메뉴 건너뛰기




Volumn 18, Issue 7, 2009, Pages 1401-1424

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

Author keywords

drkN SH3; Molecular dynamics; Paramagnetic relaxation enhancement; Segmental diffusion; Site directed spin labeling; Smoluchowski equation; Translational relaxation; Ubiquitin; Unfolded proteins

Indexed keywords

CYSTEINE; GUANIDINE; PROTEIN SH3;

EID: 67650072494     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.153     Document Type: Article
Times cited : (49)

References (115)
  • 2
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6:197-208.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 3
    • 0026672305 scopus 로고
    • NMR determination of residual structure in a urea-denatured protein, the 434-repressor
    • Neri D, Billeter M, Wider G, Wüthrich K (1992) NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science 257:1559-1563.
    • (1992) Science , vol.257 , pp. 1559-1563
    • Neri, D.1    Billeter, M.2    Wider, G.3    Wüthrich, K.4
  • 4
    • 24944542708 scopus 로고    scopus 로고
    • Statistical coil model of the unfolded state: Resolving the reconciliation problem
    • Jha AK, Colubri A, Freed KF, Sosnick TR (2005) Statistical coil model of the unfolded state: Resolving the reconciliation problem. Proc Natl Acad Sci USA 102:13099-13104.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13099-13104
    • Jha, A.K.1    Colubri, A.2    Freed, K.F.3    Sosnick, T.R.4
  • 5
    • 23744502246 scopus 로고    scopus 로고
    • Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins
    • McCarney ER, Kohn JE, Plaxco KW (2005) Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins. Crit Rev Biochem Mol Biol 40:181-189.
    • (2005) Crit Rev Biochem Mol Biol , vol.40 , pp. 181-189
    • McCarney, E.R.1    Kohn, J.E.2    Plaxco, K.W.3
  • 6
    • 0037686252 scopus 로고    scopus 로고
    • The present view of the mechanism of protein folding
    • Daggett V, Fersht A (2003) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4:497-502.
    • (2003) Nat Rev Mol Cell Biol , vol.4 , pp. 497-502
    • Daggett, V.1    Fersht, A.2
  • 7
    • 33748349224 scopus 로고    scopus 로고
    • The role of hydrophobic interactions in initiation and propagation of protein folding
    • Dyson HJ, Wright PE, Scheraga HA (2006) The role of hydrophobic interactions in initiation and propagation of protein folding. Proc Natl Acad Sci USA 103:13057-13061.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 13057-13061
    • Dyson, H.J.1    Wright, P.E.2    Scheraga, H.A.3
  • 8
    • 0029124248 scopus 로고
    • Molten globule and protein folding
    • Ptitsyn OB (1995) Molten globule and protein folding. Adv Protein Chem 47:83-229.
    • (1995) Adv Protein Chem , vol.47 , pp. 83-229
    • Ptitsyn, O.B.1
  • 9
    • 0033554852 scopus 로고    scopus 로고
    • Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques
    • Wilkins DK, Grimshaw SB, Receveur V, Dobson CM, Jones JA, Smith LJ (1999) Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. Biochemistry 38:16424-16431.
    • (1999) Biochemistry , vol.38 , pp. 16424-16431
    • Wilkins, D.K.1    Grimshaw, S.B.2    Receveur, V.3    Dobson, C.M.4    Jones, J.A.5    Smith, L.J.6
  • 11
    • 33748454896 scopus 로고    scopus 로고
    • Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions
    • Tran HT, Pappu RV (2006) Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Biophys J 91:1868-1886.
    • (2006) Biophys J , vol.91 , pp. 1868-1886
    • Tran, H.T.1    Pappu, R.V.2
  • 12
    • 0027749370 scopus 로고
    • Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin
    • Jennings PA, Wright PE (1993) Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262:892-896.
    • (1993) Science , vol.262 , pp. 892-896
    • Jennings, P.A.1    Wright, P.E.2
  • 14
    • 0028951040 scopus 로고
    • Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer
    • Farrow NA, Zhang OW, Forman-Kay JD, Kay LE (1995) Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochemistry 34:868-878.
    • (1995) Biochemistry , vol.34 , pp. 868-878
    • Farrow, N.A.1    Zhang, O.W.2    Forman-Kay, J.D.3    Kay, L.E.4
  • 15
    • 0029978353 scopus 로고    scopus 로고
    • Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations
    • Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM (1996) Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations. J Mol Biol 255:494-506.
    • (1996) J Mol Biol , vol.255 , pp. 494-506
    • Smith, L.J.1    Bolin, K.A.2    Schwalbe, H.3    MacArthur, M.W.4    Thornton, J.M.5    Dobson, C.M.6
  • 16
  • 17
    • 0030759665 scopus 로고    scopus 로고
    • Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea
    • Schwalbe H, Fiebig KM, Buck M, Jones JA, Grimshaw SB, Spencer A, Glaser SJ, Smith LJ, Dobson CM (1997) Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea. Biochemistry 36:8977-8991.
