Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study.
Proc Natl Acad Sci U S A. 2016 Jul 11;
Authors: Huang R, Ripstein ZA, Augustyniak R, Lazniewski M, Ginalski K, Kay LE, Rubinstein JL
Abstract
The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded.
PMID: 27402735 [PubMed - as supplied by publisher]
[NMR paper] Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy.
Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif Related Articles Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy.
Proc Natl Acad Sci U S A. 2015 Oct 13;
Authors: Sborgi L, Ravotti F, Dandey VP, Dick MS, Mazur A, Reckel S, Chami M, Scherer S, Huber M, Böckmann A, Egelman EH,...
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[NMR paper] Effects of nucleotide binding to LmrA: A combined MAS-NMR and solution NMR study.
Effects of nucleotide binding to LmrA: A combined MAS-NMR and solution NMR study.
Related Articles Effects of nucleotide binding to LmrA: A combined MAS-NMR and solution NMR study.
Biochim Biophys Acta. 2015 Oct 5;
Authors: Hellmich UA, Mönkemeyer L, Velamakanni S, van Veen HW, Glaubitz C
PMID: 26449340
[NMR paper] Solution NMR study of DNA recognition mechanism of IRF4 protein.
Solution NMR study of DNA recognition mechanism of IRF4 protein.
Related Articles Solution NMR study of DNA recognition mechanism of IRF4 protein.
Nucleic Acids Symp Ser (Oxf). 2004;(48):105-6
Authors: Ishizaki I, Nomura M, Yamamoto K, Matsuyama T, Mishima M, Kojima C
Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was...
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11-24-2010 09:25 PM
[NMR paper] A 19F-NMR study of the equilibrium unfolding of membrane-associated D-lactate dehydro
A 19F-NMR study of the equilibrium unfolding of membrane-associated D-lactate dehydrogenase of Escherichia coli.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A 19F-NMR study of the equilibrium unfolding of membrane-associated D-lactate dehydrogenase of Escherichia coli.
Biochemistry. 1996 Dec 24;35(51):16502-9
Authors: Sun ZY, Pratt EA, Simplaceanu V, Ho C
Partially folded protein intermediates have been observed by 19F-NMR spectroscopy during the equilibrium unfolding of the...
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08-22-2010 02:20 PM
[NMR paper] Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton
Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR.
J Mol Biol. 1995 Jul 28;250(5):689-94
Authors: Yamaguchi T, Yamada H, Akasaka K
Thermodynamic stability of ribonuclease A (6.2 mM pH 1.0, 0.15 M KCl, in 2H2O) has been studied in the pressure range of 1 to 2000 atm and in the temperature range...
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[NMR paper] NMR study of the cold, heat, and pressure unfolding of ribonuclease A.
NMR study of the cold, heat, and pressure unfolding of ribonuclease A.
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Biochemistry. 1995 Jul 11;34(27):8631-41
Authors: Zhang J, Peng X, Jonas A, Jonas J
The reversible cold, heat, and pressure unfolding of RNase A and RNase A--inhibitor complex were studied by 1D and 2D 1H NMR spectroscopy. The reversible pressure denaturation experiments in the pressure range from 1 bar to 5 kbar were carried out at pH 2.0 and 10 degrees C. The cold denaturation was...
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[NMR paper] High-resolution NMR study of the pressure-induced unfolding of lysozyme.
High-resolution NMR study of the pressure-induced unfolding of lysozyme.
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Biochemistry. 1992 Sep 1;31(34):7773-8
Authors: Samarasinghe SD, Campbell DM, Jonas A, Jonas J
The pressure-induced reversible unfolding of lysozyme was investigated by high-resolution proton magnetic resonance spectroscopy by following the proton spectra of the following residues: His-15 epsilon 1, Trp-28 epsilon 3, Leu-17 delta 2, Cys-64 alpha, and Trp-108 epsilon 3. The...