메뉴 건너뛰기




Volumn 428, Issue 2, 2016, Pages 323-331

New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy

Author keywords

conformational studies; functional dynamics; proteasome; solution NMR spectroscopy

Indexed keywords

PROTEASOME; PROTEIN; REGULATOR PROTEIN; SOLUTION AND SOLUBILITY;

EID: 84957435673     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2015.11.028     Document Type: Review
Times cited : (97)

References (49)
  • 1
    • 84924003209 scopus 로고    scopus 로고
    • Visualizing transient dark states by NMR spectroscopy
    • N.J. Anthis, and G.M. Clore Visualizing transient dark states by NMR spectroscopy Q. Rev. Biophys. 48 2015 35 116
    • (2015) Q. Rev. Biophys. , vol.48 , pp. 35-116
    • Anthis, N.J.1    Clore, G.M.2
  • 2
    • 0034919305 scopus 로고    scopus 로고
    • NMR methods for quantifying microsecond-to-millisecond motions in biological macromolecules
    • A.G. Palmer, C.D. Kroenke, and J.P. Loria NMR methods for quantifying microsecond-to-millisecond motions in biological macromolecules Methods Enzymol. 339 2001 204 238
    • (2001) Methods Enzymol. , vol.339 , pp. 204-238
    • Palmer, A.G.1    Kroenke, C.D.2    Loria, J.P.3
  • 3
    • 84902209981 scopus 로고    scopus 로고
    • Bringing dynamic molecular machines into focus by methyl-TROSY NMR
    • R. Rosenzweig, and L.E. Kay Bringing dynamic molecular machines into focus by methyl-TROSY NMR Annu. Rev. Biochem. 83 2014 291 315
    • (2014) Annu. Rev. Biochem. , vol.83 , pp. 291-315
    • Rosenzweig, R.1    Kay, L.E.2
  • 4
    • 77649179384 scopus 로고    scopus 로고
    • Methyl groups as probes of supra-molecular structure, dynamics and function
    • A.M. Ruschak, and L.E. Kay Methyl groups as probes of supra-molecular structure, dynamics and function J. Biomol. NMR 46 2009 75 87
    • (2009) J. Biomol. NMR , vol.46 , pp. 75-87
    • Ruschak, A.M.1    Kay, L.E.2
  • 5
    • 0344994534 scopus 로고    scopus 로고
    • NMR spectroscopy of large molecules and multimolecular assemblies in solution
    • G. Wider, and K. Wüthrich NMR spectroscopy of large molecules and multimolecular assemblies in solution Curr. Opin. Struct. Biol. 9 1999 594 601
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 594-601
    • Wider, G.1    Wüthrich, K.2
  • 6
    • 84934438245 scopus 로고    scopus 로고
    • Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR
    • M. Kaplan, and et al. Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR Nat. Methods 12 2015 649 652
    • (2015) Nat. Methods , vol.12 , pp. 649-652
    • Kaplan, M.1
  • 8
    • 0030612833 scopus 로고    scopus 로고
    • 2 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
    • 2 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. U. S. A. 94 1997 12366 12371
    • (1997) Proc. Natl. Acad. Sci. U. S. A. , vol.94 , pp. 12366-12371
    • Pervushin, K.1    Riek, R.2    Wider, G.3    Wüthrich, K.4
  • 9
    • 0041930989 scopus 로고    scopus 로고
    • 13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes
    • 13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes J. Am. Chem. Soc. 125 2003 10420 10428
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 10420-10428
    • Tugarinov, V.1    Hwang, P.2    Ollerenshaw, J.3    Kay, L.E.4
  • 11
    • 36049046667 scopus 로고    scopus 로고
    • Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR
    • I. Gelis, and et al. Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR Cell 131 2007 756 769
    • (2007) Cell , vol.131 , pp. 756-769
    • Gelis, I.1
  • 12
    • 0346727127 scopus 로고    scopus 로고
    • Protein degradation and protection against misfolded or damaged proteins
    • A.L. Goldberg Protein degradation and protection against misfolded or damaged proteins Nature 426 2003 895 899
    • (2003) Nature , vol.426 , pp. 895-899
    • Goldberg, A.L.1
  • 13
    • 0029042511 scopus 로고
    • Crystal structure of the 20S proteasome from the archaeon T. Acidophilum at 3.4 Å resolution
    • J. Lowe, D. Stock, B. Jap, P. Zwickl, W. Baumeister, and R. Huber Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution Science 268 1995 533 539
    • (1995) Science , vol.268 , pp. 533-539
    • Lowe, J.1    Stock, D.2    Jap, B.3    Zwickl, P.4    Baumeister, W.5    Huber, R.6
