메뉴 건너뛰기




Volumn 113, Issue 29, 2016, Pages E4090-W4199

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

Author keywords

Cryo EM; Methyl trosy NMR; Proteasome; Protein dynamics; VAT

Indexed keywords

1,10 PHENANTHROLINE COPPER; ADENOSINE TRIPHOSPHATASE; MALEIMIDE; NUCLEOTIDE; PROTEASOME; VALOSIN CONTAINING PROTEIN; ARCHAEAL PROTEIN; VAT PROTEIN, THERMOPLASMA ACIDOPHILUM;

EID: 84978842964     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1603980113     Document Type: Article
Times cited : (46)

References (97)
  • 2
    • 70350772363 scopus 로고    scopus 로고
    • Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine
    • Glynn SE, Martin A, Nager AR, Baker TA, Sauer RT (2009) Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell 139(4):744-756.
    • (2009) Cell , vol.139 , Issue.4 , pp. 744-756
    • Glynn, S.E.1    Martin, A.2    Nager, A.R.3    Baker, T.A.4    Sauer, R.T.5
  • 3
    • 0034677361 scopus 로고    scopus 로고
    • The structures of HsIU and the ATP-dependent protease HsIUHsIV
    • BochtlerM, et al. (2000) The structures of HsIU and the ATP-dependent protease HsIUHsIV. Nature 403(6771):800-805.
    • (2000) Nature , vol.403 , Issue.6771 , pp. 800-805
    • Bochtler, M.1
  • 4
    • 84949267291 scopus 로고    scopus 로고
    • Asymmetric ring structure of Vps4 required for ESCRT-III disassembly
    • Caillat C, et al. (2015) Asymmetric ring structure of Vps4 required for ESCRT-III disassembly. Nat Commun 6:8781.
    • (2015) Nat Commun , vol.6 , pp. 8781
    • Caillat, C.1
  • 5
    • 8844251486 scopus 로고    scopus 로고
    • Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB
    • Weibezahn J, et al. (2004) Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB. Cell 119(5):653-665.
    • (2004) Cell , vol.119 , Issue.5 , pp. 653-665
    • Weibezahn, J.1
  • 6
    • 0027996115 scopus 로고
    • Protein disaggregation mediated by heat-shock protein Hsp104
    • Parsell DA, Kowal AS, Singer MA, Lindquist S (1994) Protein disaggregation mediated by heat-shock protein Hsp104. Nature 372(6505):475-478.
    • (1994) Nature , vol.372 , Issue.6505 , pp. 475-478
    • Parsell, D.A.1    Kowal, A.S.2    Singer, M.A.3    Lindquist, S.4
  • 7
    • 79959389010 scopus 로고    scopus 로고
    • AAA+ proteases: ATP-fueled machines of protein destruction
    • Sauer RT, Baker TA (2011) AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem 80:587-612.
    • (2011) Annu Rev Biochem , vol.80 , pp. 587-612
    • Sauer, R.T.1    Baker, T.A.2
  • 8
    • 0346727127 scopus 로고    scopus 로고
    • Protein degradation and protection against misfolded or damaged proteins
    • Goldberg AL (2003) Protein degradation and protection against misfolded or damaged proteins. Nature 426(6968):895-899.
    • (2003) Nature , vol.426 , Issue.6968 , pp. 895-899
    • Goldberg, A.L.1
  • 9
    • 84885428073 scopus 로고    scopus 로고
    • Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase
    • Beckwith R, Estrin E, Worden EJ, Martin A (2013) Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase. Nat Struct Mol Biol 20(10):1164-1172.
    • (2013) Nat Struct Mol Biol , vol.20 , Issue.10 , pp. 1164-1172
    • Beckwith, R.1    Estrin, E.2    Worden, E.J.3    Martin, A.4
  • 10
    • 84856976866 scopus 로고    scopus 로고
    • Complete subunit architecture of the proteasome regulatory particle
    • Lander GC, et al. (2012) Complete subunit architecture of the proteasome regulatory particle. Nature 482(7384):186-191.
    • (2012) Nature , vol.482 , Issue.7384 , pp. 186-191
    • Lander, G.C.1
  • 11
    • 84898807479 scopus 로고    scopus 로고
    • Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome
    • Unverdorben P, et al. (2014) Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci USA 111(15):5544-5549.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.15 , pp. 5544-5549
    • Unverdorben, P.1
  • 12
    • 42449121085 scopus 로고    scopus 로고
    • The two PAN ATPases from Halobacterium display N-terminal heterogeneity and form labile complexes with the 20S proteasome
    • Chamieh H, Guetta D, Franzetti B (2008) The two PAN ATPases from Halobacterium display N-terminal heterogeneity and form labile complexes with the 20S proteasome. Biochem J 411(2):387-397.