    • (1997) Biochemistry , vol.36 , pp. 8977-8991
    • Schwalbe, H.1    Fiebig, K.M.2    Buck, M.3    Jones, J.A.4    Grimshaw, S.B.5    Spencer, A.6    Glaser, S.J.7    Smith, L.J.8    Dobson, C.M.9
  • 18
    • 0034705338 scopus 로고    scopus 로고
    • NMR characterization of residual structure in the denatured state of protein L
    • Yi Q, Scalley-Kim ML, Alm EJ, Baker D (2000) NMR characterization of residual structure in the denatured state of protein L. J Mol Biol 299:1341-1351.
    • (2000) J Mol Biol , vol.299 , pp. 1341-1351
    • Yi, Q.1    Scalley-Kim, M.L.2    Alm, E.J.3    Baker, D.4
  • 19
    • 0038031645 scopus 로고    scopus 로고
    • Crowhurst KA, Choy WY, Mok YK, Forman-Kay JD (2003) Corrigendum to the paper by Mok et al. (1999). NOE data demonstrating a compact unfolded state for an SH3 domain under nondenaturing conditions. J Mol Biol 329:185-187.
    • Crowhurst KA, Choy WY, Mok YK, Forman-Kay JD (2003) Corrigendum to the paper by Mok et al. (1999). NOE data demonstrating a compact unfolded state for an SH3 domain under nondenaturing conditions. J Mol Biol 329:185-187.
  • 20
    • 0041846681 scopus 로고    scopus 로고
    • Aromatic and methyl NOEs highlight hydrophobic clustering in the unfolded state of an SH3 domain
    • Crowhurst KA, Forman-Kay JD (2003) Aromatic and methyl NOEs highlight hydrophobic clustering in the unfolded state of an SH3 domain. Biochemistry 42:8687-8695.
    • (2003) Biochemistry , vol.42 , pp. 8687-8695
    • Crowhurst, K.A.1    Forman-Kay, J.D.2
  • 22
    • 0026697158 scopus 로고
    • Disulfide bond formation during the folding of influenza-virus hemagglutinin
    • Segal MS, Bye JM, Sambrook JF, Gething MJHJ (1992) Disulfide bond formation during the folding of influenza-virus hemagglutinin. Cell Biol 118:227-244.
    • (1992) Cell Biol , vol.118 , pp. 227-244
    • Segal, M.S.1    Bye, J.M.2    Sambrook, J.F.3    Gething, M.J.H.J.4
  • 23
    • 0037132584 scopus 로고    scopus 로고
    • Structural features of the cytochrome c molten globule revealed by fluorescence energy transfer kinetics
    • Lyubovitsky JG, Gray HB, Winkler JR (2002) Structural features of the cytochrome c molten globule revealed by fluorescence energy transfer kinetics. J Am Chem Soc 124:14840-14841.
    • (2002) J Am Chem Soc , vol.124 , pp. 14840-14841
    • Lyubovitsky, J.G.1    Gray, H.B.2    Winkler, J.R.3
  • 24
    • 8344224484 scopus 로고    scopus 로고
    • Inter- and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction
    • Steinhoff HJ (2004) Inter- and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction. Biol Chem 385:913-920.
    • (2004) Biol Chem , vol.385 , pp. 913-920
    • Steinhoff, H.J.1
  • 25
    • 0031585990 scopus 로고    scopus 로고
    • Characterization of long-range structure in the denatured state of staphylococcal nuclease. 1. Paramagnetic relaxation enhancement by nitroxide spin labels
    • Gillespie JR, Shortle DJ (1997) Characterization of long-range structure in the denatured state of staphylococcal nuclease. 1. Paramagnetic relaxation enhancement by nitroxide spin labels. Mol Biol 268:158-169.
    • (1997) Mol Biol , vol.268 , pp. 158-169
    • Gillespie, J.R.1    Shortle, D.J.2
  • 26
    • 0020482581 scopus 로고
    • A novel reversible thiol-specific spin label - papain active site labeling and inhibition
    • Berliner LJ, Grunwald J, Hankovszky HO, Hideg K (1982) A novel reversible thiol-specific spin label - papain active site labeling and inhibition. Anal Biochem 119:450-455.
    • (1982) Anal Biochem , vol.119 , pp. 450-455
    • Berliner, L.J.1    Grunwald, J.2    Hankovszky, H.O.3    Hideg, K.4
  • 28
    • 0031585992 scopus 로고    scopus 로고
    • Characterization of long-range structure in the denatured state of staphylococcal nuclease .2. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures
    • Gillespie JR, Shortle D (1997) Characterization of long-range structure in the denatured state of staphylococcal nuclease .2. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. J Mol Biol 268:170-184.
