메뉴 건너뛰기




Volumn 40, Issue 5, 2012, Pages 1014-1020

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

Author keywords

Chemical shift index (CSI); Intrinsically disordered protein (IDP); ncIDP; Neighbour corrected structural propensity calculator (ncSPC); Structural propensity

Indexed keywords

ALPHA SYNUCLEIN; INTRINSICALLY DISORDERED PROTEIN; PHOTOACTIVE YELLOW PROTEIN; PROTEIN; STRUCTURAL PROTEIN; UNCLASSIFIED DRUG;

EID: 84866704850     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120171     Document Type: Review
Times cited : (104)

References (51)
  • 1
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
    • Wright, P. and Dyson, H. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293, 321-331
    • (1999) J. Mol. Biol. , vol.293 , pp. 321-331
    • Wright, P.1    Dyson, H.2
  • 2
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson, C.M. (2003) Protein folding and misfolding. Nature 426, 884-890
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 3
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F. and Jones, D.T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337, 635-645
    • (2004) J. Mol. Biol. , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 4
    • 33847768609 scopus 로고    scopus 로고
    • Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions
    • Xie, H., Vucetic, S., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Uversky, V.N. and Obradovic, Z. (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 6, 1882-1898
    • (2007) J. Proteome Res. , vol.6 , pp. 1882-1898
    • Xie, H.1    Vucetic, S.2    Iakoucheva, L.M.3    Oldfield, C.J.4    Dunker, A.K.5    Uversky, V.N.6    Obradovic, Z.7
  • 6
    • 0036468397 scopus 로고    scopus 로고
    • Coupling of folding and binding for unstructured proteins
    • Dyson, H.J. and Wright, P.E. (2002) Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12, 54-60
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 54-60
    • Dyson, H.J.1    Wright, P.E.2
  • 7
    • 55949092886 scopus 로고    scopus 로고
    • α-Synuclein misfolding and neurodegenerative diseases
    • Uversky, V.N. (2008) α-Synuclein misfolding and neurodegenerative diseases. Curr. Protein Pept. Sci. 9, 507-540
    • (2008) Curr. Protein Pept. Sci. , vol.9 , pp. 507-540
    • Uversky, V.N.1
  • 8
    • 4344707281 scopus 로고    scopus 로고
    • Unfolded proteins and protein folding studied by NMR
    • Dyson, H.J. and Wright, P.E. (2004) Unfolded proteins and protein folding studied by NMR. Chem. Rev. 104, 3607-3622
    • (2004) Chem. Rev. , vol.104 , pp. 3607-3622
    • Dyson, H.J.1    Wright, P.E.2
  • 10
    • 41449109638 scopus 로고    scopus 로고
    • Conformational distributions of unfolded polypeptides from novel NMR techniques
    • Meier, S., Blackledge, M. and Grzesiek, S. (2008) Conformational distributions of unfolded polypeptides from novel NMR techniques. J. Chem. Phys. 128, 052204
    • (2008) J. Chem. Phys. , vol.128 , pp. 052204
    • Meier, S.1    Blackledge, M.2    Grzesiek, S.3
  • 11
    • 0034923356 scopus 로고    scopus 로고
    • Use of chemical shifts in macromolecular structure determination
    • Wishart, D.S. and Case, D.A. (2001) Use of chemical shifts in macromolecular structure determination. Methods Enzymol. 338, 3-34
    • (2001) Methods Enzymol. , vol.338 , pp. 3-34
    • Wishart, D.S.1    Case, D.A.2
  • 12
    • 34547679071 scopus 로고    scopus 로고
    • NMR: Prediction of protein flexibility
    • Berjanskii, M. and Wishart, D.S. (2006) NMR: prediction of protein flexibility. Nat. Protoc. 1, 683-688
    • (2006) Nat. Protoc. , vol.1 , pp. 683-688
    • Berjanskii, M.1    Wishart, D.S.2
  • 13
    • 34547563370 scopus 로고    scopus 로고
