메뉴 건너뛰기




Volumn 347, Issue 4, 2005, Pages 827-839

The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins

Author keywords

Foldability; Interresidue interactions; Intrinsically unstructured proteins; Low resolution force fields; Prediction of disordered proteins

Indexed keywords

AMINO ACID;

EID: 14844342815     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.01.071     Document Type: Article
Times cited : (830)

References (47)
  • 1
    • 0029662315 scopus 로고    scopus 로고
    • Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: Conformational disorder mediates binding diversity
    • R.W. Kriwacki, L. Hengst, L. Tennant, S.I. Reed, and P.E. Wright Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity Proc. Natl Acad. Sci. USA 93 1996 11504 11509
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 11504-11509
    • Kriwacki, R.W.1    Hengst, L.2    Tennant, L.3    Reed, S.I.4    Wright, P.E.5
  • 3
    • 0032479055 scopus 로고    scopus 로고
    • Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB
    • I. Radhakrishnan, G.C. Perez-Alvarado, H.J. Dyson, and P.E. Wright Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB FEBS Letters 430 1998 317 322
    • (1998) FEBS Letters , vol.430 , pp. 317-322
    • Radhakrishnan, I.1    Perez-Alvarado, G.C.2    Dyson, H.J.3    Wright, P.E.4
  • 4
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
    • P.E. Wright, and H.J. Dyson Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm J. Mol. Biol. 293 1999 321 331
    • (1999) J. Mol. Biol. , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 6
    • 0036803243 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins
    • P. Tompa Intrinsically unstructured proteins Trends Biochem. Sci. 27 2002 527 533
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 527-533
    • Tompa, P.1
  • 7
    • 1642533607 scopus 로고    scopus 로고
    • The functional benefits of protein disorder
    • P. Tompa The functional benefits of protein disorder J. Mol. Struct. (Theochem) 666-667 2003 361 371
    • (2003) J. Mol. Struct. (Theochem) , vol.666-667 , pp. 361-371
    • Tompa, P.1
  • 9
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • J.J. Ward, J.S. Sodhi, L.J. McGuffin, B.F. Buxton, and D.T. Jones Prediction and functional analysis of native disorder in proteins from the three kingdoms of life J. Mol. Biol. 337 2004 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
  • 10
    • 0036408751 scopus 로고    scopus 로고
    • Intrinsic disorder in cell-signaling and cancer-associated proteins
    • L. Iakoucheva, C. Brown, J. Lawson, Z. Obradovic, and A. Dunker Intrinsic disorder in cell-signaling and cancer-associated proteins J. Mol. Biol. 323 2002 573 584
    • (2002) J. Mol. Biol. , vol.323 , pp. 573-584
    • Iakoucheva, L.1    Brown, C.2    Lawson, J.3    Obradovic, Z.4    Dunker, A.5
  • 11
    • 0036968309 scopus 로고    scopus 로고
    • Loopy proteins appear conserved in evolution
    • J. Liu, H. Tan, and B. Rost Loopy proteins appear conserved in evolution J. Mol. Biol. 322 2002 53 64
    • (2002) J. Mol. Biol. , vol.322 , pp. 53-64
    • Liu, J.1    Tan, H.2    Rost, B.3
  • 12
    • 6344277430 scopus 로고    scopus 로고
    • Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein
    • E.A. Weathers, M.E. Paulaitis, T.B. Woolf, and J.H. Hoh Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein FEBS Letters 576 2004 348 352
    • (2004) FEBS Letters , vol.576 , pp. 348-352
    • Weathers, E.A.1    Paulaitis, M.E.2    Woolf, T.B.3    Hoh, J.H.4
  • 15
    • 0042622240 scopus 로고    scopus 로고
    • GlobPlot: Exploring protein sequences for globularity and disorder
    • R. Linding, R.B. Russell, V. Neduva, and T.J. Gibson GlobPlot: exploring protein sequences for globularity and disorder Nucl. Acids Res. 31 2003 3701 3708
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3701-3708
    • Linding, R.1    Russell, R.B.2    Neduva, V.3    Gibson, T.J.4
  • 17
    • 0034669882 scopus 로고    scopus 로고
    • Why are "natively unfolded" proteins unstructured under physiologic conditions?
