Sequential allosteric mechanism of ATP hydrolysis by the CCT/TRiC chaperone is revealed through Arrhenius analysis

Significance Many biological machines consist of oligomeric rings that undergo conformational changes driven by ATP binding and hydrolysis. These conformational changes can take place in a concerted, probabilistic, or sequential fashion. Knowing the mode of conformational switching is important for understanding how these machines work. Here, we show that measuring the temperature dependence of the ATPase reaction of the chaperonin CCT/TRiC provides insight into its mode of switching. Our results show that ATP hydrolysis triggers sequential ‟conformational waves” in CCT/TRiC that proceed both clockwise and counterclockwise around its rings. Knowing the mechanism of allosteric switching is important for understanding how molecular machines work. The CCT/TRiC chaperonin nanomachine undergoes ATP-driven conformational changes that are crucial for its folding function. Here, we demonstrate that insight into its allosteric mechanism of ATP hydrolysis can be achieved by Arrhenius analysis. Our results show that ATP hydrolysis triggers sequential ‟conformational waves.” They also suggest that these waves start from subunits CCT6 and CCT8 (or CCT3 and CCT6) and proceed clockwise and counterclockwise, respectively.

[1]  A. Horovitz,et al.  Probing allosteric mechanisms using native mass spectrometry. , 2015, Current opinion in structural biology.

[2]  Michael Levitt,et al.  Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling , 2012, Proceedings of the National Academy of Sciences.

[3]  W. Chiu,et al.  Dual Action of ATP Hydrolysis Couples Lid Closure to Substrate Release into the Group II Chaperonin Chamber , 2011, Cell.

[4]  Renée L. Brost,et al.  The interaction network of the chaperonin CCT , 2008, The EMBO journal.

[5]  T. Baker,et al.  Subunit asymmetry and roles of conformational switching in the hexameric AAA+ ring of ClpX , 2015, Nature Structural &Molecular Biology.

[6]  A. Horwich,et al.  Chaperone rings in protein folding and degradation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[7]  A. Horovitz,et al.  Allosteric Mechanisms in Chaperonin Machines. , 2016, Chemical reviews.

[8]  A. Horovitz,et al.  Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis , 2005, Nature Structural &Molecular Biology.

[9]  C. Bustamante,et al.  Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. , 2014, Biophysical journal.

[10]  F. Pazos,et al.  Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex , 2014, Proteins.

[11]  Fabienne Beuron,et al.  The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins , 2011, The EMBO journal.

[12]  W E Moerner,et al.  Sensing cooperativity in ATP hydrolysis for single multisubunit enzymes in solution , 2011, Proceedings of the National Academy of Sciences.

[13]  A. Horovitz,et al.  Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cellular and gene expression phenotypes. , 2010, Journal of molecular biology.

[14]  A. R. Fresht Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding , 1999 .

[15]  L. Joachimiak,et al.  A gradient of ATP affinities generates an asymmetric power stroke driving the chaperonin TRIC/CCT folding cycle. , 2012, Cell reports.

[16]  M. Levitt,et al.  The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning. , 2013, Structure.

[17]  M. Levitt,et al.  The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. , 1995, Journal of molecular biology.

[18]  J. King,et al.  Human CCT4 and CCT5 Chaperonin Subunits Expressed in Escherichia coli Form Biologically Active Homo-oligomers* , 2013, The Journal of Biological Chemistry.

[19]  Michal Sharon,et al.  Allosteric mechanisms can be distinguished using structural mass spectrometry , 2013, Proceedings of the National Academy of Sciences.

[20]  A. Horovitz,et al.  Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET. , 2008, Journal of molecular biology.

[21]  J. Corrie,et al.  Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase. , 1994, Biochemistry.

[22]  Amnon Horovitz,et al.  ATP-induced allostery in the eukaryotic chaperonin CCT is abolished by the mutation G345D in CCT4 that renders yeast temperature-sensitive for growth. , 2008, Journal of molecular biology.

[23]  A. Brunger,et al.  Recent Advances in Deciphering the Structure and Molecular Mechanism of the AAA+ ATPase N-Ethylmaleimide-Sensitive Factor (NSF). , 2016, Journal of molecular biology.

[24]  M. Gerstein,et al.  Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly-made proteins with complex topologies , 2008, Nature Structural &Molecular Biology.

[25]  Patrice Koehl,et al.  An analytical method for computing atomic contact areas in biomolecules , 2013, J. Comput. Chem..