title: Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model.
abstract: p97, a Mg-ATPase belonging to the AAA (ATPase associated with various cellular activities) super family of proteins, has been proposed to function in two distinct cellular pathways, namely homotypic membrane fusion and ubiquitin protein degradation by utilizing differing adaptor complexes. We present the cryo-electron microscopy three-dimensional reconstruction of endogenous p97 in an AMP-PNP bound state at 24 A resolution. It reveals clear nucleotide-dependent differences when compared to our previously published "p97-ADP" reconstruction, including a striking rearrangement of N domains and a positional change of the two ATPase domains, D1 and D2, with respect to each other. The docking of the X-ray structure of N-D1 domains in an ADP bound state indicates that an upward repositioning of N domain is necessary to accommodate the cryo-EM map of "p97-AMP-PNP", suggesting a change in the orientation of N domains upon nucleotide hydrolysis. Furthermore, computational analysis of the deformational motions of p97, performed on the cryo-EM density map and the atomic structure of the N-D1 domains independently, shows the existence of a negative cooperativity between the D1 and D2 rings and the flexibility of the N domains. Together these results allow the identification of functionally important features that offer molecular insights into the dynamics of the proposed p97 chaperone function.
authors.affiliation: Department of Biological Sciences, Imperial College London, South Kensington Campus, The Flowers Building, Armstrong Road, SW7 2AZ, London, UK.
authors.forename: Fabienne
authors.initials: F
authors.lastname: Beuron
authors.forename: Terence C
authors.initials: TC
authors.lastname: Flynn
authors.forename: Jianpeng
authors.initials: J
authors.lastname: Ma
authors.forename: Hisao
authors.initials: H
authors.lastname: Kondo
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhang
authors.forename: Paul S
authors.initials: PS
authors.lastname: Freemont
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry* / Q000378:metabolism*; D000818:Animals; D016880:Anisotropy; D055592:Biophysical Phenomena; D001703:Biophysics; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D004583:Electrons; D007091:Image Processing, Computer-Assisted; D008099:Liver / Q000378:metabolism; D008958:Models, Molecular; D015233:Models, Statistical; D009687:Nuclear Proteins / Q000737:chemistry* / Q000378:metabolism*; D009711:Nucleotides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D051381:Rats; D011994:Recombinant Proteins / Q000737:chemistry
chemical_list: D009687:Nuclear Proteins; D009711:Nucleotides; D011994:Recombinant Proteins; D000251:Adenosine Triphosphatases; C404942:p97 ATPase