메뉴 건너뛰기




Volumn 16, Issue 11, 2008, Pages 1627-1637

Predicting the Energetics of Conformational Fluctuations in Proteins from Sequence: A Strategy for Profiling the Proteome

Author keywords

PROTEINS

Indexed keywords

PROTEOME; STEROID RECEPTOR; TRIPEPTIDE;

EID: 55249122742     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.08.016     Document Type: Article
Times cited : (18)

References (44)
  • 2
    • 0024545638 scopus 로고
    • Gene regulation by steroid hormones
    • Beato M. Gene regulation by steroid hormones. Cell 56 (1989) 335-344
    • (1989) Cell , vol.56 , pp. 335-344
    • Beato, M.1
  • 4
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom J.D., Drummond D.A., Arnold F.H., and Wilke C.O. Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 23 (2006) 1751-1761
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 5
    • 0029900846 scopus 로고    scopus 로고
    • The magnitude of the backbone conformational entropy change in protein folding
    • D'Aquino J.A., Gomez J., Hilser V.J., Lee K.H., Amzel L.M., and Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins 25 (1996) 143-156
    • (1996) Proteins , vol.25 , pp. 143-156
    • D'Aquino, J.A.1    Gomez, J.2    Hilser, V.J.3    Lee, K.H.4    Amzel, L.M.5    Freire, E.6
  • 6
    • 35248852356 scopus 로고    scopus 로고
    • Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation
    • Daughdrill G.W., Narayanaswami P., Gilmore S.H., Belczyk A., and Brown C.J. Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation. J. Mol. Evol. 65 (2007) 277-288
    • (2007) J. Mol. Evol. , vol.65 , pp. 277-288
    • Daughdrill, G.W.1    Narayanaswami, P.2    Gilmore, S.H.3    Belczyk, A.4    Brown, C.J.5
  • 8
    • 23944490117 scopus 로고    scopus 로고
    • Missense meanderings in sequence space: a biophysical view of protein evolution
    • DePristo M.A., Weinreich D.M., and Hartl D.L. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat. Rev. Genet. 6 (2005) 678-687
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 9
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: probabilistic consistency-based multiple sequence alignment
    • Do C.B., Mahabhashyam M.S., Brudno M., and Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15 (2005) 330-340
    • (2005) Genome Res. , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 12
    • 0023913120 scopus 로고
    • The steroid and thyroid hormone receptor superfamily
    • Evans R.M. The steroid and thyroid hormone receptor superfamily. Science 240 (1988) 889-895
    • (1988) Science , vol.240 , pp. 889-895
    • Evans, R.M.1
  • 13
    • 1842539352 scopus 로고    scopus 로고
    • A linear correlation between the energetics of allosteric communication and protein flexibility in the Escherichia coli cyclic AMP receptor protein revealed by mutation-induced changes in compressibility and amide hydrogen-deuterium exchange
    • Gekko K., Obu N., Li J., and Lee J.C. A linear correlation between the energetics of allosteric communication and protein flexibility in the Escherichia coli cyclic AMP receptor protein revealed by mutation-induced changes in compressibility and amide hydrogen-deuterium exchange. Biochemistry 43 (2004) 3844-3852
    • (2004) Biochemistry , vol.43 , pp. 3844-3852
    • Gekko, K.1    Obu, N.2    Li, J.3    Lee, J.C.4
  • 14
    • 0030580089 scopus 로고    scopus 로고
    • Structure-based calculation of the equilibrium folding pathway of proteins: correlation with hydrogen exchange protection factors
    • Hilser V.J., and Freire E. Structure-based calculation of the equilibrium folding pathway of proteins: correlation with hydrogen exchange protection factors. J. Mol. Biol. 262 (1996) 756-772
    • (1996) J. Mol. Biol. , vol.262 , pp. 756-772
    • Hilser, V.J.1    Freire, E.2
  • 15
    • 34347235156 scopus 로고    scopus 로고
    • Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins
    • Hilser V.J., and Thompson E.B. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl. Acad. Sci. USA 104 (2007) 8311-8315
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 8311-8315
    • Hilser, V.J.1    Thompson, E.B.2
  • 17
    • 0242362157 scopus 로고    scopus 로고
    • Prediction of disordered regions in proteins from position specific score matrices
    • Jones D.T., and Ward J.J. Prediction of disordered regions in proteins from position specific score matrices. Proteins 53 Suppl 6 (2003) 573-578