    • (2008) Biochem J , vol.411 , Issue.2 , pp. 387-397
    • Chamieh, H.1    Guetta, D.2    Franzetti, B.3
  • 13
    • 79951707743 scopus 로고    scopus 로고
    • ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle
    • Smith DM, Fraga H, Reis C, Kafri G, Goldberg AL (2011) ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle. Cell 144(4):526-538.
    • (2011) Cell , vol.144 , Issue.4 , pp. 526-538
    • Smith, D.M.1    Fraga, H.2    Reis, C.3    Kafri, G.4    Goldberg, A.L.5
  • 14
    • 0034100371 scopus 로고    scopus 로고
    • Biochemical and physical properties of the Methanococcus jannaschii 20S proteasome and PAN, a homolog of the ATPase (Rpt) subunits of the eucaryal 26S proteasome
    • Wilson HL, Ou MS, Aldrich HC, Maupin-Furlow J (2000) Biochemical and physical properties of the Methanococcus jannaschii 20S proteasome and PAN, a homolog of the ATPase (Rpt) subunits of the eucaryal 26S proteasome. J Bacteriol 182(6):1680-1692.
    • (2000) J Bacteriol , vol.182 , Issue.6 , pp. 1680-1692
    • Wilson, H.L.1    Ou, M.S.2    Aldrich, H.C.3    Maupin-Furlow, J.4
  • 15
    • 70349770896 scopus 로고    scopus 로고
    • Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa
    • Wang T, et al. (2009) Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa. Structure 17(10):1377-1385.
    • (2009) Structure , vol.17 , Issue.10 , pp. 1377-1385
    • Wang, T.1
  • 16
    • 0031042544 scopus 로고    scopus 로고
    • Cloning, sequencing and expression of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum
    • Pamnani V, et al. (1997) Cloning, sequencing and expression of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum. FEBS Lett 404(2-3):263-268.
    • (1997) FEBS Lett , vol.404 , Issue.2-3 , pp. 263-268
    • Pamnani, V.1
  • 17
    • 0036295232 scopus 로고    scopus 로고
    • Electron cryo-microscopy of VAT, the archaeal p97/CDC48 homologue from Thermoplasma acidophilum
    • Rockel B, Jakana J, Chiu W, Baumeister W (2002) Electron cryo-microscopy of VAT, the archaeal p97/CDC48 homologue from Thermoplasma acidophilum. J Mol Biol 317(5):673-681.
    • (2002) J Mol Biol , vol.317 , Issue.5 , pp. 673-681
    • Rockel, B.1    Jakana, J.2    Chiu, W.3    Baumeister, W.4
  • 18
    • 30044443816 scopus 로고    scopus 로고
    • VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase
    • Gerega A, et al. (2005) VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase. J Biol Chem 280(52):42856-42862.
    • (2005) J Biol Chem , vol.280 , Issue.52 , pp. 42856-42862
    • Gerega, A.1
  • 19
    • 84865094127 scopus 로고    scopus 로고
    • Identification of the Cdc48•20S proteasome as an ancient AAA+ proteolytic machine
    • Barthelme D, Sauer RT (2012) Identification of the Cdc48•20S proteasome as an ancient AAA+ proteolytic machine. Science 337(6096):843-846.
    • (2012) Science , vol.337 , Issue.6096 , pp. 843-846
    • Barthelme, D.1    Sauer, R.T.2
  • 20
    • 84874452437 scopus 로고    scopus 로고
    • Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20S peptidase
    • Barthelme D, Sauer RT (2013) Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20S peptidase. Proc Natl Acad Sci USA 110(9):3327-3332.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.9 , pp. 3327-3332
    • Barthelme, D.1    Sauer, R.T.2
  • 21
    • 84869016840 scopus 로고    scopus 로고
    • The archaeal proteasome is regulated by a network of AAA ATPases
    • Forouzan D, et al. (2012) The archaeal proteasome is regulated by a network of AAA ATPases. J Biol Chem 287(46):39254-39262.
    • (2012) J Biol Chem , vol.287 , Issue.46 , pp. 39254-39262
    • Forouzan, D.1
  • 22
    • 57149130824 scopus 로고    scopus 로고
    • AAA ATPase p97/VCP: Cellular functions, disease and therapeutic potential
    • Vij N (2008) AAA ATPase p97/VCP: Cellular functions, disease and therapeutic potential. J Cell Mol Med 12(6A):2511-2518.
