메뉴 건너뛰기




Volumn 47, Issue 7, 2008, Pages 2110-2122

Conformational switching upon phosphorylation: A predictive framework based on energy landscape principles

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; HAMILTONIANS; PRINCIPAL COMPONENT ANALYSIS; PROBABILITY; PROTEINS;

EID: 39649088661     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701350v     Document Type: Article
Times cited : (54)

References (37)
  • 1
    • 0034614490 scopus 로고    scopus 로고
    • Signaling - 2000 and beyond
    • Hunter, T. (2000) Signaling - 2000 and beyond, Cell 100, 113-127.
    • (2000) Cell , vol.100 , pp. 113-127
    • Hunter, T.1
  • 2
    • 0027310848 scopus 로고
    • The effects of phosphorylation on the structure and function of proteins
    • Johnson, L. N., and Barford, D. (1993) The effects of phosphorylation on the structure and function of proteins, Annu. Rev. Biophys. Biomol. Struct. 22, 199-232.
    • (1993) Annu. Rev. Biophys. Biomol. Struct , vol.22 , pp. 199-232
    • Johnson, L.N.1    Barford, D.2
  • 3
    • 15344341157 scopus 로고    scopus 로고
    • Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS
    • Steen, H., Jebanathirajah, J. A., Springer, M., and Kirschner, M. W. (2005) Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS, Proc. Natl. Acad. Sci. U.S.A. 102, 3948-3953.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 3948-3953
    • Steen, H.1    Jebanathirajah, J.A.2    Springer, M.3    Kirschner, M.W.4
  • 4
    • 0344936739 scopus 로고    scopus 로고
    • Solution structure of the kix domain of cbp bound to the transactivation domain of creb: A model for activator:coactivator interactions
    • Radhakrishnan, I., PerezAlvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R., and Wright, P. E. (1997) Solution structure of the kix domain of cbp bound to the transactivation domain of creb: A model for activator:coactivator interactions, Cell 91, 741- 752.
    • (1997) Cell , vol.91 , pp. 741-752
    • Radhakrishnan, I.1    PerezAlvarado, G.C.2    Parker, D.3    Dyson, H.J.4    Montminy, M.R.5    Wright, P.E.6
  • 5
    • 0035937549 scopus 로고    scopus 로고
    • Flipping a switch
    • Buck, M., and Rosen, M. K. (2001) Flipping a switch, Science 291, 2329-2330.
    • (2001) Science , vol.291 , pp. 2329-2330
    • Buck, M.1    Rosen, M.K.2
  • 6
    • 0035970301 scopus 로고    scopus 로고
    • Phosphorylation-induced structural changes in the amyloid precursor protein cytoplasmic tail detected by NMR
    • Ramelot, T. A., and Nicholson, L. K. (2001) Phosphorylation-induced structural changes in the amyloid precursor protein cytoplasmic tail detected by NMR, J. Mol. Biol. 307, 871-884.
    • (2001) J. Mol. Biol , vol.307 , pp. 871-884
    • Ramelot, T.A.1    Nicholson, L.K.2
  • 7
    • 0035413607 scopus 로고    scopus 로고
    • Structural basis for control by phosphorylation
    • Johnson, L. N., and Lewis, R. J. (2001) Structural basis for control by phosphorylation, Chem. Rev. 101, 2209-2242.
    • (2001) Chem. Rev , vol.101 , pp. 2209-2242
    • Johnson, L.N.1    Lewis, R.J.2
  • 8
    • 21744436606 scopus 로고    scopus 로고
    • Variable control of ets-1 DNA binding by multiple phosphates in an unstructured region
    • Pufall, M., Lee, G. M., Nelson, M. L., K. H. S., Velyvis, A., Kay, L. E., McIntosh, L. P., and Graves, B. J. (2005) Variable control of ets-1 DNA binding by multiple phosphates in an unstructured region, Science 309, 142-145.
    • (2005) Science , vol.309 , pp. 142-145
    • Pufall, M.1    Lee, G.M.2    Nelson, M.L.K.H.S.3    Velyvis, A.4    Kay, L.E.5    McIntosh, L.P.6    Graves, B.J.7
  • 9
    • 33747592823 scopus 로고    scopus 로고
    • Graded regulation of the kv2.1 potassium channel by variable phosphorylation
    • Park, K.-S., Mohapatra, D. P., Misonou, H., and Trimmer, J. S. (2006) Graded regulation of the kv2.1 potassium channel by variable phosphorylation, Science 18, 976-979.
    • (2006) Science , vol.18 , pp. 976-979
    • Park, K.-S.1    Mohapatra, D.P.2    Misonou, H.3    Trimmer, J.S.4
  • 10
  • 11
    • 0035830403 scopus 로고    scopus 로고
    • Influence of myristoylation, phosphorylation, and deamidation on the structural behavior of the N-terminus of the catalytic subunit of CAMP-dependent protein kinase
    • Tholey, A., Pipkorn, R., Bossemeyer, D., Kinzel, V., and Reed, J. (2001) Influence of myristoylation, phosphorylation, and deamidation on the structural behavior of the N-terminus of the catalytic subunit of CAMP-dependent protein kinase, Biochemistry 40, 225-231.
