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Volumn 287, Issue 4, 2012, Pages 2731-2738

Trimming down a protein structure to its bare foldons: Spatial organization of the cooperative unit

Author keywords

[No Author keywords available]

Indexed keywords

CHEVRON PLOT; COOPERATIVE UNIT; COOPERATIVITY; FOLDING NUCLEI; FOLDING TRANSITION STATE; HETERONUCLEAR SINGLE QUANTUM CORRELATIONS; INTERMOLECULAR BINDING; NATIVE STATE; PROTEIN STRUCTURES; REDUCED SIZE; RIBOSOMAL PROTEINS; SPATIAL ORGANIZATION; WELL-DISPERSED;

EID: 84856068609     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.312447     Document Type: Article
Times cited : (18)

References (45)
  • 1
    • 33747592347 scopus 로고    scopus 로고
    • The experimental survey of protein-folding energy landscapes
    • DOI 10.1017/S0033583506004185, PII S0033583506004185
    • Oliveberg, M., and Wolynes, P. G. (2005) The experimental survey of protein folding energy landscapes. Q. Rev. Biophys. 38, 245-288 (Pubitemid 44268537)
    • (2005) Quarterly Reviews of Biophysics , vol.38 , Issue.3 , pp. 245-288
    • Oliveberg, M.1    Wolynes, P.G.2
  • 2
    • 36749078792 scopus 로고    scopus 로고
    • Folding versus aggregation: Polypeptide conformations on competing pathways
    • DOI 10.1016/j.abb.2007.05.015, PII S0003986107002731, Highlight Issue: Protein Folding
    • Jahn, T. R., and Radford, S. E. (2008) Folding versus aggregation: polypeptide conformations on competing pathways. Arch. Biochem. Biophys. 469, 100-117 (Pubitemid 350214559)
    • (2008) Archives of Biochemistry and Biophysics , vol.469 , Issue.1 , pp. 100-117
    • Jahn, T.R.1    Radford, S.E.2
  • 3
    • 33846678063 scopus 로고    scopus 로고
    • How do ALS-associated mutations in superoxide dismutase 1 promote aggregation of the protein?
    • DOI 10.1016/j.tibs.2006.12.005, PII S0968000406003331
    • Shaw, B. F., and Valentine, J. S. (2007) How do ALS-associated mutations in superoxide dismutase 1 promote aggregation of the protein? Trends Biochem. Sci. 32, 78-85 (Pubitemid 46199198)
    • (2007) Trends in Biochemical Sciences , vol.32 , Issue.2 , pp. 78-85
    • Shaw, B.F.1    Valentine, J.S.2
  • 4
    • 77953532917 scopus 로고    scopus 로고
    • SOD1 mutations targeting surface hydrogen bonds promote amyotrophic lateral sclerosis without reducing apo-state stability
    • Byström, R., Andersen, P. M., Gröbner, G., and Oliveberg, M. (2010) SOD1 mutations targeting surface hydrogen bonds promote amyotrophic lateral sclerosis without reducing apo-state stability. J. Biol. Chem. 285, 19544-19552
    • (2010) J. Biol. Chem. , vol.285 , pp. 19544-19552
    • Byström, R.1    Andersen, P.M.2    Gröbner, G.3    Oliveberg, M.4
  • 5
    • 0032842870 scopus 로고    scopus 로고
    • The fundamentals of protein folding: Bringing together theory and experiment
    • DOI 10.1016/S0959-440X(99)80012-8
    • Dobson, C. M., and Karplus, M. (1999) The fundamentals of protein folding: bringing together theory and experiment. Curr. Opin Struct. Biol. 9, 92-101 (Pubitemid 29471980)
    • (1999) Current Opinion in Structural Biology , vol.9 , Issue.1 , pp. 92-101
    • Dobson, C.M.1    Karplus, M.2
  • 6
    • 0036829967 scopus 로고    scopus 로고
    • Complete change of the protein folding transition state upon circular permutation
    • Lindberg, M., Tångrot, J., and Oliveberg, M. (2002) Complete change of the protein folding transition state upon circular permutation. Nat. Struct. Biol. 9, 818-822 (Pubitemid 35257780)
    • (2002) Nature Structural Biology , vol.9 , Issue.11 , pp. 818-822
    • Lindberg, M.1    Tangrot, J.2    Oliveberg, M.3
  • 8
    • 33846916730 scopus 로고    scopus 로고
    • Malleability of protein folding pathways: A simple reason for complex behaviour
    • DOI 10.1016/j.sbi.2007.01.008, PII S0959440X07000097, Foldinf and Binding / Protein-Nucleic Interactions
    • Lindberg, M. O., and Oliveberg, M. (2007) Malleability of protein folding pathways: a simple reason for complex behavior. Curr. Opin Struct. Biol. 17, 21-29 (Pubitemid 46240818)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.1 , pp. 21-29
    • Lindberg, M.O.1    Oliveberg, M.2
  • 9
    • 76049096608 scopus 로고    scopus 로고
    • The HD-exchange motions of ribosomal protein S6 are insensitive to reversal of the protein folding pathway