    • (1997) J Mol Biol , vol.268 , pp. 170-184
    • Gillespie, J.R.1    Shortle, D.2
  • 29
    • 0036389787 scopus 로고    scopus 로고
    • Mapping long-range contacts in a highly unfolded protein
    • Lietzow MA, Jamin M, Dyson HJ, Wright PE (2002) Mapping long-range contacts in a highly unfolded protein. J Mol Biol 322:655-662.
    • (2002) J Mol Biol , vol.322 , pp. 655-662
    • Lietzow, M.A.1    Jamin, M.2    Dyson, H.J.3    Wright, P.E.4
  • 30
    • 0036438881 scopus 로고    scopus 로고
    • Transient structure formation in unfolded acyl-coenzyme A-binding protein observed by site-directed spin labelling
    • Teilum K, Kragelund BB, Poulsen FM (2002) Transient structure formation in unfolded acyl-coenzyme A-binding protein observed by site-directed spin labelling. J Mol Biol 324:349-357.
    • (2002) J Mol Biol , vol.324 , pp. 349-357
    • Teilum, K.1    Kragelund, B.B.2    Poulsen, F.M.3
  • 32
    • 12944304172 scopus 로고    scopus 로고
    • Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations
    • Dedmon MM, Lindorff-Larsen K, Christodoulou J, Vendruscolo M, Dobson CM (2005) Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J Am Chem Soc 127:476-477.
    • (2005) J Am Chem Soc , vol.127 , pp. 476-477
    • Dedmon, M.M.1    Lindorff-Larsen, K.2    Christodoulou, J.3    Vendruscolo, M.4    Dobson, C.M.5
  • 33
    • 36749113906 scopus 로고
    • 1 processes
    • 1 processes. J Chem Phys 68:4034-4037.
    • (1978) J Chem Phys , vol.68 , pp. 4034-4037
    • Freed, J.H.1
  • 34
    • 24144482595 scopus 로고    scopus 로고
    • Accessibility and dynamics of nitroxide side chains in T4 lysozyme measured by saturation recovery EPR
    • Pyka J, Ilnicki J, Altenbach C, Hubbell WL, Froncisz W (2005) Accessibility and dynamics of nitroxide side chains in T4 lysozyme measured by saturation recovery EPR. Biophys J 89:2059-2068.
    • (2005) Biophys J , vol.89 , pp. 2059-2068
    • Pyka, J.1    Ilnicki, J.2    Altenbach, C.3    Hubbell, W.L.4    Froncisz, W.5
  • 35
    • 33749013594 scopus 로고    scopus 로고
    • Unfolding of alanine-based peptides using electron spin resonance distance measurements
    • Jun S, Becker JS, Yonkunas M, Coalson R, Saxena S (2006) Unfolding of alanine-based peptides using electron spin resonance distance measurements. Biochemistry 45:11666-11673.
    • (2006) Biochemistry , vol.45 , pp. 11666-11673
    • Jun, S.1    Becker, J.S.2    Yonkunas, M.3    Coalson, R.4    Saxena, S.5
  • 37
    • 19944417905 scopus 로고    scopus 로고
    • Explanation of spin-lattice relaxation rates of spin labels obtained with multifrequency saturation recovery EPR
    • Mailer C, Nielsen RD, Robinson BH (2005) Explanation of spin-lattice relaxation rates of spin labels obtained with multifrequency saturation recovery EPR. J Phys Chem A 109:4049-4061.
    • (2005) J Phys Chem A , vol.109 , pp. 4049-4061
    • Mailer, C.1    Nielsen, R.D.2    Robinson, B.H.3
  • 39
    • 15244342213 scopus 로고    scopus 로고
    • Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies
    • Kristjansdottir S, Lindorff-Larsen K, Fieber W, Dobson CM, Vendruscolo M, Poulsen FM (2005) Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies. J Mol Biol 347:1053-1062.
    • (2005) J Mol Biol , vol.347 , pp. 1053-1062
    • Kristjansdottir, S.1    Lindorff-Larsen, K.2    Fieber, W.3    Dobson, C.M.4    Vendruscolo, M.5    Poulsen, F.M.6
  • 40
    • 44049097465 scopus 로고    scopus 로고
    • Modeling transient collapsed states of an unfolded protein to provide insights into early folding events
    • Felitsky DJ, Lietzow MA, Dyson HJ, Wright PE (2008) Modeling transient collapsed states of an unfolded protein to provide insights into early folding events. Proc Natl Acad Sci USA 105:6278-6283.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 6278-6283
    • Felitsky, D.J.1    Lietzow, M.A.2    Dyson, H.J.3    Wright, P.E.4
  • 41
    • 0000807746 scopus 로고
    • Dynamic effects of pair correlation functions on spin relaxation by translational diffusion in liquids
    • Hwang LP, Freed JH (1975) Dynamic effects of pair correlation functions on spin relaxation by translational diffusion in liquids. J Chem Phys 63:4017-4025.