    • (2001) Biochemistry , vol.40 , pp. 225-231
    • Tholey, A.1    Pipkorn, R.2    Bossemeyer, D.3    Kinzel, V.4    Reed, J.5
  • 12
    • 0035913754 scopus 로고    scopus 로고
    • Atomistic Brownian dynamics simulation of peptide phosphorylation
    • Shen, T., Wong, C. F., and McCammon, J. A. (2001) Atomistic Brownian dynamics simulation of peptide phosphorylation, J. Am. Chem. Soc. 123, 9107-9111.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 9107-9111
    • Shen, T.1    Wong, C.F.2    McCammon, J.A.3
  • 13
    • 33646266474 scopus 로고    scopus 로고
    • Conformational changes in protein loops and helices induced by post-translational phosphorylation
    • Groban, E. S., Narayanan, A., and Jacobson, M. P. (2006) Conformational changes in protein loops and helices induced by post-translational phosphorylation, PLoS Comput. Biol. 2, 238-250.
    • (2006) PLoS Comput. Biol , vol.2 , pp. 238-250
    • Groban, E.S.1    Narayanan, A.2    Jacobson, M.P.3
  • 14
    • 0027731168 scopus 로고
    • The structures of native phosphorylated chicken cystatin and of a recombinant unphosphorylated variant in solution
    • Dieckmann, T., Mitschang, L., Hofmann, M., Kos, J., Turk, V., Auerswald, E. A., Jaenicke, R., and Oschkinat, H. (1993) The structures of native phosphorylated chicken cystatin and of a recombinant unphosphorylated variant in solution, J. Mol. Biol. 234, 1048-1059.
    • (1993) J. Mol. Biol , vol.234 , pp. 1048-1059
    • Dieckmann, T.1    Mitschang, L.2    Hofmann, M.3    Kos, J.4    Turk, V.5    Auerswald, E.A.6    Jaenicke, R.7    Oschkinat, H.8
  • 16
    • 0033599026 scopus 로고    scopus 로고
    • Structure of a transiently phosphorylated switch in bacterial signal transduction
    • Kern, D., Volkman, B. F., Luginbuhl, P., Nohaile, M. J., Kustu, S., and Wemmer, D. E. (1999) Structure of a transiently phosphorylated switch in bacterial signal transduction, Nature 402, 894-898.
    • (1999) Nature , vol.402 , pp. 894-898
    • Kern, D.1    Volkman, B.F.2    Luginbuhl, P.3    Nohaile, M.J.4    Kustu, S.5    Wemmer, D.E.6
  • 17
    • 4243291206 scopus 로고    scopus 로고
    • A signaling protein 'in action' - structure and dynamics of a transiently phosphorylated switch
    • Kern, D., Volkman, B. F., and Wemmer, D. E. (2001) A signaling protein 'in action' - structure and dynamics of a transiently phosphorylated switch, Biophys. J. 80, 13a.
    • (2001) Biophys. J , vol.80
    • Kern, D.1    Volkman, B.F.2    Wemmer, D.E.3
  • 18
    • 0034687712 scopus 로고    scopus 로고
    • Associative memory hamiltonians for structure prediction without homology: Alpha-helical proteins
    • Hardin, C., Eastwood, M. P., Luthey-Schulten, Z., and Wolynes, P. G. (2000) Associative memory hamiltonians for structure prediction without homology: Alpha-helical proteins, Proc. Natl. Acad. Sci. U.S.A. 97, 14235-14240.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.97 , pp. 14235-14240
    • Hardin, C.1    Eastwood, M.P.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 21
    • 24644442164 scopus 로고    scopus 로고
    • The folding energy landscape and phosphorylation: Modeling the conformational switch of the nfat regulatory domain
    • Shen, T. Y., Zong, C. H., Hamelberg, D., McCammon, J. A., and Wolynes, P. G. (2005) The folding energy landscape and phosphorylation: modeling the conformational switch of the nfat regulatory domain, FASEB J. 19, 1389-1395.
    • (2005) FASEB J , vol.19 , pp. 1389-1395
    • Shen, T.Y.1    Zong, C.H.2    Hamelberg, D.3    McCammon, J.A.4    Wolynes, P.G.5
  • 22
    • 0035327183 scopus 로고    scopus 로고
    • Evaluating protein structure-prediction schemes using energy landscape theory
    • Eastwood, M. P., Hardin, C., Luthey-Schulten, Z., and Wolynes, P. G. (2001) Evaluating protein structure-prediction schemes using energy landscape theory, IBM J. Res. Dev. 45, 475-497.
    • (2001) IBM J. Res. Dev , vol.45 , pp. 475-497
    • Eastwood, M.P.1    Hardin, C.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 23
    • 0037452701 scopus 로고    scopus 로고
    • Associative memory hamiltonians for structure prediction without homology:alpha/beta proteins
    • Hardin, C., Eastwood, M., Luthey-Schulten, Z., and Wolynes, P. G. (2003) Associative memory hamiltonians for structure prediction without homology:alpha/beta proteins, Proc. Natl. Acad. Sci. U.S.A. 100, 1679-1684.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 1679-1684