    • Haglund, E., Lind, J., Oman, T., Ohman, A., Mäler, L., and Oliveberg, M. (2009) The HD-exchange motions of ribosomal protein S6 are insensitive to reversal of the protein folding pathway. Proc. Natl. Acad. Sci. U.S.A. 106, 21619-21624
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 21619-21624
    • Haglund, E.1    Lind, J.2    Oman, T.3    Ohman, A.4    Mäler, L.5    Oliveberg, M.6
  • 10
    • 55549098922 scopus 로고    scopus 로고
    • Changes of protein folding pathways by circular permutation. Overlapping nuclei promote global cooperativity
    • Haglund, E., Lindberg, M. O., and Oliveberg, M. (2008) Changes of protein folding pathways by circular permutation. Overlapping nuclei promote global cooperativity. J. Biol. Chem. 283, 27904-27915
    • (2008) J. Biol. Chem. , vol.283 , pp. 27904-27915
    • Haglund, E.1    Lindberg, M.O.2    Oliveberg, M.3
  • 11
    • 0033580679 scopus 로고    scopus 로고
    • Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
    • Otzen, D. E., Kristensen, O., Proctor, M., and Oliveberg, M. (1999) Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry 38, 6499-6511
    • (1999) Biochemistry , vol.38 , pp. 6499-6511
    • Otzen, D.E.1    Kristensen, O.2    Proctor, M.3    Oliveberg, M.4
  • 12
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293
    • (1995) J. Biomol. NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5    Bax, A.6
  • 19
    • 37549039510 scopus 로고    scopus 로고
    • A short history of SHELX
    • Sheldrick, G. M. (2008) A short history of SHELX. Acta Crystallogr. A. 64, 112-122
    • (2008) Acta Crystallogr. A. , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 21
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • DOI 10.1107/S0907444904026460
    • Krissinel, E., and Henrick, K. (2004) Secondary structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D. Biol. Crystallogr. 60, 2256-2268 (Pubitemid 41742778)
    • (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.12 I , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 23
    • 0034730203 scopus 로고    scopus 로고
    • Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: A structural clue to amyloid assembly
    • Otzen, D. E., Kristensen, O., and Oliveberg, M. (2000) Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly. Proc. Natl. Acad. Sci. U.S.A. 97, 9907-9912
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 9907-9912
    • Otzen, D.E.1    Kristensen, O.2    Oliveberg, M.3
  • 24
    • 0033054043 scopus 로고    scopus 로고
    • High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor
    • DOI 10.1006/jmbi.1999.2818
    • Baber, J. L., Libutti, D., Levens, D., and Tjandra, N. (1999) High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor. J. Mol. Biol. 289, 949-962 (Pubitemid 29306662)
    • (1999) Journal of Molecular Biology , vol.289 , Issue.4 , pp. 949-962
    • Baber, J.L.1    Libutti, D.2    Levens, D.3    Tjandra, N.4
  • 25
    • 75149193285 scopus 로고    scopus 로고
    • Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P54-55
    • Ohman, A., Oman, T., and Oliveberg, M. (2010) Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P54-55. Protein Sci. 19, 183-189
    • (2010) Protein Sci. , vol.19 , pp. 183-189
    • Ohman, A.1    Oman, T.2    Oliveberg, M.3
  • 26
    • 0027991494 scopus 로고
    • Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using molecular dynamics simulations and NMR relaxation data
    • Fushman, D., Ohlenschläger, O., and Rüterjans, H. (1994) Determination of the backbone mobility of ribonuclease T1 and its 2 -GMP complex using molecular dynamics simulations and NMR relaxation data. J. Biomol. Struct. Dyn. 11, 1377-1402 (Pubitemid 24250964)
    • (1994) Journal of Biomolecular Structure and Dynamics , vol.11 , Issue.6 , pp. 1377-1402
    • Fushman, D.1    Ohlenschlager, O.2    Ruterjans, H.3
  • 27
    • 0029185933 scopus 로고
    • CRYSOL - A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • DOI 10.1107/S0021889895007047
    • Svergun, D. I., Barberato, C., and Koch M. H. (1995) CRYSOL: a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768-773 (Pubitemid 3014671)
    • (1995) Journal of Applied Crystallography , vol.28 , Issue.6 , pp. 768-773
    • Svergun, D.1    Barberato, C.2    Koch, M.H.3
  • 28
    • 0014718113 scopus 로고