    • (2008) J Cell Mol Med , vol.12 , Issue.6 A , pp. 2511-2518
    • Vij, N.1
  • 23
    • 33847711447 scopus 로고    scopus 로고
    • Mutations in p97/VCP induce unfolding activity
    • Rothballer A, Tzvetkov N, Zwickl P (2007) Mutations in p97/VCP induce unfolding activity. FEBS Lett 581(6):1197-1201.
    • (2007) FEBS Lett , vol.581 , Issue.6 , pp. 1197-1201
    • Rothballer, A.1    Tzvetkov, N.2    Zwickl, P.3
  • 24
    • 84855198520 scopus 로고    scopus 로고
    • Structure and function of the AAA+ nucleotide binding pocket
    • Wendler P, Ciniawsky S, Kock M, Kube S (2012) Structure and function of the AAA+ nucleotide binding pocket. Biochim Biophys Acta 1823(1):2-14.
    • (2012) Biochim Biophys Acta , vol.1823 , Issue.1 , pp. 2-14
    • Wendler, P.1    Ciniawsky, S.2    Kock, M.3    Kube, S.4
  • 25
    • 84855199977 scopus 로고    scopus 로고
    • Proteasomal AAA-ATPases: Structure and function
    • Bar-Nun S, Glickman MH (2012) Proteasomal AAA-ATPases: Structure and function. Biochim Biophys Acta 1823(1):67-82.
    • (2012) Biochim Biophys Acta , vol.1823 , Issue.1 , pp. 67-82
    • Bar-Nun, S.1    Glickman, M.H.2
  • 26
    • 33745041480 scopus 로고    scopus 로고
    • Evolutionary relationships and structural mechanisms of AAA+ proteins
    • Erzberger JP, Berger JM (2006) Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu Rev Biophys Biomol Struct 35(1):93-114.
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , Issue.1 , pp. 93-114
    • Erzberger, J.P.1    Berger, J.M.2
  • 27
    • 84897000286 scopus 로고    scopus 로고
    • Biochemistry. The resolution revolution
    • Kühlbrandt W (2014) Biochemistry. The resolution revolution. Science 343(6178):1443-1444.
    • (2014) Science , vol.343 , Issue.6178 , pp. 1443-1444
    • Kühlbrandt, W.1
  • 28
    • 84905911542 scopus 로고    scopus 로고
    • Structural biology. Beyond blob-ology
    • Smith MTJ, Rubinstein JL (2014) Structural biology. Beyond blob-ology. Science 345(6197):617-619.
    • (2014) Science , vol.345 , Issue.6197 , pp. 617-619
    • Smith, M.T.J.1    Rubinstein, J.L.2
  • 29
    • 0037062977 scopus 로고    scopus 로고
    • NMR analysis of a 900K GroEL GroES complex
    • Fiaux J, Bertelsen EB, Horwich AL, Wuthrich K (2002) NMR analysis of a 900K GroEL GroES complex. Nature 418(6894):207-211.
    • (2002) Nature , vol.418 , Issue.6894 , pp. 207-211
    • Fiaux, J.1    Bertelsen, E.B.2    Horwich, A.L.3    Wuthrich, K.4
  • 30
    • 33846928691 scopus 로고    scopus 로고
    • Quantitative dynamics and binding studies of the 20S proteasome by NMR
    • Sprangers R, Kay LE (2007) Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445(7128):618-622.
    • (2007) Nature , vol.445 , Issue.7128 , pp. 618-622
    • Sprangers, R.1    Kay, L.E.2
  • 31
    • 84941254172 scopus 로고    scopus 로고
    • An atomic structure of human γ-secretase
    • Bai XC, et al. (2015) An atomic structure of human γ-secretase. Nature 525(7568):212-217.
    • (2015) Nature , vol.525 , Issue.7568 , pp. 212-217
    • Bai, X.C.1
  • 32
    • 84929335211 scopus 로고    scopus 로고
    • Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase
    • Zhao J, Benlekbir S, Rubinstein JL (2015) Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature 521(7551):241-245.
    • (2015) Nature , vol.521 , Issue.7551 , pp. 241-245
    • Zhao, J.1    Benlekbir, S.2    Rubinstein, J.L.3
  • 33
    • 84938742519 scopus 로고    scopus 로고
    • Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex
    • Llacer JL, et al. (2015) Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Mol Cell 59(3):399-412.
    • (2015) Mol Cell , vol.59 , Issue.3 , pp. 399-412
    • Llacer, J.L.1
  • 34
    • 0030612833 scopus 로고    scopus 로고
    • Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution
    • Pervushin K, Riek R, Wider G, Wuthrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94(23):12366-12371.
