: Saio, Tomohide Browse this author
Hiramatsu, Soya Browse this author
Asada, Mizue Browse this author
Nakagawa, Hiroshi Browse this author
Shimizu, Kazumi Browse this author
Kumeta, Hiroyuki Browse this author
Nakamura, Toshikazu Browse this author
Ishimori, Koichiro Browse this author →KAKEN DB
Issue Date: 3-Aug-2021
Publisher: Cell Press
Journal Title: Biophysical journal
Volume: 120
Issue: 15
Start Page: 2943
End Page: 2951
Publisher DOI: 10.1016/j.bpj.2021.06.033
Abstract: Despite their importance in function, the conformational state of proteins and its changes are often poorly understood, mainly because of the lack of an efficient tool. MurD, a 47-kDa protein enzyme responsible for peptidoglycan biosynthesis, is one of those proteins whose conformational states and changes during their catalytic cycle are not well understood. Although it has been considered that MurD takes a single conformational state in solution as shown by a crystal structure, the solution nuclear magnetic resonance (NMR) study suggested the existence of multiple conformational state of apo MurD in solution. However, the conformational distribution has not been evaluated. In this work, we investigate the conformational states of MurD by the use of electron paramagnetic resonance (EPR), especially intergadolinium distance measurement using double electron-electron resonance (DEER) measurement. The gadolinium ions are fixed on specific positions on MurD via a rigid double-arm paramagnetic lanthanide tag that has been originally developed for paramagnetic NMR. The combined use of NMR and EPR enables accurate interpretation of the DEER distance information to the structural information of MurD. The DEER distance measurement for apo MurD shows a broad distance distribution, whereas the presence of the inhibitor narrows the distance distribution. The results suggest that MurD exists in a wide variety of conformational states in the absence of ligands, whereas binding of the inhibitor eliminates variation in conformational states. The multiple conformational states of MurD were previously implied by NMR experiments, but our DEER data provided structural characterization of the conformational variety of MurD.
Rights: ©2021.This manuscript version is made available under the CC-BY-NC-ND 4.0 license
Type: article (author version)
Appears in Collections:理学院・理学研究院 (Graduate School of Science / Faculty of Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 石森 浩一郎

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