  • 15
    • 0028985861 scopus 로고
    • Conformational constraints in protein degradation by the 20S proteasome
    • T. Wenzel, and W. Baumeister Conformational constraints in protein degradation by the 20S proteasome Nat. Struct. Biol. 2 1995 199 204
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 199-204
    • Wenzel, T.1    Baumeister, W.2
  • 16
    • 33846928691 scopus 로고    scopus 로고
    • Quantitative dynamics and binding studies of the 20S proteasome by NMR
    • R. Sprangers, and L.E. Kay Quantitative dynamics and binding studies of the 20S proteasome by NMR Nature 445 2007 618 622
    • (2007) Nature , vol.445 , pp. 618-622
    • Sprangers, R.1    Kay, L.E.2
  • 17
    • 1242308875 scopus 로고    scopus 로고
    • An isotope labeling strategy for methyl TROSY spectroscopy
    • V. Tugarinov, and L.E. Kay An isotope labeling strategy for methyl TROSY spectroscopy J. Biomol. NMR 28 2004 165 172
    • (2004) J. Biomol. NMR , vol.28 , pp. 165-172
    • Tugarinov, V.1    Kay, L.E.2
  • 18
    • 28044440088 scopus 로고    scopus 로고
    • Quantitative NMR spectroscopy of supramolecular complexes: Dynamic side pores in ClpP are important for product release
    • R. Sprangers, A. Gribun, P.M. Hwang, W.A. Houry, and L.E. Kay Quantitative NMR spectroscopy of supramolecular complexes: Dynamic side pores in ClpP are important for product release Proc. Natl. Acad. Sci. U. S. A. 102 2005 16678 16683
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 16678-16683
    • Sprangers, R.1    Gribun, A.2    Hwang, P.M.3    Houry, W.A.4    Kay, L.E.5
  • 19
    • 84893842501 scopus 로고    scopus 로고
    • Tracing an allosteric pathway regulating the activity of the HslV protease
    • L. Shi, and L.E. Kay Tracing an allosteric pathway regulating the activity of the HslV protease Proc. Natl. Acad. Sci. U. S. A. 111 2014 2140 2145
    • (2014) Proc. Natl. Acad. Sci. U. S. A. , vol.111 , pp. 2140-2145
    • Shi, L.1    Kay, L.E.2
  • 20
    • 77950497745 scopus 로고    scopus 로고
    • Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR
    • T.L. Religa, R. Sprangers, and L.E. Kay Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR Science 328 2010 98 102
    • (2010) Science , vol.328 , pp. 98-102
    • Religa, T.L.1    Sprangers, R.2    Kay, L.E.3
  • 21
    • 0034625121 scopus 로고    scopus 로고
    • Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data
    • J.L. Battiste, and G. Wagner Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data Biochemistry 39 2000 5355 5365
    • (2000) Biochemistry , vol.39 , pp. 5355-5365
    • Battiste, J.L.1    Wagner, G.2
  • 22
    • 42949096020 scopus 로고    scopus 로고
    • Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases
    • J. Rabl, D.M. Smith, Y. Yu, S.C. Chang, A.L. Goldberg, and Y. Cheng Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases Mol. Cell 30 2008 360 368
    • (2008) Mol. Cell , vol.30 , pp. 360-368
    • Rabl, J.1    Smith, D.M.2    Yu, Y.3    Chang, S.C.4    Goldberg, A.L.5    Cheng, Y.6
  • 23
    • 34548274872 scopus 로고    scopus 로고
    • Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's alpha ring opens the gate for substrate entry
    • D.M. Smith, S.C. Chang, S. Park, D. Finley, Y. Cheng, and A.L. Goldberg Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's alpha ring opens the gate for substrate entry Mol. Cell 27 2007 731 744
    • (2007) Mol. Cell , vol.27 , pp. 731-744
    • Smith, D.M.1    Chang, S.C.2    Park, S.3    Finley, D.4    Cheng, Y.5    Goldberg, A.L.6
  • 24
    • 84870938343 scopus 로고    scopus 로고
    • Proteasome allostery as a population shift between interchanging conformers
    • A.M. Ruschak, and L.E. Kay Proteasome allostery as a population shift between interchanging conformers Proc. Natl. Acad. Sci. U. S. A. 109 2012 E3454 E3462
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. E3454-E3462
    • Ruschak, A.M.1    Kay, L.E.2
  • 26
    • 84879529913 scopus 로고    scopus 로고
    • Measurement of active site ionization equilibria in the 670 kDa proteasome core particle using methyl-TROSY NMR
