Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, [2000-

Adenosine Triphosphatases*/metabolism; ATPases Associated with Diverse Cellular Activities/metabolism ; Protein Structure, Tertiary ; Models, Molecular ; Cryoelectron Microscopy/methods

Single-particle cryo-electron microscopy (cryo-EM) has been shown to be effective in defining the structure of macromolecules, including protein complexes. Complexes adopt different conformations and compositions to perform their biological functions. In cryo-EM, the protein complexes are observed in solution, enabling the recording of images of the protein in multiple conformations. Various methods exist for capturing the conformational variability through analysis of cryo-EM data. Here, we analyzed the conformational variability in the hexameric AAA + ATPase p97, a complex with a six-fold rotational symmetric core surrounded by six flexible N-domains. We compared the performance of discrete classification methods with our recently developed method, MDSPACE, which uses 3D-to-2D flexible fitting of an atomic structure to images based on molecular dynamics (MD) simulations. Our analysis detected a novel conformation adopted by approximately 2% of the particles in the dataset and determined that the N-domains of p97 sway by up to 60° around a central position. This study demonstrates the application of MDSPACE in analyzing the continuous conformational changes in partially symmetrical protein complexes, systems notoriously difficult to analyze due to the alignment errors caused by their partial symmetry.

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Start-up and MRS The University of Melbourne; ANR-19-CE11-0008 French National Research Agency-ANR; A0100710998R; A0100710998; A0070710998; AP010712190; AD011012188 GENCI; The University of Melbourne start-up fund; Melbourne Research Scholarship; CNRS PRC 2889; CNRS 80 Prime; joint PhD scholarship Melbourne-CNRS Network

Keywords: AAA+ ATPase p97; MDSPACE; continuous conformational variability; partially symmetrical protein complexes; single-particle cryo-electron microscopy

EC 3.6.4.- (ATPases Associated with Diverse Cellular Activities)
EC 3.6.1.- (Adenosine Triphosphatases)

Date Created: 20240328 Date Completed: 20240329 Latest Revision: 20240330

20240330

PMC10970294

10.3390/ijms25063371

38542345