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 573-578
    • Jones, D.T.1    Ward, J.J.2
  • 18
    • 0038265311 scopus 로고    scopus 로고
    • The three-dimensional structures of antagonistic and agonistic forms of the glucocorticoid receptor ligand-binding domain: RU-486 induces a transconformation that leads to active antagonism
    • Kauppi B., Jakob C., Farnegardh M., Yang J., Ahola H., Alarcon M., Calles K., Engstrom O., Harlan J., Muchmore S., et al. The three-dimensional structures of antagonistic and agonistic forms of the glucocorticoid receptor ligand-binding domain: RU-486 induces a transconformation that leads to active antagonism. J. Biol. Chem. 278 (2003) 22748-22754
    • (2003) J. Biol. Chem. , vol.278 , pp. 22748-22754
    • Kauppi, B.1    Jakob, C.2    Farnegardh, M.3    Yang, J.4    Ahola, H.5    Alarcon, M.6    Calles, K.7    Engstrom, O.8    Harlan, J.9    Muchmore, S.10
  • 20
  • 21
    • 34548396816 scopus 로고    scopus 로고
    • Effects of different osmolytes on the induced folding of the N-terminal activation domain (AF1) of the glucocorticoid receptor
    • Kumar R., Serrette J.M., Khan S.H., Miller A.L., and Thompson E.B. Effects of different osmolytes on the induced folding of the N-terminal activation domain (AF1) of the glucocorticoid receptor. Arch. Biochem. Biophys. 465 (2007) 452-460
    • (2007) Arch. Biochem. Biophys. , vol.465 , pp. 452-460
    • Kumar, R.1    Serrette, J.M.2    Khan, S.H.3    Miller, A.L.4    Thompson, E.B.5
  • 22
    • 46649105245 scopus 로고    scopus 로고
    • Allosteric signaling in the biotin repressor occurs via local folding coupled to global dampening of protein dynamics
    • Laine O., Streaker E.D., Nabavi M., Fenselau C.C., and Beckett D. Allosteric signaling in the biotin repressor occurs via local folding coupled to global dampening of protein dynamics. J. Mol. Biol. 381 (2008) 89-101
    • (2008) J. Mol. Biol. , vol.381 , pp. 89-101
    • Laine, O.1    Streaker, E.D.2    Nabavi, M.3    Fenselau, C.C.4    Beckett, D.5
  • 23
    • 3042572569 scopus 로고    scopus 로고
    • Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization
    • Larson S.A., and Hilser V.J. Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization. Protein Sci. 13 (2004) 1787-1801
    • (2004) Protein Sci. , vol.13 , pp. 1787-1801
    • Larson, S.A.1    Hilser, V.J.2
  • 24
    • 27744511919 scopus 로고    scopus 로고
    • Structure and function of steroid receptor AF1 transactivation domains: induction of active conformations
    • Lavery D.N., and McEwan I.J. Structure and function of steroid receptor AF1 transactivation domains: induction of active conformations. Biochem. J. 391 (2005) 449-464
    • (2005) Biochem. J. , vol.391 , pp. 449-464
    • Lavery, D.N.1    McEwan, I.J.2
  • 27
    • 0034808117 scopus 로고    scopus 로고
    • Comparing function and structure between entire proteomes
    • Liu J., and Rost B. Comparing function and structure between entire proteomes. Protein Sci. 10 (2001) 1970-1979
    • (2001) Protein Sci. , vol.10 , pp. 1970-1979
    • Liu, J.1    Rost, B.2
  • 29
    • 0025780755 scopus 로고
    • Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA
    • Luisi B.F., Xu W.X., Otwinowski Z., Freedman L.P., Yamamoto K.R., and Sigler P.B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature 352 (1991) 497-505
    • (1991) Nature , vol.352 , pp. 497-505
    • Luisi, B.F.1    Xu, W.X.2    Otwinowski, Z.3    Freedman, L.P.4    Yamamoto, K.R.5    Sigler, P.B.6
  • 30
    • 34347394165 scopus 로고    scopus 로고
    • Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
    • Marsden R.L., Lewis T.A., and Orengo C.A. Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics 8 (2007) 86
    • (2007) BMC Bioinformatics , vol.8 , pp. 86
    • Marsden, R.L.1    Lewis, T.A.2    Orengo, C.A.3
  • 31
    • 34249667205 scopus 로고    scopus 로고
    • Natural disordered sequences in the amino terminal domain of nuclear receptors: lessons from the androgen and glucocorticoid receptors
    • McEwan I.J., Lavery D., Fischer K., and Watt K. Natural disordered sequences in the amino terminal domain of nuclear receptors: lessons from the androgen and glucocorticoid receptors. Nucl Recept Signal 5 (2007) e001
    • (2007) Nucl Recept Signal , vol.5
    • McEwan, I.J.1    Lavery, D.2    Fischer, K.3    Watt, K.4
  • 33
    • 0000332920 scopus 로고    scopus 로고