    • (1975) J Chem Phys , vol.63 , pp. 4017-4025
    • Hwang, L.P.1    Freed, J.H.2
  • 42
    • 0012974617 scopus 로고
    • NMR study of spectral densities over a large frequency range for intermolecular relaxation in liquids: Pair correlation effects
    • Albrand JP, Taieb MC, Fries PH, Belorizky E (1983) NMR study of spectral densities over a large frequency range for intermolecular relaxation in liquids: Pair correlation effects. J Chem Phys 78:5809-5815.
    • (1983) J Chem Phys , vol.78 , pp. 5809-5815
    • Albrand, J.P.1    Taieb, M.C.2    Fries, P.H.3    Belorizky, E.4
  • 46
    • 0024121530 scopus 로고
    • Diffusion in a rough potential
    • Zwanzig R (1988) Diffusion in a rough potential. Proc Natl Acad Sci USA 85:2029-2030.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 2029-2030
    • Zwanzig, R.1
  • 48
    • 0032209310 scopus 로고    scopus 로고
    • Model-free analysis of stretched relaxation dispersions
    • Halle B, Jóhannesson H, Venu K (1998) Model-free analysis of stretched relaxation dispersions. J Magn Reson 135:1-13.
    • (1998) J Magn Reson , vol.135 , pp. 1-13
    • Halle, B.1    Jóhannesson, H.2    Venu, K.3
  • 49
    • 0346212520 scopus 로고    scopus 로고
    • Cross-relaxation between macromolecular and solvent spins: The role of long-range dipole couplings
    • Halle B (2003) Cross-relaxation between macromolecular and solvent spins: The role of long-range dipole couplings. J Chem Phys 119:12372-12385.
    • (2003) J Chem Phys , vol.119 , pp. 12372-12385
    • Halle, B.1
  • 50
    • 0000875969 scopus 로고
    • Calculation of spectral densities for relaxation resulting from random molecular translational modulation of magnetic dipolar coupling in liquids
    • Ayant Y, Belorizky E, Alizon J, Gallice J (1975) Calculation of spectral densities for relaxation resulting from random molecular translational modulation of magnetic dipolar coupling in liquids. J Phys (Paris) 36:991-1004.
    • (1975) J Phys (Paris) , vol.36 , pp. 991-1004
    • Ayant, Y.1    Belorizky, E.2    Alizon, J.3    Gallice, J.4
  • 51
    • 36149047220 scopus 로고
    • Nuclear spin relaxation by translational diffusion in liquids and solids: High and low-frequency limits
    • Sholl CA (1981) Nuclear spin relaxation by translational diffusion in liquids and solids: high and low-frequency limits. J Phys C: Solid State Phys 14:447-464.
    • (1981) J Phys C: Solid State Phys , vol.14 , pp. 447-464
    • Sholl, C.A.1
  • 52
    • 0004235292 scopus 로고    scopus 로고
    • MathWorks , MA, Natick
    • MathWorks (2001) Using MATLAB. MA, Natick.
    • (2001) Using MATLAB
  • 53
    • 0037012374 scopus 로고    scopus 로고
    • 13C} 2D NMR: A novel strategy for the study of paramagnetic proteins with slow electronic relaxation rates
    • 13C} 2D NMR: a novel strategy for the study of paramagnetic proteins with slow electronic relaxation rates. J Am Chem Soc 124:3204-3205.
    • (2002) J Am Chem Soc , vol.124 , pp. 3204-3205
    • Machonkin, T.E.1    Westler, W.M.2    Markley, J.L.3
  • 54
    • 0346434110 scopus 로고    scopus 로고
    • 13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase
    • 13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase. J Am Chem Soc 125:16423-16429.
    • (2003) J Am Chem Soc , vol.125 , pp. 16423-16429
    • Bermel, W.1    Bertini, I.2    Felli, I.C.3    Kümmerle, R.4    Pierattelli, R.5
  • 55
    • 0011521731 scopus 로고
    • Nuclear magnetic relaxation of polymer solutions
    • Ullman R (1965) Nuclear magnetic relaxation of polymer solutions. J Chem Phys 43:3161-3177.
    • (1965) J Chem Phys , vol.43 , pp. 3161-3177
    • Ullman, R.1
  • 57
    • 36749116443 scopus 로고
    • 1st passage time approach to diffusion controlled reactions
    • Szabo A, Schulten K, Schulten Z (1980) 1st passage time approach to diffusion controlled reactions. J Chem Phys 72:4350-4357.