    • A. Velyvis, and L.E. Kay Measurement of active site ionization equilibria in the 670 kDa proteasome core particle using methyl-TROSY NMR J. Am. Chem. Soc. 135 2013 9259 9262
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 9259-9262
    • Velyvis, A.1    Kay, L.E.2
  • 28
    • 84881450365 scopus 로고    scopus 로고
    • NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers
    • A. Sekhar, and L.E. Kay NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers Proc. Natl. Acad. Sci. U. S. A. 110 2013 12867 12874
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 12867-12874
    • Sekhar, A.1    Kay, L.E.2
  • 29
    • 33846851242 scopus 로고
    • Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance
    • S. Forsen, and R.A. Hoffman Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance J. Chem. Phys. 39 1963 2892 2901
    • (1963) J. Chem. Phys. , vol.39 , pp. 2892-2901
    • Forsen, S.1    Hoffman, R.A.2
  • 30
    • 0037427449 scopus 로고    scopus 로고
    • The structure of holo and metal-deficient wild-type human Cu, Zn superoxide dismutase and its relevance to familial amyotrophic lateral sclerosis
    • R.W. Strange, and et al. The structure of holo and metal-deficient wild-type human Cu, Zn superoxide dismutase and its relevance to familial amyotrophic lateral sclerosis J. Mol. Biol. 328 2003 877 891
    • (2003) J. Mol. Biol. , vol.328 , pp. 877-891
    • Strange, R.W.1
  • 32
    • 84862061967 scopus 로고    scopus 로고
    • Studying "invisible" excited protein states in slow exchange with a major conformation
    • P. Vallurupalli, G. Bouvignies, and L.E. Kay Studying "invisible" excited protein states in slow exchange with a major conformation J. Am. Chem. Soc. 134 2012 8148 8161
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 8148-8161
    • Vallurupalli, P.1    Bouvignies, G.2    Kay, L.E.3
  • 33
    • 33847534249 scopus 로고
    • Effects of diffusion on free precession in nuclear magnetic resonance experiments
    • H.Y. Carr, and E.M. Purcell Effects of diffusion on free precession in nuclear magnetic resonance experiments Phys. Rev. 54 1954 630 638
    • (1954) Phys. Rev. , vol.54 , pp. 630-638
    • Carr, H.Y.1    Purcell, E.M.2
  • 34
    • 0002899752 scopus 로고
    • Modified spin-echo method for measuring nuclear magnetic relaxation times
    • S. Meiboom, and D. Gill Modified spin-echo method for measuring nuclear magnetic relaxation times Rev. Sci. Instrum. 29 1958 688 691
    • (1958) Rev. Sci. Instrum. , vol.29 , pp. 688-691
    • Meiboom, S.1    Gill, D.2
  • 35
    • 77956501272 scopus 로고    scopus 로고
    • A transient and low-populated protein-folding intermediate at atomic resolution
    • D.M. Korzhnev, T.L. Religa, W. Banachewicz, A.R. Fersht, and L.E. Kay A transient and low-populated protein-folding intermediate at atomic resolution Science 329 2010 1312 1316
    • (2010) Science , vol.329 , pp. 1312-1316
    • Korzhnev, D.M.1    Religa, T.L.2    Banachewicz, W.3    Fersht, A.R.4    Kay, L.E.5
  • 36
    • 33646356250 scopus 로고    scopus 로고
    • Detecting transient intermediates in macromolecular binding by paramagnetic NMR
    • J. Iwahara, and G.M. Clore Detecting transient intermediates in macromolecular binding by paramagnetic NMR Nature 440 2006 1227 1230
    • (2006) Nature , vol.440 , pp. 1227-1230
    • Iwahara, J.1    Clore, G.M.2
  • 37
    • 22244479388 scopus 로고    scopus 로고
    • Copper-zinc superoxide dismutase and amyotrophic lateral sclerosis
    • J.S. Valentine, P.A. Doucette, and S. Zittin Potter Copper-zinc superoxide dismutase and amyotrophic lateral sclerosis Annu. Rev. Biochem. 74 2005 563 593
    • (2005) Annu. Rev. Biochem. , vol.74 , pp. 563-593
    • Valentine, J.S.1    Doucette, P.A.2    Zittin Potter, S.3
  • 38
    • 84874754257 scopus 로고    scopus 로고
    • Composition of soluble misfolded superoxide dismutase-1 in murine models of amyotrophic lateral sclerosis
    • P. Zetterstrom, K.S. Graffmo, P.M. Andersen, T. Brannstrom, and S.L. Marklund Composition of soluble misfolded superoxide dismutase-1 in murine models of amyotrophic lateral sclerosis Neruomol. Med. 15 2013 147 158
    • (2013) Neruomol. Med. , vol.15 , pp. 147-158
    • Zetterstrom, P.1    Graffmo, K.S.2    Andersen, P.M.3    Brannstrom, T.4    Marklund, S.L.5