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.23 , pp. 12366-12371
    • Pervushin, K.1    Riek, R.2    Wider, G.3    Wuthrich, K.4
  • 35
    • 0041930989 scopus 로고    scopus 로고
    • Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes
    • Tugarinov V, Hwang PM, Ollerenshaw JE, Kay LE (2003) Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J Am Chem Soc 125(34):10420-10428.
    • (2003) J Am Chem Soc , vol.125 , Issue.34 , pp. 10420-10428
    • Tugarinov, V.1    Hwang, P.M.2    Ollerenshaw, J.E.3    Kay, L.E.4
  • 36
    • 1242308875 scopus 로고    scopus 로고
    • An isotope labeling strategy for methyl TROSY spectroscopy
    • Tugarinov V, Kay LE (2004) An isotope labeling strategy for methyl TROSY spectroscopy. J Biomol NMR 28(2):165-172.
    • (2004) J Biomol NMR , vol.28 , Issue.2 , pp. 165-172
    • Tugarinov, V.1    Kay, L.E.2
  • 37
    • 84958205941 scopus 로고    scopus 로고
    • Solution NMR spectroscopy provides an avenue for the study of functionally dynamic molecular machines: The example of protein disaggregation
    • Rosenzweig R, Kay LE (2016) Solution NMR Spectroscopy Provides an Avenue for the Study of Functionally Dynamic Molecular Machines: The Example of Protein Disaggregation. J Am Chem Soc 138(5):1466-1477.
    • (2016) J Am Chem Soc , vol.138 , Issue.5 , pp. 1466-1477
    • Rosenzweig, R.1    Kay, L.E.2
  • 38
    • 84958883175 scopus 로고    scopus 로고
    • 2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition
    • Banerjee S, et al. (2016) 2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 351(6275):871-875.
    • (2016) Science , vol.351 , Issue.6275 , pp. 871-875
    • Banerjee, S.1
  • 39
    • 84960799533 scopus 로고    scopus 로고
    • Nucleotide-dependent conformational changes of the AAA+ ATPase p97 revisited
    • Schuller JM, Beck F, Lossl P, Heck AJR, Forster F (2016) Nucleotide-dependent conformational changes of the AAA+ ATPase p97 revisited. FEBS Lett 590(5):595-604.
    • (2016) FEBS Lett , vol.590 , Issue.5 , pp. 595-604
    • Schuller, J.M.1    Beck, F.2    Lossl, P.3    Heck, A.J.R.4    Forster, F.5
  • 40
    • 42949164124 scopus 로고    scopus 로고
    • Improved structures of full-length p97, an AAA ATPase: Implications for mechanisms of nucleotide-dependent conformational change
    • Davies JM, Brunger AT, Weis WI (2008) Improved structures of full-length p97, an AAA ATPase: Implications for mechanisms of nucleotide-dependent conformational change. Structure 16(5):715-726.
    • (2008) Structure , vol.16 , Issue.5 , pp. 715-726
    • Davies, J.M.1    Brunger, A.T.2    Weis, W.I.3
  • 41
    • 0344983310 scopus 로고    scopus 로고
    • The crystal structure of murine p97/VCP at 3.6A
    • Huyton T, et al. (2003) The crystal structure of murine p97/VCP at 3.6A. J Struct Biol 144(3):337-348.
    • (2003) J Struct Biol , vol.144 , Issue.3 , pp. 337-348
    • Huyton, T.1
  • 42
    • 0141507032 scopus 로고    scopus 로고
    • Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains
    • DeLaBarre B, Brunger AT (2003) Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat Struct Biol 10(10):856-863.
    • (2003) Nat Struct Biol , vol.10 , Issue.10 , pp. 856-863
    • DeLaBarre, B.1    Brunger, A.T.2
  • 43
    • 42949089487 scopus 로고    scopus 로고
    • Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
    • Trabuco LG, Villa E, Mitra K, Frank J, Schulten K (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16(5):673-683.
    • (2008) Structure , vol.16 , Issue.5 , pp. 673-683
    • Trabuco, L.G.1    Villa, E.2    Mitra, K.3    Frank, J.4    Schulten, K.5
  • 45
    • 84894623755 scopus 로고    scopus 로고
    • Quantifying the local resolution of cryo-EM density maps
    • Kucukelbir A, Sigworth FJ, Tagare HD (2014) Quantifying the local resolution of cryo-EM density maps. Nat Methods 11(1):63-65.
    • (2014) Nat Methods , vol.11 , Issue.1 , pp. 63-65
    • Kucukelbir, A.1    Sigworth, F.J.2    Tagare, H.D.3
  • 46
    • 79958789586 scopus 로고    scopus 로고
    • Site-directed methyl group labeling as an NMR probe of structure and dynamics in supramolecular protein systems: Applications to the proteasome and to the ClpP protease
    • Religa TL, Ruschak AM, Rosenzweig R, Kay LE (2011) Site-directed methyl group labeling as an NMR probe of structure and dynamics in supramolecular protein systems: Applications to the proteasome and to the ClpP protease. J Am Chem Soc 133(23):9063-9068.
