論文

国際誌
2021年7月7日

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

Biophysical journal
  • Tomohide Saio
  • ,
  • Soya Hiramatsu
  • ,
  • Mizue Asada
  • ,
  • Hiroshi Nakagawa
  • ,
  • Kazumi Shimizu
  • ,
  • Hiroyuki Kumeta
  • ,
  • Toshikazu Nakamura
  • ,
  • Koichiro Ishimori

120
15
開始ページ
2943
終了ページ
2951
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1016/j.bpj.2021.06.033

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.

リンク情報
DOI
https://doi.org/10.1016/j.bpj.2021.06.033
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/34242587
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8391054
ID情報
  • DOI : 10.1016/j.bpj.2021.06.033
  • PubMed ID : 34242587
  • PubMed Central 記事ID : PMC8391054

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