  • 39
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • C. Dominguez, R. Boelens, and A.M. Bonvin HADDOCK: A protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 40
    • 0037473750 scopus 로고    scopus 로고
    • Prevention of transthyretin amyloid disease by changing protein misfolding energetics
    • P. Hammarström, R.L. Wiseman, E.T. Powers, and J.W. Kelly Prevention of transthyretin amyloid disease by changing protein misfolding energetics Science 299 2003 713 716
    • (2003) Science , vol.299 , pp. 713-716
    • Hammarström, P.1    Wiseman, R.L.2    Powers, E.T.3    Kelly, J.W.4
  • 41
    • 0030004644 scopus 로고    scopus 로고
    • The acid-mediated denaturation pathway of transthyretin yields a conformational intermediate that can self-assemble into amyloid
    • Z. Lai, W. Colón, and J.W. Kelly The acid-mediated denaturation pathway of transthyretin yields a conformational intermediate that can self-assemble into amyloid Biochemistry (Mosc) 35 1996 6470 6482
    • (1996) Biochemistry (Mosc) , vol.35 , pp. 6470-6482
    • Lai, Z.1    Colón, W.2    Kelly, J.W.3
  • 42
    • 0035920156 scopus 로고    scopus 로고
    • Tetramer dissociation and monomer partial unfolding precedes protofibril formation in amyloidogenic transthyretin variants
    • A. Quintas, D.C. Vaz, I. Cardoso, M.J.M. Saraiva, and R.M. Brito Tetramer dissociation and monomer partial unfolding precedes protofibril formation in amyloidogenic transthyretin variants J. Biol. Chem. 276 2001 27207 27213
    • (2001) J. Biol. Chem. , vol.276 , pp. 27207-27213
    • Quintas, A.1    Vaz, D.C.2    Cardoso, I.3    Saraiva, M.J.M.4    Brito, R.M.5
  • 43
    • 0036220131 scopus 로고    scopus 로고
    • Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme
    • D. Canet, and et al. Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme Nat. Struct. Mol. Biol. 9 2002 308 315
    • (2002) Nat. Struct. Mol. Biol. , vol.9 , pp. 308-315
    • Canet, D.1
  • 44
    • 33144467755 scopus 로고    scopus 로고
    • Amyloid formation under physiological conditions proceeds via a native-like folding intermediate
    • T.R. Jahn, M.J. Parker, S.W. Homans, and S.E. Radford Amyloid formation under physiological conditions proceeds via a native-like folding intermediate Nat. Struct. Mol. Biol. 13 2006 195 201
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 195-201
    • Jahn, T.R.1    Parker, M.J.2    Homans, S.W.3    Radford, S.E.4
  • 45
    • 77949363063 scopus 로고    scopus 로고
    • Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high molecular weight proteins
    • P. Gans, and et al. Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high molecular weight proteins Angew. Chem. Int. Ed. 49 2010 1958 1962
    • (2010) Angew. Chem. Int. Ed. , vol.49 , pp. 1958-1962
    • Gans, P.1
  • 46
    • 0034924188 scopus 로고    scopus 로고
    • Segmental isotopic labeling using expressed protein ligation
    • D. Cowburn, and T.W. Muir Segmental isotopic labeling using expressed protein ligation Methods Enzymol. 339 2001 41 54
    • (2001) Methods Enzymol. , vol.339 , pp. 41-54
    • Cowburn, D.1    Muir, T.W.2
  • 47
    • 84885658230 scopus 로고    scopus 로고
    • LEGO-NMR spectroscopy: A method to visualize individual subunits in large heteromeric complexes
    • M. Mund, J.H. Overbeck, J. Ullmann, and R. Sprangers LEGO-NMR spectroscopy: A method to visualize individual subunits in large heteromeric complexes Angew. Chem. Int. Ed. Engl. 52 2013 11401 11405
    • (2013) Angew. Chem. Int. Ed. Engl. , vol.52 , pp. 11401-11405
    • Mund, M.1    Overbeck, J.H.2    Ullmann, J.3    Sprangers, R.4
  • 48
    • 77957937199 scopus 로고    scopus 로고
    • Atomic-level characterization of the structural dynamics of proteins
    • D.E. Shaw, and et al. Atomic-level characterization of the structural dynamics of proteins Science 330 2010 341 346
    • (2010) Science , vol.330 , pp. 341-346
    • Shaw, D.E.1
  • 49
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • J.S. Fraser, M.W. Clarkson, S.C. Degnan, R. Erion, D. Kern, and T. Alber Hidden alternative structures of proline isomerase essential for catalysis Nature 462 2009 669 673
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.