    • (2011) J Am Chem Soc , vol.133 , Issue.23 , pp. 9063-9068
    • Religa, T.L.1    Ruschak, A.M.2    Rosenzweig, R.3    Kay, L.E.4
  • 47
    • 0036300690 scopus 로고    scopus 로고
    • Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques
    • Choy WY, et al. (2002) Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques. J Mol Biol 316(1):101-112.
    • (2002) J Mol Biol , vol.316 , Issue.1 , pp. 101-112
    • Choy, W.Y.1
  • 48
    • 51649131592 scopus 로고    scopus 로고
    • NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd (III) (DTPA-BMA) as paramagnetic probes
    • Bernini A, et al. (2008) NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd (III) (DTPA-BMA) as paramagnetic probes. Biophys Chem 137(2-3):71-75.
    • (2008) Biophys Chem , vol.137 , Issue.2-3 , pp. 71-75
    • Bernini, A.1
  • 49
    • 33744944532 scopus 로고    scopus 로고
    • Relaxation rates of degenerate 1H transitions in methyl groups of proteins as reporters of side-chain dynamics
    • Tugarinov V, Kay LE (2006) Relaxation rates of degenerate 1H transitions in methyl groups of proteins as reporters of side-chain dynamics. J Am Chem Soc 128(22):7299-7308.
    • (2006) J Am Chem Soc , vol.128 , Issue.22 , pp. 7299-7308
    • Tugarinov, V.1    Kay, L.E.2
  • 50
    • 0034993445 scopus 로고    scopus 로고
    • Multiplet component separation for measurement of methyl 13C-1H dipolar couplings in weakly aligned proteins
    • Kontaxis G, Bax A (2001) Multiplet component separation for measurement of methyl 13C-1H dipolar couplings in weakly aligned proteins. J Biomol NMR 20(1):77-82.
    • (2001) J Biomol NMR , vol.20 , Issue.1 , pp. 77-82
    • Kontaxis, G.1    Bax, A.2
  • 51
    • 85023511576 scopus 로고
    • Intramolecular dipolar relaxation in multispin systems
    • Werbelow LG, Grant DM (1977) Intramolecular dipolar relaxation in multispin systems. Adv Magn Opt Reson 9:189-299.
    • (1977) Adv Magn Opt Reson , vol.9 , pp. 189-299
    • Werbelow, L.G.1    Grant, D.M.2
  • 52
    • 44949272393 scopus 로고
    • The effects of dipolar cross correlation on 13C methyl-carbon T1, T2, and NOE measurements in macromolecules
    • Kay LE, Torchia D (1991) The effects of dipolar cross correlation on 13C methyl-carbon T1, T2, and NOE measurements in macromolecules. J Magn Reson 95(3):536-547.
    • (1991) J Magn Reson , vol.95 , Issue.3 , pp. 536-547
    • Kay, L.E.1    Torchia, D.2
  • 53
    • 0028503463 scopus 로고
    • A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium
    • Farrow NA, Zhang O, Forman-Kay JD, Kay LE (1994) A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium. J Biomol NMR 4(5):727-734.
    • (1994) J Biomol NMR , vol.4 , Issue.5 , pp. 727-734
    • Farrow, N.A.1    Zhang, O.2    Forman-Kay, J.D.3    Kay, L.E.4
  • 54
    • 33845939047 scopus 로고    scopus 로고
    • Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization
    • Scheres SHW, et al. (2007) Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat Methods 4(1):27-29.
    • (2007) Nat Methods , vol.4 , Issue.1 , pp. 27-29
    • Scheres, S.H.W.1
  • 55
    • 84868444740 scopus 로고    scopus 로고
    • RELION: Implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres SHW (2012) RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180(3):519-530.
    • (2012) J Struct Biol , vol.180 , Issue.3 , pp. 519-530
    • Scheres, S.H.W.1
  • 56
    • 0033517351 scopus 로고    scopus 로고
    • Global unfolding of a substrate protein by the Hsp100 chaperone ClpA
    • Weber-Ban EU, Reid BG, Miranker AD, Horwich AL (1999) Global unfolding of a substrate protein by the Hsp100 chaperone ClpA. Nature 401(6748):90-93.