    • (1980) J Chem Phys , vol.72 , pp. 4350-4357
    • Szabo, A.1    Schulten, K.2    Schulten, Z.3
  • 59
    • 33846438226 scopus 로고    scopus 로고
    • End-to-end vs interior loop formation kinetics in unfolded polypeptide chains
    • Fierz B, Kiefhaber T (2007) End-to-end vs interior loop formation kinetics in unfolded polypeptide chains. J Am Chem Soc 129:672-679.
    • (2007) J Am Chem Soc , vol.129 , pp. 672-679
    • Fierz, B.1    Kiefhaber, T.2
  • 60
    • 0034193509 scopus 로고    scopus 로고
    • A fast method to sample real protein conformational space
    • Feldman HJ, Hogue CWV (2000) A fast method to sample real protein conformational space. Protein Struct Funct Genet 39:112-131.
    • (2000) Protein Struct Funct Genet , vol.39 , pp. 112-131
    • Feldman, H.J.1    Hogue, C.W.V.2
  • 61
    • 45749088164 scopus 로고    scopus 로고
    • Calculation of residual dipolar couplings from disordered state ensembles using local alignment
    • Marsh JA, Baker JMR, Tollinger M, Forman-Kay JD (2008) Calculation of residual dipolar couplings from disordered state ensembles using local alignment. J Am Chem Soc 130:7804-7805.
    • (2008) J Am Chem Soc , vol.130 , pp. 7804-7805
    • Marsh, J.A.1    Baker, J.M.R.2    Tollinger, M.3    Forman-Kay, J.D.4
  • 62
    • 0036139188 scopus 로고    scopus 로고
    • Probabilistic sampling of protein conformations: New hope for brute force?
    • Feldman HJ, Hogue CWV (2002) Probabilistic sampling of protein conformations: New hope for brute force? Protein Struct Funct Genet 46:8-23.
    • (2002) Protein Struct Funct Genet , vol.46 , pp. 8-23
    • Feldman, H.J.1    Hogue, C.W.V.2
  • 63
    • 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
    • Battiste JL, Wagner G (2000) 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 39:5355-5365.
    • (2000) Biochemistry , vol.39 , pp. 5355-5365
    • Battiste, J.L.1    Wagner, G.2
  • 68
    • 0002387901 scopus 로고
    • Ed, Spin labeling: theory and applications. New York: Academic Press, pp
    • Nordio PL, General magnetic resonance theory. In: Berliner LJ, Ed. (1976) Spin labeling: theory and applications. New York: Academic Press, pp 5-52.
    • (1976) General magnetic resonance theory , pp. 5-52
    • Nordio, P.L.1
  • 70
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
    • Garcia AE, Onuchic JN (2003) Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc Natl Acad Sci USA 100:13898-13903.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13898-13903
    • Garcia, A.E.1    Onuchic, J.N.2
  • 71
    • 0035742323 scopus 로고    scopus 로고
    • Internal coordinates for molecular dynamics and minimization in structure determination and refinement
    • Schwieters CD, Clore GM (2001) Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J Magn Reson 152:288-302.
    • (2001) J Magn Reson , vol.152 , pp. 288-302
    • Schwieters, C.D.1    Clore, G.M.2
  • 72
    • 0033577269 scopus 로고    scopus 로고
    • Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration
    • Kuszewski J, Gronenborn AM, Clore GM (1999) Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J Am Chem Soc 121:2337-2338.
    • (1999) J Am Chem Soc , vol.121 , pp. 2337-2338
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 73
    • 0037433504 scopus 로고    scopus 로고
    • 1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics
    • 1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics. J Am Chem Soc 125:2902-2912.
    • (2003) J Am Chem Soc , vol.125 , pp. 2902-2912
    • Clore, G.M.1    Schwieters, C.D.2
  • 74
    • 0001767250 scopus 로고
    • Influence of rapid intramolecular motion on NMR cross-relaxation rates. A Molecular Dynamics study of antamanide in solution
    • Brüschweiler R, Roux B, Blackledge M, Griesinger C, Karplus M, Ernst RR (1992) Influence of rapid intramolecular motion on NMR cross-relaxation rates. A Molecular Dynamics study of antamanide in solution. J Am Chem Soc 114:2289-2302.
    • (1992) J Am Chem Soc , vol.114 , pp. 2289-2302
    • Brüschweiler, R.1    Roux, B.2    Blackledge, M.3    Griesinger, C.4    Karplus, M.5    Ernst, R.R.6
  • 76
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • Day R, Bennion BJ, Ham S, Daggett V (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J Mol Biol 322:189-203.