    • The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts
    • Berjanskii, M.V. and Wishart, D.S. (2007) The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res. 35, W531-W537
    • (2007) Nucleic Acids Res. , vol.35
    • Berjanskii, M.V.1    Wishart, D.S.2
  • 14
    • 0026597879 scopus 로고
    • The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy
    • Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31, 1647-1651
    • (1992) Biochemistry , vol.31 , pp. 1647-1651
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 15
    • 33751552347 scopus 로고    scopus 로고
    • Sensitivity of secondary structure propensities to sequence differences between α- and γ-synuclein: Implications for fibrillation
    • Marsh, J.A., Singh, V.K., Jia, Z. and Forman-Kay, J.D. (2006) Sensitivity of secondary structure propensities to sequence differences between α- and γ-synuclein: implications for fibrillation. Protein Sci. 15, 2795-2804
    • (2006) Protein Sci. , vol.15 , pp. 2795-2804
    • Marsh, J.A.1    Singh, V.K.2    Jia, Z.3    Forman-Kay, J.D.4
  • 16
    • 0000084729 scopus 로고
    • Sequence-corrected 15N "random coil" chemical shifts
    • Braun, D., Wider, G. and Ẅuthrich, K. (1994) Sequence-corrected 15N "random coil" chemical shifts. J. Am. Chem. Soc. 116, 8466-8469
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 8466-8469
    • Braun, D.1    Wider, G.2    Ẅuthrich, K.3
  • 17
    • 0029181728 scopus 로고
    • H-1, C-13 and N-15 random coil NMR chemical shifts of the common amino acids. 1. Investigation of nearest-neighbor effects
    • Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) H-1, C-13 and N-15 random coil NMR chemical shifts of the common amino acids. 1. Investigation of nearest-neighbor effects. J. Biomol. NMR 5, 67-81
    • (1995) J. Biomol. NMR , vol.5 , pp. 67-81
    • Wishart, D.S.1    Bigam, C.G.2    Holm, A.3    Hodges, R.S.4    Sykes, B.D.5
  • 19
    • 80051704532 scopus 로고    scopus 로고
    • Sequence correction of random coil chemical shifts: Correlation between neighbor correction factors and changes in the Ramachandran distribution
    • Kjaergaard, M. and Poulsen, F.M. (2011) Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J. Biomol. NMR 50, 157-165
    • (2011) J. Biomol. NMR , vol.50 , pp. 157-165
    • Kjaergaard, M.1    Poulsen, F.M.2
  • 20
    • 0037184476 scopus 로고    scopus 로고
    • Investigation of the neighboring residue effects on protein chemical shifts
    • Wang, Y. and Jardetzky, O. (2002) Investigation of the neighboring residue effects on protein chemical shifts. J. Am. Chem. Soc. 124, 14075-14084
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 14075-14084
    • Wang, Y.1    Jardetzky, O.2
  • 21
    • 70450194574 scopus 로고    scopus 로고
    • Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins
    • Simone, A.D., Cavalli, A., Hsu, S.D., Vranken, W. and Vendruscolo, M. (2009) Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins. J. Am. Chem. Soc. 131, 16332-16333
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 16332-16333
    • Simone, A.D.1    Cavalli, A.2    Hsu, S.D.3    Vranken, W.4    Vendruscolo, M.5
  • 22
    • 78650615363 scopus 로고    scopus 로고
    • Sequence-specific random coil chemical shifts of intrinsically disordered proteins
    • Tamiola, K., Acar, B. and Mulder, F.A.A. (2010) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J. Am. Chem. Soc. 132, 18000-18003
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 18000-18003
    • Tamiola, K.1    Acar, B.2    Mulder, F.A.A.3
  • 23
    • 0029904487 scopus 로고    scopus 로고
    • NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded
    • Weinreb, P.H., Zhen, W., Poon, A.W., Conway, K.A. and Lansbury, P.T. (1996) NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded. Biochemistry 35, 13709-13715
    • (1996) Biochemistry , vol.35 , pp. 13709-13715
    • Weinreb, P.H.1    Zhen, W.2    Poon, A.W.3    Conway, K.A.4    Lansbury, P.T.5
  • 24
    • 0141677840 scopus 로고    scopus 로고
    • A protein-chameleon: Conformational plasticity of α-synuclein, a disordered protein involved in neurodegenerative disorders
    • Uversky, V.N. (2003) A protein-chameleon: conformational plasticity of α-synuclein, a disordered protein involved in neurodegenerative disorders. J. Biomol. Struct. Dyn. 21, 211-234
    • (2003) J. Biomol. Struct. Dyn. , vol.21 , pp. 211-234
    • Uversky, V.N.1
  • 27
    • 77953906592 scopus 로고    scopus 로고
    • A combinatorial NMR and EPR approach for evaluating the structural ensemble of partially folded proteins
    • Rao, J.N., Jao, C.C., Hegde, B.G., Langen, R. and Ulmer, T.S. (2010) A combinatorial NMR and EPR approach for evaluating the structural ensemble of partially folded proteins. J. Am. Chem. Soc. 132, 8657-8668
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 8657-8668
    • Rao, J.N.1    Jao, C.C.2    Hegde, B.G.3    Langen, R.4    Ulmer, T.S.5
  • 28
    • 0037354231 scopus 로고    scopus 로고
    • RefDB: A database of uniformly referenced protein chemical shifts
    • Zhang, H., Neal, S. and Wishart, D.S. (2003) RefDB: a database of uniformly referenced protein chemical shifts. J. Biomol. NMR 25, 173-195
    • (2003) J. Biomol. NMR , vol.25 , pp. 173-195
    • Zhang, H.1    Neal, S.2    Wishart, D.S.3
  • 29
    • 0038407231 scopus 로고    scopus 로고
    • Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts
    • Neal, S., Nip, A.M., Zhang, H. and Wishart, D.S. (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J. Biomol. NMR 26, 215-240
    • (2003) J. Biomol. NMR , vol.26 , pp. 215-240
    • Neal, S.1    Nip, A.M.2    Zhang, H.3    Wishart, D.S.4
  • 30
    • 67349276645 scopus 로고    scopus 로고
    • Amyloid precursor protein and α-synuclein translation, implications for iron and inflammation in neurodegenerative diseases
    • Cahill, C.M., Lahiri, D.K., Huang, X. and Rogers, J.T. (2009) Amyloid precursor protein and α-synuclein translation, implications for iron and inflammation in neurodegenerative diseases. Biochim. Biophys. Acta 1790, 615-628
    • (2009) Biochim. Biophys. Acta , vol.1790 , pp. 615-628
    • Cahill, C.M.1    Lahiri, D.K.2    Huang, X.3    Rogers, J.T.4
  • 31
    • 70349481750 scopus 로고    scopus 로고
    • Enhanced α-synuclein expression in human neurodegenerative diseases: Pathogenetic and therapeutic implications
    • McCormack, A.L. and Monte, D.A.D. (2009) Enhanced α-synuclein expression in human neurodegenerative diseases: pathogenetic and therapeutic implications. Curr. Protein Pept. Sci. 10, 476-482
    • (2009) Curr. Protein Pept. Sci. , vol.10 , pp. 476-482
    • McCormack, A.L.1    Monte, D.A.D.2
  • 32
    • 0028277520 scopus 로고
    • Identification of two distinct synucleins from human brain
    • Jakes, R., Spillantini, M.G. and Goedert, M. (1994) Identification of two distinct synucleins from human brain. FEBS Lett. 345, 27-32
    • (1994) FEBS Lett. , vol.345 , pp. 27-32
    • Jakes, R.1    Spillantini, M.G.2    Goedert, M.3
  • 36
    • 77956393934 scopus 로고    scopus 로고
    • α-Synuclein, lipids and Parkinson's disease
    • Ruipérez, V., Darios, F. and Davletov, B. (2010) α-Synuclein, lipids and Parkinson's disease. Prog. Lipid Res. 49, 420-428
    • (2010) Prog. Lipid Res. , vol.49 , pp. 420-428
    • Ruipérez, V.1    Darios, F.2    Davletov, B.3
  • 38
    • 0032584686 scopus 로고    scopus 로고