    • (1999) Nature , vol.401 , Issue.6748 , pp. 90-93
    • Weber-Ban, E.U.1    Reid, B.G.2    Miranker, A.D.3    Horwich, A.L.4
  • 57
    • 84902209981 scopus 로고    scopus 로고
    • Bringing dynamic molecular machines into focus by methyl-TROSY NMR
    • Rosenzweig R, Kay LE (2014) Bringing dynamic molecular machines into focus by methyl-TROSY NMR. Annu Rev Biochem 83:291-315.
    • (2014) Annu Rev Biochem , vol.83 , pp. 291-315
    • Rosenzweig, R.1    Kay, L.E.2
  • 58
    • 84881450365 scopus 로고    scopus 로고
    • NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers
    • Sekhar A, Kay LE (2013) NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Proc Natl Acad Sci USA 110(32):12867-12874.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.32 , pp. 12867-12874
    • Sekhar, A.1    Kay, L.E.2
  • 59
    • 33646535590 scopus 로고    scopus 로고
    • Central pore residues mediate the p97/VCP activity required for ERAD
    • DeLaBarre B, Christianson JC, Kopito RR, Brunger AT (2006) Central pore residues mediate the p97/VCP activity required for ERAD. Mol Cell 22(4):451-462.
    • (2006) Mol Cell , vol.22 , Issue.4 , pp. 451-462
    • DeLaBarre, B.1    Christianson, J.C.2    Kopito, R.R.3    Brunger, A.T.4
  • 60
    • 84923096947 scopus 로고    scopus 로고
    • Mechanistic insights into the recycling machine of the SNARE complex
    • Zhao M, et al. (2015) Mechanistic insights into the recycling machine of the SNARE complex. Nature 518(7537):61-67.
    • (2015) Nature , vol.518 , Issue.7537 , pp. 61-67
    • Zhao, M.1
  • 61
    • 3042588011 scopus 로고    scopus 로고
    • Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex
    • Bowman GD, O'Donnell M, Kuriyan J (2004) Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature 429(6993):724-730.
    • (2004) Nature , vol.429 , Issue.6993 , pp. 724-730
    • Bowman, G.D.1    O'Donnell, M.2    Kuriyan, J.3
  • 62
    • 33746860263 scopus 로고    scopus 로고
    • Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling
    • Erzberger JP, Mott ML, Berger JM (2006) Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol 13(8):676-683.
    • (2006) Nat Struct Mol Biol , vol.13 , Issue.8 , pp. 676-683
    • Erzberger, J.P.1    Mott, M.L.2    Berger, J.M.3
  • 63
    • 84939215665 scopus 로고    scopus 로고
    • An Atypical AAA+ ATPase assembly controls efficient transposition through DNA remodeling and transposase recruitment
    • Arias-Palomo E, Berger JM (2015) An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment. Cell 162(4):860-871.
    • (2015) Cell , vol.162 , Issue.4 , pp. 860-871
    • Arias-Palomo, E.1    Berger, J.M.2
  • 64
    • 33746375404 scopus 로고    scopus 로고
    • Mechanism of DNA translocation in a replicative hexameric helicase
    • Enemark EJ, Joshua-Tor L (2006) Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442(7100):270-275.
    • (2006) Nature , vol.442 , Issue.7100 , pp. 270-275
    • Enemark, E.J.1    Joshua-Tor, L.2
  • 66
    • 84905390155 scopus 로고    scopus 로고
    • Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine
    • Cordova JC, et al. (2014) Stochastic but highly coordinated protein unfolding and translocation by the ClpXP proteolytic machine. Cell 158(3):647-658.
    • (2014) Cell , vol.158 , Issue.3 , pp. 647-658
    • Cordova, J.C.1
  • 67
    • 0348010363 scopus 로고    scopus 로고
    • Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis
    • Yamada-Inagawa T, Okuno T, Karata K, Yamanaka K, Ogura T (2003) Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis. J Biol Chem 278(50):50182-50187.
    • (2003) J Biol Chem , vol.278 , Issue.50 , pp. 50182-50187
    • Yamada-Inagawa, T.1    Okuno, T.2    Karata, K.3    Yamanaka, K.4    Ogura, T.5
  • 68
    • 84925496573 scopus 로고    scopus 로고
    • Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine
    • Iosefson O, Nager AR, Baker TA, Sauer RT (2015) Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine. Nat Chem Biol 11(3):201-206.
    • (2015) Nat Chem Biol , vol.11 , Issue.3 , pp. 201-206
    • Iosefson, O.1    Nager, A.R.2    Baker, T.A.3    Sauer, R.T.4
  • 69
    • 84947035580 scopus 로고    scopus 로고
    • Dissection of axial-pore loop function during unfolding and translocation by a AAA+ proteolytic machine
    • Iosefson O, Olivares AO, Baker TA, Sauer RT (2015) Dissection of Axial-Pore Loop Function during Unfolding and Translocation by a AAA+ Proteolytic Machine. Cell Reports 12(6):1032-1041.
