Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E.

doi:10.1063/1.5005930

Title: Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

Journal Article · Wed Mar 28 00:00:00 EDT 2018 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.5005930· OSTI ID:1512950

Wang, Quan ^[1]; Serban, Andrew J. ^[2]; Wachter, Rebekka M. ^[2];

^[1]

Stanford Univ., CA (United States). Dept. of Chemistry
Arizona State Univ., Tempe, AZ (United States)

Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here in this paper, we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 $$μ$$M range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ∼0.1 s^-1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

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Research Organization:: Stanford Univ., CA (United States); Arizona State Univ., Tempe, AZ (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: FG02-07ER15892; FG02-09ER16123

OSTI ID:: 1512950

Alternate ID(s):: OSTI ID: 1416215

Journal Information:: Journal of Chemical Physics, Vol. 148, Issue 12; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 19 works

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References (40)

Protein aggregation and neurodegenerative disease Ross, Christopher A.; Poirier, Michelle A. Nature Medicine, Vol. 10, Issue S7 https://doi.org/10.1038/nm1066	journal	July 2004
Regulation of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase: PRODUCT INHIBITION, COOPERATIVITY, AND MAGNESIUM ACTIVATION Hazra, Suratna; Henderson, J. Nathan; Liles, Kevin Journal of Biological Chemistry, Vol. 290, Issue 40 https://doi.org/10.1074/jbc.m115.651745	journal	August 2015
Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA+ Machine Stinson, Benjamin M.; Nager, Andrew R.; Glynn, Steven E. Cell, Vol. 153, Issue 3 https://doi.org/10.1016/j.cell.2013.03.029	journal	April 2013
Protein Oligomerization Monitored by Fluorescence Fluctuation Spectroscopy: Self-Assembly of Rubisco Activase Chakraborty, Manas; Kuriata, Agnieszka M.; Nathan Henderson, J. Biophysical Journal, Vol. 103, Issue 5 https://doi.org/10.1016/j.bpj.2012.07.034	journal	September 2012
Single-Molecule characterization of oligomerization kinetics and equilibria of the tumor suppressor p53 Rajagopalan, S.; Huang, F.; Fersht, A. R. Nucleic Acids Research, Vol. 39, Issue 6 https://doi.org/10.1093/nar/gkq800	journal	November 2010
Dynamic light scattering: a practical guide and applications in biomedical sciences Stetefeld, Jörg; McKenna, Sean A.; Patel, Trushar R. Biophysical Reviews, Vol. 8, Issue 4 https://doi.org/10.1007/s12551-016-0218-6	journal	October 2016
Breaking the concentration limit of optical single-molecule detection Holzmeister, Phil; Acuna, Guillermo P.; Grohmann, Dina Chem. Soc. Rev., Vol. 43, Issue 4 https://doi.org/10.1039/c3cs60207a	journal	January 2014
Sensing cooperativity in ATP hydrolysis for single multisubunit enzymes in solution Jiang, Y.; Douglas, N. R.; Conley, N. R. Proceedings of the National Academy of Sciences, Vol. 108, Issue 41 https://doi.org/10.1073/pnas.1112244108	journal	September 2011
Small-angle scattering studies of biological macromolecules in solution Svergun, Dmitri I.; Koch, Michel H. J. Reports on Progress in Physics, Vol. 66, Issue 10 https://doi.org/10.1088/0034-4885/66/10/R05	journal	September 2003
Elucidating the Aggregation Number of Dopamine-Induced α-Synuclein Oligomeric Assemblies Zijlstra, Niels; Claessens, Mireille M. A. E.; Blum, Christian Biophysical Journal, Vol. 106, Issue 2 https://doi.org/10.1016/j.bpj.2013.12.009	journal	January 2014