    • Filamentous α-synuclein inclusions link multiple system atrophy with Parkinson's disease and dementia with Lewy bodies
    • Spillantini, M.G., Crowther, R.A., Jakes, R., Cairns, N.J., Lantos, P.L. and Goedert, M. (1998) Filamentous α-synuclein inclusions link multiple system atrophy with Parkinson's disease and dementia with Lewy bodies. Neurosci. Lett. 251, 205-208
    • (1998) Neurosci. Lett. , vol.251 , pp. 205-208
    • Spillantini, M.G.1    Crowther, R.A.2    Jakes, R.3    Cairns, N.J.4    Lantos, P.L.5    Goedert, M.6
  • 40
    • 77952571567 scopus 로고    scopus 로고
    • Detection of transient interchain interactions in the intrinsically disordered protein α-synuclein by NMR paramagnetic relaxation enhancement
    • Wu, K. and Baum, J. (2010) Detection of transient interchain interactions in the intrinsically disordered protein α-synuclein by NMR paramagnetic relaxation enhancement. J. Am. Chem. Soc. 132, 5546-5547
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 5546-5547
    • Wu, K.1    Baum, J.2
  • 43
    • 2942555022 scopus 로고    scopus 로고
    • Structure of membrane-bound α-synuclein studied by site-directed spin labeling
    • Jao, C.C. (2004) Structure of membrane-bound α-synuclein studied by site-directed spin labeling. Proc. Natl. Acad. Sci. U.S.A. 101, 8331-8336
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 8331-8336
    • Jao, C.C.1
  • 44
    • 44349100972 scopus 로고    scopus 로고
    • Broken helix in vesicle and micelle-bound α-synuclein: Insights from site-directed spin labeling-EPR experiments and MD simulations
    • Bortolus, M., Tombolato, F., Tessari, I., Bisaglia, M., Mammi, S., Bubacco, L., Ferrarini, A. and Maniero, A.L. (2008) Broken helix in vesicle and micelle-bound α-synuclein: insights from site-directed spin labeling-EPR experiments and MD simulations. J. Am. Chem. Soc. 130, 6690-6691
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 6690-6691
    • Bortolus, M.1    Tombolato, F.2    Tessari, I.3    Bisaglia, M.4    Mammi, S.5    Bubacco, L.6    Ferrarini, A.7    Maniero, A.L.8
  • 45
    • 33744788870 scopus 로고    scopus 로고
    • Quantification of α-synuclein binding to lipid vesicles using fluorescence correlation spectroscopy
    • Rhoades, E., Ramlall, T., Webb, W. and Eliezer, D. (2006) Quantification of α-synuclein binding to lipid vesicles using fluorescence correlation spectroscopy. Biophys. J. 90, 4692-4700
    • (2006) Biophys. J. , vol.90 , pp. 4692-4700
    • Rhoades, E.1    Ramlall, T.2    Webb, W.3    Eliezer, D.4
  • 46
    • 15744362063 scopus 로고    scopus 로고
    • Structure and dynamics of micelle-bound human α-synuclein
    • Ulmer, T.S., Bax, A., Cole, N.B. and Nussbaum, R.L. (2005) Structure and dynamics of micelle-bound human α-synuclein. J. Biol. Chem. 280, 9595-9603
    • (2005) J. Biol. Chem. , vol.280 , pp. 9595-9603
    • Ulmer, T.S.1    Bax, A.2    Cole, N.B.3    Nussbaum, R.L.4
  • 47
    • 78149272906 scopus 로고    scopus 로고
    • Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain
    • Philip, A.F., Kumauchi, M. and Hoff, W.D. (2010) Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain. Proc. Natl. Acad. Sci. U.S.A. 107, 17986-17991
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 17986-17991
    • Philip, A.F.1    Kumauchi, M.2    Hoff, W.D.3
  • 51
    • 0001258823 scopus 로고
    • Isotope labeling in solution protein assignment and structural analysis
    • LeMaster, D.M. (1994) Isotope labeling in solution protein assignment and structural analysis. Prog. Nucl. Magn. Reson. Spectrosc. 26, 371-419
    • (1994) Prog. Nucl. Magn. Reson. Spectrosc. , vol.26 , pp. 371-419
    • LeMaster, D.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.