    • (2015) Cell Reports , vol.12 , Issue.6 , pp. 1032-1041
    • Iosefson, O.1    Olivares, A.O.2    Baker, T.A.3    Sauer, R.T.4
  • 70
    • 55549088522 scopus 로고    scopus 로고
    • Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding
    • Martin A, Baker TA, Sauer RT (2008) Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat Struct Mol Biol 15(11):1147-1151.
    • (2008) Nat Struct Mol Biol , vol.15 , Issue.11 , pp. 1147-1151
    • Martin, A.1    Baker, T.A.2    Sauer, R.T.3
  • 71
    • 1542283751 scopus 로고    scopus 로고
    • Role of the processing pore of the ClpX AAA+ ATPase in the recognition and engagement of specific protein substrates
    • Siddiqui SM, Sauer RT, Baker TA (2004) Role of the processing pore of the ClpX AAA+ ATPase in the recognition and engagement of specific protein substrates. Genes Dev 18(4):369-374.
    • (2004) Genes Dev , vol.18 , Issue.4 , pp. 369-374
    • Siddiqui, S.M.1    Sauer, R.T.2    Baker, T.A.3
  • 72
    • 0035845498 scopus 로고    scopus 로고
    • Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis
    • Flynn JM, et al. (2001) Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc Natl Acad Sci USA 98(19):10584-10589.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.19 , pp. 10584-10589
    • Flynn, J.M.1
  • 73
    • 3042642040 scopus 로고    scopus 로고
    • Substrate recognition by the AAA+ chaperone ClpB
    • Schlieker C, et al. (2004) Substrate recognition by the AAA+ chaperone ClpB. Nat Struct Mol Biol 11(7):607-615.
    • (2004) Nat Struct Mol Biol , vol.11 , Issue.7 , pp. 607-615
    • Schlieker, C.1
  • 74
    • 84891001553 scopus 로고    scopus 로고
    • Fabrication of carbon films with ∼ 500nm holes for cryo-EM with a direct detector device
    • Marr CR, Benlekbir S, Rubinstein JL (2014) Fabrication of carbon films with ∼ 500nm holes for cryo-EM with a direct detector device. J Struct Biol 185(1):42-47.
    • (2014) J Struct Biol , vol.185 , Issue.1 , pp. 42-47
    • Marr, C.R.1    Benlekbir, S.2    Rubinstein, J.L.3
  • 75
    • 80052401629 scopus 로고    scopus 로고
    • Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
    • Bouvignies G, et al. (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477(7362):111-114.
    • (2011) Nature , vol.477 , Issue.7362 , pp. 111-114
    • Bouvignies, G.1
  • 76
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • Delaglio F, et al. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6(3):277-293.
    • (1995) J Biomol NMR , vol.6 , Issue.3 , pp. 277-293
    • Delaglio, F.1
  • 77
    • 84871444338 scopus 로고    scopus 로고
    • University of California, San Francisco
    • Goddard TD, Kneller DG (2008) SPARKY 3 (University of California, San Francisco).
    • (2008) SPARKY 3
    • Goddard, T.D.1    Kneller, D.G.2
  • 78
    • 84946473054 scopus 로고    scopus 로고
    • Alignment of cryo-EM movies of individual particles by optimization of image translations
    • Rubinstein JL, Brubaker MA (2015) Alignment of cryo-EM movies of individual particles by optimization of image translations. J Struct Biol 192(2):188-195.
    • (2015) J Struct Biol , vol.192 , Issue.2 , pp. 188-195
    • Rubinstein, J.L.1    Brubaker, M.A.2
  • 79
    • 84946488108 scopus 로고    scopus 로고
    • CTFFIND4: Fast and accurate defocus estimation from electron micrographs
    • Rohou A, Grigorieff N (2015) CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol 192(2):216-221.
    • (2015) J Struct Biol , vol.192 , Issue.2 , pp. 216-221
    • Rohou, A.1    Grigorieff, N.2
  • 80
    • 84922727036 scopus 로고    scopus 로고
    • Semi-automated selection of cryo-EM particles in RELION-1.3
    • Scheres SHW (2015) Semi-automated selection of cryo-EM particles in RELION-1.3. J Struct Biol 189(2):114-122.
    • (2015) J Struct Biol , vol.189 , Issue.2 , pp. 114-122
    • Scheres, S.H.W.1
  • 81
    • 84946486192 scopus 로고    scopus 로고
    • Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images
    • Zhao J, Brubaker MA, Benlekbir S, Rubinstein JL (2015) Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images. J Struct Biol 192(2):209-215.