    • V.N. Uversky, J.R. Gillespie, and A.L. Fink Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41 2000 415 427
    • (2000) Proteins , vol.41 , pp. 415-427
    • Uversky, V.N.1    Gillespie, J.R.2    Fink, A.L.3
  • 18
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • S. Miyazawa, and R.L. Jernigan Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation Macromolecules 18 1985 534 552
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 19
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • M.J. Sippl Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins J. Mol. Biol. 213 1990 859 883
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 20
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • P.D. Thomas, and K.A. Dill An iterative method for extracting energy-like quantities from protein structures Proc. Natl Acad. Sci. USA 93 1996 11628 11633
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 22
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? a new approach to an old problem
    • L.A. Mirny, and E.I. Shakhnovich How to derive a protein folding potential? A new approach to an old problem J. Mol. Biol. 264 1996 1164 1179
    • (1996) J. Mol. Biol. , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 23
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • S. Miyazawa, and R.L. Jernigan Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading J. Mol. Biol. 256 1996 623 644
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 24
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • F. Melo, R. Sanchez, and A. Sali Statistical potentials for fold assessment Protein Sci. 11 2002 430 448
    • (2002) Protein Sci. , vol.11 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 25
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • D.T. Jones, W.R. Taylor, and J.M. Thornton A new approach to protein fold recognition Nature 358 1992 86 89
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 26
    • 0030967586 scopus 로고    scopus 로고
    • Perspectives in protein-fold recognition
    • A.E. Torda Perspectives in protein-fold recognition Curr. Opin. Struct. Biol. 7 1997 200 205
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 200-205
    • Torda, A.E.1
  • 27
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • H. Gohlke, M. Hendlich, and G. Klebe Knowledge-based scoring function to predict protein-ligand interactions J. Mol. Biol. 295 2000 337 356
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 28
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • A. Kolinski, and J. Skolnick Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme Proteins: Struct. Funct. Genet. 18 1994 338 352
    • (1994) Proteins: Struct. Funct. Genet. , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 29
    • 1242294472 scopus 로고    scopus 로고
    • Can contact potentials reliably predict stability of proteins?
    • J. Khatun, S.D. Khare, and N.V. Dokholyan Can contact potentials reliably predict stability of proteins? J. Mol. Biol. 336 2004 1223 1238
    • (2004) J. Mol. Biol. , vol.336 , pp. 1223-1238
    • Khatun, J.1    Khare, S.D.2    Dokholyan, N.V.3
  • 30
    • 0036128797 scopus 로고    scopus 로고
    • Natively unfolded proteins: A point where biology waits for physics
    • V.N. Uversky Natively unfolded proteins: a point where biology waits for physics Protein Sci. 11 2002 739 756
    • (2002) Protein Sci. , vol.11 , pp. 739-756
    • Uversky, V.N.1
  • 32
    • 0021112868 scopus 로고
    • Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure
    • R.M. Sweet, and D. Eisenberg Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure J. Mol. Biol. 171 1983 479 488
    • (1983) J. Mol. Biol. , vol.171 , pp. 479-488
    • Sweet, R.M.1    Eisenberg, D.2
  • 33
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • J.C. Wootton, and S. Federhen Analysis of compositionally biased regions in sequence databases Methods Enzymol. 266 1996 554 571
    • (1996) Methods Enzymol. , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 34
    • 0036153571 scopus 로고    scopus 로고
