title: A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site.
abstract: The turnstile motion of two neighboring threonines sets up a dynamic side chain interplay that can accommodate both polar and apolar ligands in a small molecule allosteric protein binding site. A computational model based on SAR data and both X-ray and cryo-EM structures of the AAA ATPase p97 was used to analyze the effects of paired threonines at the inhibitor site. Specifically, the Thr side chain hydroxyl groups form a hydrogen bonding network that readily accommodates small, highly polar ligand substituents. Conversely, diametric rotation of the χ1torsion by 150-180° orients the side chain β-methyl groups into the binding cleft, creating a hydrophobic pocket that can accommodate small, apolar substituents. This motif was found to be critical for rationalizing the affinities of a structurally focused set of inhibitors of p97 covering a > 2000-fold variation in potencies, with a preference for either small-highly polar or small-apolar groups. The threonine turnstile motif was further validated by a PDB search that identified analogous binding modes in ligand interactions in PKB, as well as by an analysis of NMR structures demonstrating additional gear-like interactions between adjacent Thr pairs. Combined, these data suggest that the threonine turnstile motif may be a general feature of interest in protein binding pockets.
authors.affiliation: Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Burnett
authors.forename: Chaemin
authors.initials: C
authors.lastname: Lim
authors.forename: Brian D
authors.initials: BD
authors.lastname: Peyser
authors.forename: Lalith P
authors.initials: LP
authors.lastname: Samankumara
authors.forename: Marina
authors.initials: M
authors.lastname: Kovaliov
authors.forename: Raffaele
authors.initials: R
authors.lastname: Colombo
authors.forename: Stacie L
authors.initials: SL
authors.lastname: Bulfer
authors.forename: Matthew G
authors.initials: MG
authors.lastname: LaPorte
authors.forename: Ann R
authors.initials: AR
authors.lastname: Hermone
authors.forename: Connor F
authors.initials: CF
authors.lastname: McGrath
authors.forename: Michelle R
authors.initials: MR
authors.lastname: Arkin
authors.forename: Rick
authors.initials: R
authors.lastname: Gussio
authors.forename: Donna M
authors.initials: DM
authors.lastname: Huryn
authors.forename: Peter
authors.initials: P
authors.lastname: Wipf
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry* / Q000378:metabolism*; D000495:Allosteric Site; D020816:Amino Acid Motifs; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D009687:Nuclear Proteins / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D013912:Threonine
chemical_list: D008024:Ligands; D009687:Nuclear Proteins; D013912:Threonine; D000251:Adenosine Triphosphatases; C404942:p97 ATPase