    • (2015) J Struct Biol , vol.192 , Issue.2 , pp. 209-215
    • Zhao, J.1    Brubaker, M.A.2    Benlekbir, S.3    Rubinstein, J.L.4
  • 82
    • 84901044474 scopus 로고    scopus 로고
    • Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy
    • Yeung HO, et al. (2014) Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy. Open Biol 4:130142.
    • (2014) Open Biol , vol.4 , pp. 130142
    • Yeung, H.O.1
  • 83
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1
  • 84
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658-1659.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 85
    • 0037433034 scopus 로고    scopus 로고
    • PCMA: Fast and accurate multiple sequence alignment based on profile consistency
    • Pei J, Sadreyev R, Grishin NV (2003) PCMA: Fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 19(3):427-428.
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 427-428
    • Pei, J.1    Sadreyev, R.2    Grishin, N.V.3
  • 86
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404-405.
    • (2000) Bioinformatics , vol.16 , Issue.4 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 87
    • 0043123216 scopus 로고    scopus 로고
    • GeneSilico protein structure prediction meta-server
    • Kurowski MA, Bujnicki JM (2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res 31(13):3305-3307.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3305-3307
    • Kurowski, M.A.1    Bujnicki, J.M.2
  • 88
    • 0242267511 scopus 로고    scopus 로고
    • Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
    • Ginalski K, Rychlewski L (2003) Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. Proteins 53(Suppl 6):410-417.
    • (2003) Proteins , vol.53 , pp. 410-417
    • Ginalski, K.1    Rychlewski, L.2
  • 89
    • 79960001809 scopus 로고    scopus 로고
    • FFAS server: Novel features and applications
    • Web Server issue
    • Jaroszewski L, Li Z, Cai XH, Weber C, Godzik A (2011) FFAS server: Novel features and applications. Nucleic Acids Res 39(Web Server issue, Suppl 2):W38-W44.
    • (2011) Nucleic Acids Res , vol.39 , pp. W38-W44
    • Jaroszewski, L.1    Li, Z.2    Cai, X.H.3    Weber, C.4    Godzik, A.5
  • 90
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951-960.
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 951-960
    • Soding, J.1
  • 91
    • 0347383758 scopus 로고    scopus 로고
    • Modeller: Generation and refinement of homology-based protein structure models
    • Fiser A, Sali A (2003) Modeller: Generation and refinement of homology-based protein structure models. Methods Enzymol 374:461-491.
    • (2003) Methods Enzymol , vol.374 , pp. 461-491
    • Fiser, A.1    Sali, A.2
  • 92
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Web Server issue
    • Wiederstein M, Sippl MJ (2007) ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(Web Server issue, Suppl 2):W407-W410.
    • (2007) Nucleic Acids Res , vol.35 , pp. W407-W410
    • Wiederstein, M.1    Sippl, M.J.2
  • 93
    • 33845345287 scopus 로고    scopus 로고
    • Visualizing density maps with UCSF Chimera
    • Goddard TD, Huang CC, Ferrin TE (2007) Visualizing density maps with UCSF Chimera. J Struct Biol 157(1):281-287.
    • (2007) J Struct Biol , vol.157 , Issue.1 , pp. 281-287
    • Goddard, T.D.1    Huang, C.C.2    Ferrin, T.E.3
  • 94
    • 77952581453 scopus 로고    scopus 로고
    • Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
    • Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC (2010) Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol 170(3):427-438.
    • (2010) J Struct Biol , vol.170 , Issue.3 , pp. 427-438
    • Pintilie, G.D.1    Zhang, J.2    Goddard, T.D.3    Chiu, W.4    Gossard, D.C.5
  • 95
    • 0023809599 scopus 로고
    • Coupled assay of Na+, K+-ATPase activity
    • Nørby JG (1988) Coupled assay of Na+, K+-ATPase activity. Methods Enzymol 156:116-119.
    • (1988) Methods Enzymol , vol.156 , pp. 116-119
    • Nørby, J.G.1
  • 96
    • 84874393637 scopus 로고    scopus 로고
    • Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction
    • Rosenzweig R, Moradi S, Zarrine-Afsar A, Glover JR, Kay LE (2013) Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction. Science 339(6123):1080-1083.
    • (2013) Science , vol.339 , Issue.6123 , pp. 1080-1083
    • Rosenzweig, R.1    Moradi, S.2    Zarrine-Afsar, A.3    Glover, J.R.4    Kay, L.E.5
  • 97
    • 0010957050 scopus 로고
    • Reaction rates by nuclear magnetic resonance
    • McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28(3):430-431.
    • (1958) J Chem Phys , vol.28 , Issue.3 , pp. 430-431
    • McConnell, H.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.