| Journal Title /掲載ジャーナル名 |
Journal of the American Chemical Society |
| Publication Year and Month /掲載年月 |
July, 2023 |
| Paper Title /論文タイトル |
Electrostatic ratchet for successive peptide synthesis in non-ribosomal molecular machine Rimk |
| DOI /論文DOI |
10.1021/jacs.3c03926 |
| Author of Waseda University /本学の著者 |
TAKANO, Mitsunori(Professor, Faculty of Science and Engineering, School of Advanced Science and Engineering):Correspoinding Author, Last Author |
| Related Websites /関連Web |
– |
| Abstract /抄録 |
A nonribosomal peptide-synthesizing molecular machine, RimK, adds l-glutamic acids to the C-terminus of ribosomal protein S6 (RpsF) in vivo and synthesizes poly-α-glutamates in vitro. However, the mechanism of the successive glutamate addition, which is fueled by ATP, remains unclear. Here, we investigate the successive peptide-synthesizing mechanism of RimK via the molecular dynamics (MD) simulation of glutamate binding. We first show that RimK adopts three stable structural states with respect to the ATP-binding loop and the triphosphate chain of the bound ATP. We then show that a glutamate in solution preferentially binds to a positively charged belt-like region of RimK and the bound glutamate exhibits Brownian motion along the belt. The binding-energy landscape shows that the open-to-closed transition of the ATP-binding loop and the bent-to-straight transition of the triphosphate chain of ATP can function as an electrostatic ratchet that guides the bound glutamate to the active site. We then show the binding site of the second glutamate, which allows us to infer the ligation mechanism. Consistent with MD results, the crystal structure of RimK we obtained in the presence of RpsF presents an electron density that is presumed to correspond to the C-terminus of RpsF. We finally propose a mechanism for the successive peptide synthesis by RimK and discuss its similarity to other molecular machines. |