    • (2002) J Mol Biol , vol.322 , pp. 189-203
    • Day, R.1    Bennion, B.J.2    Ham, S.3    Daggett, V.4
  • 78
    • 26444608613 scopus 로고    scopus 로고
    • Ensemble versus single-molecule protein unfolding
    • Day R, Daggett V (2005) Ensemble versus single-molecule protein unfolding. Proc Natl Acad Sci USA 102:13445-13450.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13445-13450
    • Day, R.1    Daggett, V.2
  • 79
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613-4621.
    • (1995) J Chem Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 80
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
    • Qiu D, Shenkin PS, Hollinger FP, Still WC (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 101:3005-3014.
    • (1997) J Phys Chem A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 81
    • 84961985307 scopus 로고    scopus 로고
    • Development of a generalized Born model parametrization for proteins and nucleic acids
    • Dominy BN, Brooks CL (1999) Development of a generalized Born model parametrization for proteins and nucleic acids. J Phys Chem B 103:3765-3773.
    • (1999) J Phys Chem B , vol.103 , pp. 3765-3773
    • Dominy, B.N.1    Brooks, C.L.2
  • 82
    • 0035501755 scopus 로고    scopus 로고
    • Protein molecular dynamics with the generalized Born/ACE solvent model
    • Calimet N, Schaefer M, Simonson T (2001) Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins: Struct Funct Bioinf 45:144-158.
    • (2001) Proteins: Struct Funct Bioinf , vol.45 , pp. 144-158
    • Calimet, N.1    Schaefer, M.2    Simonson, T.3
  • 83
    • 33748268107 scopus 로고    scopus 로고
    • Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease
    • Francis CJ, Lindorff-Larsen K, Best RB, Vendruscolo M (2006) Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease. Proteins: Struct Funct Bioinf 65:145-152.
    • (2006) Proteins: Struct Funct Bioinf , vol.65 , pp. 145-152
    • Francis, C.J.1    Lindorff-Larsen, K.2    Best, R.B.3    Vendruscolo, M.4
  • 84
    • 0035906650 scopus 로고    scopus 로고
    • Calculation of ensembles of structures representing the unfolded state of an SH3 domain
    • Choy WY, Forman-Kay JD (2001) Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J Mol Biol 308:1011-1032.
    • (2001) J Mol Biol , vol.308 , pp. 1011-1032
    • Choy, W.Y.1    Forman-Kay, J.D.2
  • 85
    • 0026992556 scopus 로고
    • Nonlocal interactions stabilize compact folding intermediates in reduced unfolded Bovine Pancreatic Trypsin Inhibitor
    • Gottfried DS, Haas E (1992) Nonlocal interactions stabilize compact folding intermediates in reduced unfolded Bovine Pancreatic Trypsin Inhibitor. Biochemistry 31:12353-12362.
    • (1992) Biochemistry , vol.31 , pp. 12353-12362
    • Gottfried, D.S.1    Haas, E.2
  • 86
    • 0028800425 scopus 로고
    • Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved nonradiative dynamic excitation energy transfer between site-specific extrinsic probes
    • Buckler DR, Haas E, Scheraga HA (1995) Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved nonradiative dynamic excitation energy transfer between site-specific extrinsic probes. Biochemistry 34:15965-15978.
    • (1995) Biochemistry , vol.34 , pp. 15965-15978
    • Buckler, D.R.1    Haas, E.2    Scheraga, H.A.3
  • 87
    • 0029010695 scopus 로고
    • Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
    • Guo ZY, Thirumalai D (1995) Kinetics of protein folding: nucleation mechanism, time scales, and pathways. Biopolymers 36:83-102.
    • (1995) Biopolymers , vol.36 , pp. 83-102
    • Guo, Z.Y.1    Thirumalai, D.2
  • 88
    • 0034691198 scopus 로고    scopus 로고
    • Measuring the rate of intramolecular contact formation in polypeptides
    • Lapidus LJ, Eaton WA, Hofrichter J (2000) Measuring the rate of intramolecular contact formation in polypeptides. Proc Natl Acad Sci USA 97:7220-7225.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 7220-7225
    • Lapidus, L.J.1    Eaton, W.A.2    Hofrichter, J.3
  • 89
    • 0037038514 scopus 로고    scopus 로고
    • Effects of chain stiffness on the dynamics of loop formation in polypeptides. Appendix: Testing a 1-dimensional diffusion model for peptide dynamics
    • Lapidus LJ, Steinbach PJ, Eaton WA, Szabo A, Hofrichter J (2002) Effects of chain stiffness on the dynamics of loop formation in polypeptides. Appendix: testing a 1-dimensional diffusion model for peptide dynamics. J Phys Chem B 106:11628-11640.