    • Hardin, C.1    Eastwood, M.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 24
    • 0036733958 scopus 로고    scopus 로고
    • Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach
    • Eastwood, M. P., Hardin, C., Luthey-Schulten, Z., and Wolynes, P. G. (2002) Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach, J. Chem. Phys. 117, 4602-4615.
    • (2002) J. Chem. Phys , vol.117 , pp. 4602-4615
    • Eastwood, M.P.1    Hardin, C.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 25
    • 84860040254 scopus 로고    scopus 로고
    • Simulation studies of the fidelity of biomolecular structure ensemble recreation
    • Latzer, J., Eastwood, M. P., and Wolynes, P. G. (2006) Simulation studies of the fidelity of biomolecular structure ensemble recreation, J. Chem. Phys. 125, 214905-1-214905-12.
    • (2006) J. Chem. Phys , vol.125
    • Latzer, J.1    Eastwood, M.P.2    Wolynes, P.G.3
  • 26
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding: Linear response theory
    • Ikeguchi, M., Ueno, J., Sato, M., and Kidera, A. (2005) Protein structural change upon ligand binding: Linear response theory, Phys. Rev. Lett. 94, 078102-1-078102-4.
    • (2005) Phys. Rev. Lett , vol.94
    • Ikeguchi, M.1    Ueno, J.2    Sato, M.3    Kidera, A.4
  • 28
    • 32044451299 scopus 로고    scopus 로고
    • A phosphorylation-induced conformation change in dematin headpiece
    • Jiang, Z. H. G., and McKnight, C. J. (2006) A phosphorylation-induced conformation change in dematin headpiece, Structure 14, 379-387.
    • (2006) Structure , vol.14 , pp. 379-387
    • Jiang, Z.H.G.1    McKnight, C.J.2
  • 29
    • 0029027040 scopus 로고
    • Two distinct signaling pathways activate the latent DNA binding function of p53 in a casein kinase ii-independent manner
    • Hupp, T. R., and Lane, D. P. (1995) Two distinct signaling pathways activate the latent DNA binding function of p53 in a casein kinase ii-independent manner, J. Biol. Chem. 270, 18165-18174.
    • (1995) J. Biol. Chem , vol.270 , pp. 18165-18174
    • Hupp, T.R.1    Lane, D.P.2
  • 30
    • 28344449719 scopus 로고    scopus 로고
    • Statistical theory for protein ensembles with designed energy landscapes
    • Biswas, P., Zou, J. M., and Saven, J. G. (2005) Statistical theory for protein ensembles with designed energy landscapes, J. Chem. Phys. 123, 154908-1-154908-12.
    • (2005) J. Chem. Phys , vol.123
    • Biswas, P.1    Zou, J.M.2    Saven, J.G.3
  • 31
  • 32
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • Miyashita, O., Onuchic, J. N., and Wolynes, P. G. (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins, Proc. Natl. Acad. Sci. U.S.A. 100, 12570-12575.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 33
    • 0022114079 scopus 로고    scopus 로고
    • Ansari, A., Berendzen, J., Bowne, S. F., Frauenfelder, H., Iben, I. E. T., Sauke, T. B., Shyamsunder, E., and Young, R. D. (1985) Protein States and Proteinquakes, PNAS 82, 5000-5004.
    • Ansari, A., Berendzen, J., Bowne, S. F., Frauenfelder, H., Iben, I. E. T., Sauke, T. B., Shyamsunder, E., and Young, R. D. (1985) Protein States and Proteinquakes, PNAS 82, 5000-5004.
  • 34
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with rosetta can be more accurate than their templates
    • Misura, K. M. S., Chivian, D., Rohl, C. A., Kim, D. E., and Baker, D. (2006) Physically realistic homology models built with rosetta can be more accurate than their templates, Proc. Natl. Acad. Sci. U.S.A. 103, 5361-5366.
    • (2006) Proc. Natl. Acad. Sci. U.S.A , vol.103 , pp. 5361-5366
    • Misura, K.M.S.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 35
    • 33846104376 scopus 로고    scopus 로고
    • All-atom ab initio folding of a diverse set of proteins
    • Yang, J. S., Chen, W. W., Skolnick, J., and Shakhnovich, E. I. (2007) All-atom ab initio folding of a diverse set of proteins. Structure 15, 53-63.
    • (2007) Structure , vol.15 , pp. 53-63
    • Yang, J.S.1    Chen, W.W.2    Skolnick, J.3    Shakhnovich, E.I.4
  • 37
    • 0029864372 scopus 로고    scopus 로고
    • Local conformation signals and the statistical thermodynamics of collapsed helical proteins
    • Saven, J. G., and Wolynes, P. G. (1996) Local conformation signals and the statistical thermodynamics of collapsed helical proteins. J. Mol. Biol. 257, 199-216.
    • (1996) J. Mol. Biol , vol.257 , pp. 199-216
    • Saven, J.G.1    Wolynes, P.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.