Assembly Pathway of an AAA+ Protein: Tracking ClpA and ClpAP Complex Formation in Real Time ^† Kress, Wolfgang; Mutschler, Hannes; Weber-Ban, Eilika Biochemistry, Vol. 46, Issue 21 https://doi.org/10.1021/bi602616t	journal	May 2007
Design principles of biochemical oscillators Novák, Béla; Tyson, John J. Nature Reviews Molecular Cell Biology, Vol. 9, Issue 12 https://doi.org/10.1038/nrm2530	journal	October 2008
AAA+ proteins: have engine, will work Hanson, Phyllis I.; Whiteheart, Sidney W. Nature Reviews Molecular Cell Biology, Vol. 6, Issue 7 https://doi.org/10.1038/nrm1684	journal	July 2005
Rubisco activity and regulation as targets for crop improvement Parry, M. A. J.; Andralojc, P. J.; Scales, J. C. Journal of Experimental Botany, Vol. 64, Issue 3 https://doi.org/10.1093/jxb/ers336	journal	November 2012
Structure of green-type Rubisco activase from tobacco Stotz, Mathias; Mueller-Cajar, Oliver; Ciniawsky, Susanne Nature Structural & Molecular Biology, Vol. 18, Issue 12 https://doi.org/10.1038/nsmb.2171	journal	November 2011
Fuzzy Nanoassemblies: Toward Layered Polymeric Multicomposites Decher, G. Science, Vol. 277, Issue 5330 https://doi.org/10.1126/science.277.5330.1232	journal	August 1997
Biophysical characterization of higher plant Rubisco activase Henderson, J. Nathan; Hazra, Suratna; Dunkle, Alison M. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 1 https://doi.org/10.1016/j.bbapap.2012.09.006	journal	January 2013
Characterization of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase activase isoforms reveals hexameric assemblies with increased thermal stability Keown, Jeremy R.; Pearce, Frederick Grant Biochemical Journal, Vol. 464, Issue 3 https://doi.org/10.1042/bj20140676	journal	December 2014
Nucleotide Dependence of Subunit Rearrangements in Short-Form Rubisco Activase from Spinach Peterson-Forbrook, Dayna S.; Hilton, Matthew T.; Tichacek, Laura Biochemistry, Vol. 56, Issue 36 https://doi.org/10.1021/acs.biochem.7b00574	journal	August 2017
An Oxygen Scavenging System for Improvement of Dye Stability in Single-Molecule Fluorescence Experiments Aitken, Colin Echeverría; Marshall, R. Andrew; Puglisi, Joseph D. Biophysical Journal, Vol. 94, Issue 5 https://doi.org/10.1529/biophysj.107.117689	journal	March 2008
Detection of Intensity Change Points in Time-Resolved Single-Molecule Measurements Watkins, Lucas P.; Yang, Haw The Journal of Physical Chemistry B, Vol. 109, Issue 1 https://doi.org/10.1021/jp0467548	journal	January 2005
Single-molecule FRET studies on alpha-synuclein oligomerization of Parkinson’s disease genetically related mutants Tosatto, Laura; Horrocks, Mathew H.; Dear, Alexander J. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep16696	journal	November 2015
ATP and Magnesium Promote Cotton Short-Form Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Hexamer Formation at Low Micromolar Concentrations Kuriata, Agnieszka M.; Chakraborty, Manas; Henderson, J. Nathan Biochemistry, Vol. 53, Issue 46 https://doi.org/10.1021/bi500968h	journal	November 2014
Structural Symmetry and Protein Function Goodsell, David S.; Olson, Arthur J. Annual Review of Biophysics and Biomolecular Structure, Vol. 29, Issue 1 https://doi.org/10.1146/annurev.biophys.29.1.105	journal	June 2000
Small Oligomers of Ribulose-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Are Required for Biological Activity Keown, Jeremy R.; Griffin, Michael D. W.; Mertens, Haydyn D. T. Journal of Biological Chemistry, Vol. 288, Issue 28 https://doi.org/10.1074/jbc.m113.466383	journal	May 2013