    • Sequence data analysis for long disordered regions prediction in the calcineurin family
    • Romero P., Obradovic Z., and Dunker A.K. Sequence data analysis for long disordered regions prediction in the calcineurin family. Genome Inform. Ser. Workshop Genome Inform. 8 (1997) 110-124
    • (1997) Genome Inform. Ser. Workshop Genome Inform. , vol.8 , pp. 110-124
    • Romero, P.1    Obradovic, Z.2    Dunker, A.K.3
  • 34
    • 0030691703 scopus 로고    scopus 로고
    • Romero, P., Obradovic, Z., Kissinger, C.R., Villafranca, J.E., and Dunker, A.K. (1997b). Identifying disordered regions in proteins from amino acid sequences. Proc. I.E.E.E. International Conference on Neural Networks 1, 90-95.
    • Romero, P., Obradovic, Z., Kissinger, C.R., Villafranca, J.E., and Dunker, A.K. (1997b). Identifying disordered regions in proteins from amino acid sequences. Proc. I.E.E.E. International Conference on Neural Networks 1, 90-95.
  • 35
    • 15544390249 scopus 로고    scopus 로고
    • Protein structure and evolutionary history determine sequence space topology
    • Shakhnovich B.E., Deeds E., Delisi C., and Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 15 (2005) 385-392
    • (2005) Genome Res. , vol.15 , pp. 385-392
    • Shakhnovich, B.E.1    Deeds, E.2    Delisi, C.3    Shakhnovich, E.4
  • 36
    • 0036128797 scopus 로고    scopus 로고
    • Natively unfolded proteins: a point where biology waits for physics
    • Uversky V.N. 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
  • 37
    • 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. 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
  • 38
    • 0035061715 scopus 로고    scopus 로고
    • Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition
    • Wrabl J.O., Larson S.A., and Hilser V.J. Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition. Protein Sci. 10 (2001) 1032-1045
    • (2001) Protein Sci. , vol.10 , pp. 1032-1045
    • Wrabl, J.O.1    Larson, S.A.2    Hilser, V.J.3
  • 39
    • 0036076716 scopus 로고    scopus 로고
    • Thermodynamic environments in proteins: fundamental determinants of fold specificity
    • Wrabl J.O., Larson S.A., and Hilser V.J. Thermodynamic environments in proteins: fundamental determinants of fold specificity. Protein Sci. 11 (2002) 1945-1957
    • (2002) Protein Sci. , vol.11 , pp. 1945-1957
    • Wrabl, J.O.1    Larson, S.A.2    Hilser, V.J.3
  • 40
    • 19444384291 scopus 로고    scopus 로고
    • Transient structural disorder as a facilitator of protein-ligand binding: native H/D exchange-mass spectrometry study of cellular retinoic acid binding protein I
    • Xiao H., and Kaltashov I.A. Transient structural disorder as a facilitator of protein-ligand binding: native H/D exchange-mass spectrometry study of cellular retinoic acid binding protein I. J. Am. Soc. Mass Spectrom. 16 (2005) 869-879
    • (2005) J. Am. Soc. Mass Spectrom. , vol.16 , pp. 869-879
    • Xiao, H.1    Kaltashov, I.A.2
  • 41
    • 33847783298 scopus 로고    scopus 로고
    • Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins
    • Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., and Uversky V.N. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J. Proteome Res. 6 (2007) 1917-1932
    • (2007) J. Proteome Res. , vol.6 , pp. 1917-1932
    • Xie, H.1    Vucetic, S.2    Iakoucheva, L.M.3    Oldfield, C.J.4    Dunker, A.K.5    Obradovic, Z.6    Uversky, V.N.7
  • 42
    • 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. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 6 (2007) 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
  • 43
    • 0022327612 scopus 로고
    • Steroid receptor regulated transcription of specific genes and gene networks
    • Yamamoto K.R. Steroid receptor regulated transcription of specific genes and gene networks. Annu. Rev. Genet. 19 (1985) 209-252
    • (1985) Annu. Rev. Genet. , vol.19 , pp. 209-252
    • Yamamoto, K.R.1
  • 44
    • 36048990877 scopus 로고    scopus 로고
    • Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch
    • Yi S., Boys B.L., Brickenden A., Konermann L., and Choy W.Y. Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch. Biochemistry 46 (2007) 13120-13130
    • (2007) Biochemistry , vol.46 , pp. 13120-13130
    • Yi, S.1    Boys, B.L.2    Brickenden, A.3    Konermann, L.4    Choy, W.Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.