    • (2002) J Phys Chem B , vol.106 , pp. 11628-11640
    • Lapidus, L.J.1    Steinbach, P.J.2    Eaton, W.A.3    Szabo, A.4    Hofrichter, J.5
  • 90
    • 0037067120 scopus 로고    scopus 로고
    • Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
    • Yeh IC, Hummer G (2002) Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J Am Chem Soc 124:6563-6568.
    • (2002) J Am Chem Soc , vol.124 , pp. 6563-6568
    • Yeh, I.C.1    Hummer, G.2
  • 91
    • 44449119077 scopus 로고    scopus 로고
    • End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation (vol 103, pg 12394, 2006)
    • Möglich A, Joder K, Kiefhaber T (2008) End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation (vol 103, pg 12394, 2006). Proc Natl Acad Sci USA 105:6787-6787.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 6787-6787
    • Möglich, A.1    Joder, K.2    Kiefhaber, T.3
  • 94
    • 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, Mulder FAA, Crowhurst KA, Muhandiram DR, Millett IS, Doniach S, Forman-Kay JD, Kay LE (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 316:101-112.
    • (2002) J Mol Biol , vol.316 , pp. 101-112
    • Choy, W.Y.1    Mulder, F.A.A.2    Crowhurst, K.A.3    Muhandiram, D.R.4    Millett, I.S.5    Doniach, S.6    Forman-Kay, J.D.7    Kay, L.E.8
  • 95
    • 0034823219 scopus 로고    scopus 로고
    • Validity of using the radius of gyration as a restraint in NMR protein structure determination
    • Huang XM, Powers R (2001) Validity of using the radius of gyration as a restraint in NMR protein structure determination. J Am Chem Soc 123:3834-3835.
    • (2001) J Am Chem Soc , vol.123 , pp. 3834-3835
    • Huang, X.M.1    Powers, R.2
  • 96
    • 0029884694 scopus 로고    scopus 로고
    • GOR method for predicting protein secondary structure from amino acid sequence
    • Garnier J, Gibrat JF, Robson B (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266:540-553.
    • (1996) Methods Enzymol , vol.266 , pp. 540-553
    • Garnier, J.1    Gibrat, J.F.2    Robson, B.3
  • 97
    • 0242299098 scopus 로고    scopus 로고
    • Shuttling device for high-resolution measurements of relaxation and related phenomena in solution at low field, using a shared commercial 500 MHz NMR instrument
    • Redfield AG (2003) Shuttling device for high-resolution measurements of relaxation and related phenomena in solution at low field, using a shared commercial 500 MHz NMR instrument. Magn Reson Chem 41:753-768.
    • (2003) Magn Reson Chem , vol.41 , pp. 753-768
    • Redfield, A.G.1
  • 99
    • 0036966026 scopus 로고    scopus 로고
    • Cooperative interactions and a non-native buried Trp in the unfolded state of an SH3 domain
    • Crowhurst KA, Tollinger M, Forman-Kay JD (2002) Cooperative interactions and a non-native buried Trp in the unfolded state of an SH3 domain. J Mol Biol 322:163-178.
    • (2002) J Mol Biol , vol.322 , pp. 163-178
    • Crowhurst, K.A.1    Tollinger, M.2    Forman-Kay, J.D.3
  • 100
    • 0035970299 scopus 로고    scopus 로고
    • Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states
    • Mok YK, Elisseeva EL, Davidson AR, Forman-Kay JD (2001) Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states. J Mol Biol 307:913-928.
    • (2001) J Mol Biol , vol.307 , pp. 913-928
    • Mok, Y.K.1    Elisseeva, E.L.2    Davidson, A.R.3    Forman-Kay, J.D.4
  • 101
    • 0030900199 scopus 로고    scopus 로고
    • NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions
    • Zhang OW, Forman-Kay JD (1997) NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. Biochemistry 36:3959-3970.
    • (1997) Biochemistry , vol.36 , pp. 3959-3970
    • Zhang, O.W.1    Forman-Kay, J.D.2
  • 102
    • 44049109615 scopus 로고
    • An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins
    • Grzesiek S, Bax A (1992) An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. J Magn Reson 99:201-207.
    • (1992) J Magn Reson , vol.99 , pp. 201-207
    • Grzesiek, S.1    Bax, A.2
  • 103
    • 0035840960 scopus 로고    scopus 로고
    • Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy
    • Donaldson LW, Skrynnikov NR, Choy WY, Muhandiram DR, Sarkar B, Forman-Kay JD, Kay LE (2001) Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy. J Am Chem Soc 123:9843-9847.