An efficient system for high-level expression and easy purification of authentic recombinant proteins Catanzariti, Ann-Maree; Soboleva, Tatiana A.; Jans, David A. Protein Science, Vol. 13, Issue 5 https://doi.org/10.1110/ps.04618904	journal	May 2004
Native Mass Spectrometry: What is in the Name? Leney, Aneika C.; Heck, Albert J. R. Journal of The American Society for Mass Spectrometry, Vol. 28, Issue 1 https://doi.org/10.1007/s13361-016-1545-3	journal	December 2016
Direct characterization of amyloidogenic oligomers by single-molecule fluorescence Orte, A.; Birkett, N. R.; Clarke, R. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 38 https://doi.org/10.1073/pnas.0803086105	journal	September 2008
Prediction of diffusion coefficients of proteins Tyn, Myo T.; Gusek, Todd W. Biotechnology and Bioengineering, Vol. 35, Issue 4 https://doi.org/10.1002/bit.260350402	journal	February 1990
Structure of Arabidopsis thaliana Rubisco activase Hasse, Dirk; Larsson, Anna M.; Andersson, Inger Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 4 https://doi.org/10.1107/s1399004715001182	journal	March 2015
Single-molecule motions enable direct visualization of biomolecular interactions in solution Wang, Quan; Moerner, W. E. Nature Methods, Vol. 11, Issue 5 https://doi.org/10.1038/nmeth.2882	journal	March 2014
Rubisco Activases: AAA+ Chaperones Adapted to Enzyme Repair Bhat, Javaid Y.; Thieulin-Pardo, Gabriel; Hartl, F. Ulrich Frontiers in Molecular Biosciences, Vol. 4 https://doi.org/10.3389/fmolb.2017.00020	journal	April 2017
Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models Ortega, A.; Amorós, D.; García de la Torre, J. Biophysical Journal, Vol. 101, Issue 4 https://doi.org/10.1016/j.bpj.2011.06.046	journal	August 2011
Resolution of Fluorescence Correlation Measurements Meseth, Ulrich; Wohland, Thorsten; Rigler, Rudolf Biophysical Journal, Vol. 76, Issue 3 https://doi.org/10.1016/s0006-3495(99)77321-2	journal	March 1999
Mg2+ and ATP or adenosine 5′-[γ-thio]-triphosphate (ATPγS) enhances intrinsic fluorescence and induces aggregation which increases the activity of spinach Rubisco activase Wang, Zhen Y.; Ramage, Robert T.; Portis, Archie R. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1202, Issue 1 https://doi.org/10.1016/0167-4838(93)90061-u	journal	September 1993
Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid β-peptide Haass, Christian; Selkoe, Dennis J. Nature Reviews Molecular Cell Biology, Vol. 8, Issue 2 https://doi.org/10.1038/nrm2101	journal	February 2007
An Adaptive Anti-Brownian Electrokinetic Trap with Real-Time Information on Single-Molecule Diffusivity and Mobility Wang, Quan; Moerner, W. E. ACS Nano, Vol. 5, Issue 7 https://doi.org/10.1021/nn2014968	journal	June 2011
Polyelectrolyte Surface Interface for Single-Molecule Fluorescence Studies of DNA Polymerase Kartalov, Emil P.; Unger, Marc A.; Quake, Stephen R. BioTechniques, Vol. 34, Issue 3 https://doi.org/10.2144/03343st02	journal	March 2003
Sensing Cooperativity in ATP Hydrolysis for Single Multisubunit Enzymes in Solution Jiang, Yan; Douglas, Nicholai R.; Conley, Nicholas R. Biophysical Journal, Vol. 102, Issue 3 https://doi.org/10.1016/j.bpj.2011.11.967	journal	January 2012
Kernel density estimation via diffusion Botev, Z. I.; Grotowski, J. F.; Kroese, D. P. arXiv https://doi.org/10.48550/arxiv.1011.2602	text	January 2010

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