    • Protein denaturation. C. Theoretical models for the mechanism of denaturation
    • Tanford, C. (1970) Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 24, 1-95
    • (1970) Adv. Protein Chem. , vol.24 , pp. 1-95
    • Tanford, C.1
  • 29
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson, S. E., and Fersht, A. R. (1991) Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30, 10428-10435
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 32
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin, N. V. (2001) Fold change in evolution of protein structures. J. Struct. Biol. 134, 167-185
    • (2001) J. Struct. Biol. , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 33
    • 33751411136 scopus 로고    scopus 로고
    • Folding of S6 Structures with Divergent Amino Acid Composition: Pathway Flexibility Within Partly Overlapping Foldons
    • DOI 10.1016/j.jmb.2006.09.016, PII S0022283606012058
    • Olofsson, M., Hansson, S., Hedberg, L., Logan, D. T., and Oliveberg, M. (2007) Folding of S6 structures with divergent amino acid composition: pathway flexibility within partly overlapping foldons. J. Mol. Biol. 365, 237-248 (Pubitemid 44821198)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.1 , pp. 237-248
    • Olofsson, M.1    Hansson, S.2    Hedberg, L.3    Logan, D.T.4    Oliveberg, M.5
  • 37
    • 61949448788 scopus 로고    scopus 로고
    • Energy landscape along an enzymatic reaction trajectory: Hinges or cracks?
    • Whitford, P. C., Onuchic, J. N., and Wolynes, P. G. (2008) Energy landscape along an enzymatic reaction trajectory: hinges or cracks? HFSP J. 2, 61-64
    • (2008) HFSP J. , vol.2 , pp. 61-64
    • Whitford, P.C.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 38
    • 6344285316 scopus 로고    scopus 로고
    • Probing the high energy states in proteins by proteolysis
    • DOI 10.1016/j.jmb.2004.08.085, PII S002228360401085X
    • Park, C., and Marqusee, S. (2004) Probing the high energy states in proteins by proteolysis. J. Mol. Biol. 343, 1467-1476 (Pubitemid 39387837)
    • (2004) Journal of Molecular Biology , vol.343 , Issue.5 , pp. 1467-1476
    • Park, C.1    Marqusee, S.2
  • 39
    • 18744391410 scopus 로고    scopus 로고
    • Pulse proteolysis: A simple method for quantitative determination of protein stability and ligand binding
    • DOI 10.1038/nmeth740
    • Park, C., and Marqusee, S. (2005) Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding. Nat. Methods 2, 207-212 (Pubitemid 41122128)
    • (2005) Nature Methods , vol.2 , Issue.3 , pp. 207-212
    • Park, C.1    Marqusee, S.2
  • 40
    • 0026522991 scopus 로고
    • Three-dimensional structure of acylphosphatase. Refinement and structure analysis
    • Pastore, A., Saudek, V., Ramponi, G., and Williams, R. J. (1992) Three-dimensional structure of acylphosphatase. Refinement and structure analysis. J. Mol. Biol. 224, 427-440
    • (1992) J. Mol. Biol. , vol.224 , pp. 427-440
    • Pastore, A.1    Saudek, V.2    Ramponi, G.3    Williams, R.J.4
  • 41
    • 0032708771 scopus 로고    scopus 로고
    • Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
    • DOI 10.1038/14890
    • Chiti, F., Taddei, N., White, P. M., Bucciantini, M., Magherini, F., Stefani, M., and Dobson, C. M. (1999) Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat. Struct. Biol. 6, 1005-1009 (Pubitemid 29519592)
    • (1999) Nature Structural Biology , vol.6 , Issue.11 , pp. 1005-1009
    • Chiti, F.1    Taddei, N.2    White, P.M.3    Bucciantini, M.4    Magherini, F.5    Stefani, M.6    Dobson, C.M.7
  • 43
    • 12444278965 scopus 로고    scopus 로고
    • Crystal structure of halophilic dodecin: A novel, dodecameric flavin binding protein from Halobacterium salinarum
    • DOI 10.1016/S0969-2126(03)00048-0
    • Bieger, B., Essen, L. O., and Oesterhelt, D. (2003) Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum. Structure 11, 375-385 (Pubitemid 36419565)
    • (2003) Structure , vol.11 , Issue.4 , pp. 375-385
    • Bieger, B.1    Essen, L.-O.2    Oesterhelt, D.3
  • 45
    • 0004040543 scopus 로고    scopus 로고
    • University of California, San Francisco
    • Goddard, T. D., and Kneller, D. G. (2007) SPARKY 3, University of California, San Francisco
    • (2007) SPARKY 3
    • Goddard, T.D.1    Kneller, D.G.2


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