    • (2001) J Am Chem Soc , vol.123 , pp. 9843-9847
    • Donaldson, L.W.1    Skrynnikov, N.R.2    Choy, W.Y.3    Muhandiram, D.R.4    Sarkar, B.5    Forman-Kay, J.D.6    Kay, L.E.7
  • 104
    • 33846561471 scopus 로고    scopus 로고
    • 1H transverse paramagnetic relaxation enhancement measurements on macromolecules
    • 1H transverse paramagnetic relaxation enhancement measurements on macromolecules. J Magn Reson 184:185-195.
    • (2007) J Magn Reson , vol.184 , pp. 185-195
    • Iwahara, J.1    Tang, C.2    Clore, G.M.3
  • 106
    • 0030864895 scopus 로고    scopus 로고
    • Conversion of nitroxide radicals by phenolic and thiol antioxidants
    • Hiramoto K, Ojima N, Kikugawa K (1997) Conversion of nitroxide radicals by phenolic and thiol antioxidants. Free Radical Res 27:45-53.
    • (1997) Free Radical Res , vol.27 , pp. 45-53
    • Hiramoto, K.1    Ojima, N.2    Kikugawa, K.3
  • 107
    • 0024689021 scopus 로고
    • Exchange and shuttling of electrons by nitroxide spin labels
    • Nettleton DO, Morse PD, Swartz HM (1989) Exchange and shuttling of electrons by nitroxide spin labels. Arch Biochem Biophys 271:414-423.
    • (1989) Arch Biochem Biophys , vol.271 , pp. 414-423
    • Nettleton, D.O.1    Morse, P.D.2    Swartz, H.M.3
  • 108
    • 0026652023 scopus 로고
    • Inhibition of radical adduct reduction and reoxidation of the corresponding hydroxylamines in in-vivo spin trapping of carbon tetrachloride-derived radicals
    • Sentjurc M, Mason RP (1992) Inhibition of radical adduct reduction and reoxidation of the corresponding hydroxylamines in in-vivo spin trapping of carbon tetrachloride-derived radicals. Free Radical Bio Med 13:151-160.
    • (1992) Free Radical Bio Med , vol.13 , pp. 151-160
    • Sentjurc, M.1    Mason, R.P.2
  • 110
    • 33645472931 scopus 로고    scopus 로고
    • Site-directed parallel spin-labeling and paramagnetic relaxation enhancement in structure determination of membrane proteins by solution NMR spectroscopy
    • Liang BY, Bushweller JH, Tamm LK (2006) Site-directed parallel spin-labeling and paramagnetic relaxation enhancement in structure determination of membrane proteins by solution NMR spectroscopy. J Am Chem Soc 128:4389-4397.
    • (2006) J Am Chem Soc , vol.128 , pp. 4389-4397
    • Liang, B.Y.1    Bushweller, J.H.2    Tamm, L.K.3
  • 111
    • 0030070225 scopus 로고    scopus 로고
    • Mutagenic and thermodynamic analyses of residual structure in the alpha subunit of tryptophan synthase
    • Saab-Rincón G, Gualfetti PJ, Matthews CR (1996) Mutagenic and thermodynamic analyses of residual structure in the alpha subunit of tryptophan synthase. Biochemistry 35:1988-1994.
    • (1996) Biochemistry , vol.35 , pp. 1988-1994
    • Saab-Rincón, G.1    Gualfetti, P.J.2    Matthews, C.R.3
  • 113
    • 33746592145 scopus 로고    scopus 로고
    • Motional properties of unfolded ubiquitin: A model for a random coil protein
    • Wirmer J, Peti W, Schwalbe H (2006) Motional properties of unfolded ubiquitin: a model for a random coil protein. J Biomol NMR 35:175-186.
    • (2006) J Biomol NMR , vol.35 , pp. 175-186
    • Wirmer, J.1    Peti, W.2    Schwalbe, H.3
  • 114
    • 0035119625 scopus 로고    scopus 로고
    • Chemical shifts in denatured proteins: Resonance assignments for denatured ubiquitin and comparisons with other denatured proteins
    • Peti W, Smith LJ, Redfield C, Schwalbe H (2001) Chemical shifts in denatured proteins: Resonance assignments for denatured ubiquitin and comparisons with other denatured proteins. J Biomol NMR 19:153-165.
    • (2001) J Biomol NMR , vol.19 , pp. 153-165
    • Peti, W.1    Smith, L.J.2    Redfield, C.3    Schwalbe, H.4
  • 115
    • 0035743931 scopus 로고    scopus 로고
    • NMR paramagnetic relaxation enhancement: Test of the controlling influence of ZFS rhombicity for S=1
    • Miller JC, Lohr LL, Sharp RR (2001) NMR paramagnetic relaxation enhancement: test of the controlling influence of ZFS rhombicity for S=1. J Magn Reson 148:267-276.
    • (2001) J Magn Reson , vol.148 , pp. 267-276
    • Miller, J.C.1    Lohr, L.L.2    Sharp, R.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.