title: Ligand-driven conformational changes of MurD visualized by paramagnetic NMR.
abstract: Proteins, especially multi-domain proteins, often undergo drastic conformational changes upon binding to ligands or by post-translational modifications, which is a key step to regulate their function. However, the detailed mechanisms of such dynamic regulation of the functional processes are poorly understood because of the lack of an efficient tool. We here demonstrate detailed characterization of conformational changes of MurD, a 47 kDa protein enzyme consisting of three domains, by the use of solution NMR equipped with paramagnetic lanthanide probe. Quantitative analysis of pseudocontact shifts has identified a novel conformational state of MurD, named semi-closed conformation, which is found to be the key to understand how MurD regulates the binding of the ligands. The modulation of the affinity coupled with conformational changes accentuates the importance of conformational state to be evaluated in drug design.
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.|Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.|PRESTO, JST, Tokyo, 135-0063, Japan.
authors.forename: Tomohide
authors.initials: T
authors.lastname: Saio
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Ogura
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kumeta
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kobashigawa
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
authors.forename: Kazumi
authors.initials: K
authors.lastname: Shimizu
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
authors.forename: Masashi
authors.initials: M
authors.lastname: Yokochi
authors.affiliation: Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
authors.forename: Kota
authors.initials: K
authors.lastname: Kodama
authors.affiliation: Shionogi Pharmaceutical Research Center, Shionogi &Co., Ltd, Toyonaka 561-0825, Japan.
authors.forename: Hiroto
authors.initials: H
authors.lastname: Yamaguchi
authors.affiliation: Shionogi Pharmaceutical Research Center, Shionogi &Co., Ltd, Osaka 541-0045, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Tsujishita
authors.affiliation: Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
authors.forename: Fuyuhiko
authors.initials: F
authors.lastname: Inagaki
mesh_terms: D002151:Calorimetry; D007477:Ions; D028581:Lanthanoid Series Elements / Q000737:chemistry; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D010453:Peptide Synthases / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D007477:Ions; D028581:Lanthanoid Series Elements; D008024:Ligands; D010453:Peptide Synthases; C053379:UDP-N-acetylmuramoylalanine-D-glutamate ligase