    • What does it mean to be natively unfolded?
    • V.N. Uversky What does it mean to be natively unfolded? Eur. J. Biochem. 269 2002 2 12
    • (2002) Eur. J. Biochem. , vol.269 , pp. 2-12
    • Uversky, V.N.1
  • 35
    • 2142757231 scopus 로고    scopus 로고
    • Preformed structural elements feature in partner recognition by intrinsically unstructured proteins
    • M. Fuxreiter, I. Simon, P. Friedrich, and P. Tompa Preformed structural elements feature in partner recognition by intrinsically unstructured proteins J. Mol. Biol. 338 2004 1015 1026
    • (2004) J. Mol. Biol. , vol.338 , pp. 1015-1026
    • Fuxreiter, M.1    Simon, I.2    Friedrich, P.3    Tompa, P.4
  • 37
    • 0036415663 scopus 로고    scopus 로고
    • P53 contains large unstructured regions in its native state
    • S. Bell, C. Klein, L. Muller, S. Hansen, and J. Buchner p53 contains large unstructured regions in its native state J. Mol. Biol. 322 2002 917
    • (2002) J. Mol. Biol. , vol.322 , pp. 917
    • Bell, S.1    Klein, C.2    Muller, L.3    Hansen, S.4    Buchner, J.5
  • 38
    • 0030980926 scopus 로고    scopus 로고
    • The C-terminal half of the anti-sigma factor. FlgM, becomes structured when bound to its target, sigma 28
    • G.W. Daughdrill, M.S. Chadsey, J.E. Karlinsey, K.T. Hughes, and F.W. Dahlquist The C-terminal half of the anti-sigma factor. FlgM, becomes structured when bound to its target, sigma 28 Nature Struct. Biol. 4 1997 285 291
    • (1997) Nature Struct. Biol. , vol.4 , pp. 285-291
    • Daughdrill, G.W.1    Chadsey, M.S.2    Karlinsey, J.E.3    Hughes, K.T.4    Dahlquist, F.W.5
  • 39
    • 0032570318 scopus 로고    scopus 로고
    • The C-terminal half of the anti-sigma factor FlgM contains a dynamic equilibrium solution structure favoring helical conformations
    • G.W. Daughdrill, L.J. Hanely, and F.W. Dahlquist The C-terminal half of the anti-sigma factor FlgM contains a dynamic equilibrium solution structure favoring helical conformations Biochemistry 37 1998 1076 1082
    • (1998) Biochemistry , vol.37 , pp. 1076-1082
    • Daughdrill, G.W.1    Hanely, L.J.2    Dahlquist, F.W.3
  • 41
    • 0033602932 scopus 로고    scopus 로고
    • Binding-dependent disorder-order transition in PKI alpha: A fluorescence anisotropy study
    • J.A. Hauer, S.S. Taylor, and D.A. Johnson Binding-dependent disorder-order transition in PKI alpha: a fluorescence anisotropy study Biochemistry 38 1999 6774 6780
    • (1999) Biochemistry , vol.38 , pp. 6774-6780
    • Hauer, J.A.1    Taylor, S.S.2    Johnson, D.A.3
  • 42
    • 0033011875 scopus 로고    scopus 로고
    • Two well-defined motifs in the cAMP-dependent protein kinase inhibitor (PKIalpha) correlate with inhibitory and nuclear export function
    • J.A. Hauer, P. Barthe, S.S. Taylor, J. Parello, and A. Padilla Two well-defined motifs in the cAMP-dependent protein kinase inhibitor (PKIalpha) correlate with inhibitory and nuclear export function Protein Sci. 8 1999 545 553
    • (1999) Protein Sci. , vol.8 , pp. 545-553
    • Hauer, J.A.1    Barthe, P.2    Taylor, S.S.3    Parello, J.4    Padilla, A.5
  • 43
    • 0028170411 scopus 로고
    • Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure
    • O. Schweers, E. Schonbrunn-Hanebeck, A. Marx, and E. Mandelkow Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure J. Biol. Chem. 269 1994 24290 24297
    • (1994) J. Biol. Chem. , vol.269 , pp. 24290-24297
    • Schweers, O.1    Schonbrunn-Hanebeck, E.2    Marx, A.3    Mandelkow, E.4
  • 44
    • 0027234766 scopus 로고
    • Engineering of stable and fast-folding sequences of model proteins
    • E.I. Shakhnovich, and A.M. Gutin Engineering of stable and fast-folding sequences of model proteins Proc. Natl Acad. Sci. USA 90 1993 7195 7199
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 7195-7199
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 47
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • U. Hobohm, and C. Sander Enlarged representative set of protein structures Protein Sci. 3 1994 522 524
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.