메뉴 건너뛰기




Volumn 101, Issue 6, 2011, Pages 1450-1458

Multiscale ensemble modeling of intrinsically disordered proteins: P53 N-terminal domain

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE FRAGMENT; PROTEIN P53;

EID: 80053120944     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.08.003     Document Type: Article
Times cited : (87)

References (51)
  • 2
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • DOI 10.1038/nrm1589
    • H.J. Dyson, and P.E. Wright Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell Biol. 6 2005 197 208 (Pubitemid 40314921)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.3 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 6
    • 34250821717 scopus 로고    scopus 로고
    • Mechanism of coupled folding and binding of an intrinsically disordered protein
    • DOI 10.1038/nature05858, PII NATURE05858
    • K. Sugase, H.J. Dyson, and P.E. Wright Mechanism of coupled folding and binding of an intrinsically disordered protein Nature 447 2007 1021 1025 (Pubitemid 46975749)
    • (2007) Nature , vol.447 , Issue.7147 , pp. 1021-1025
    • Sugase, K.1    Dyson, H.J.2    Wright, P.E.3
  • 7
    • 42949161558 scopus 로고    scopus 로고
    • Binding-induced folding of a natively unstructured transcription factor
    • A.G. Turjanski, and J.S. Gutkind G. Hummer Binding-induced folding of a natively unstructured transcription factor PLOS Comput. Biol. 4 2008 e1000060
    • (2008) PLOS Comput. Biol. , vol.4 , pp. 1000060
    • Turjanski, A.G.1    Gutkind, J.S.2    Hummer, G.3
  • 8
    • 67650684936 scopus 로고    scopus 로고
    • Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints
    • J.A. Marsh, and J.D. Forman-Kay Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints J. Mol. Biol. 391 2009 359 374
    • (2009) J. Mol. Biol. , vol.391 , pp. 359-374
    • Marsh, J.A.1    Forman-Kay, J.D.2
  • 9
    • 67849133810 scopus 로고    scopus 로고
    • Toward an accurate determination of free energy landscapes in solution states of proteins
    • A. De Simone, and B. Richter M. Vendruscolo Toward an accurate determination of free energy landscapes in solution states of proteins J. Am. Chem. Soc. 131 2009 3810 3811
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 3810-3811
    • De Simone, A.1    Richter, B.2    Vendruscolo, M.3
  • 10
  • 11
    • 78650453629 scopus 로고    scopus 로고
    • DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail
    • D. Vuzman, and Y. Levy DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail Proc. Natl. Acad. Sci. USA 107 2010 21004 21009
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 21004-21009
    • Vuzman, D.1    Levy, Y.2
  • 13
    • 0031585990 scopus 로고    scopus 로고
    • Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels
    • DOI 10.1006/jmbi.1997.0954
    • J.R. Gillespie, and D. Shortle Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels J. Mol. Biol. 268 1997 158 169 (Pubitemid 27192686)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 158-169
    • Gillespie, J.R.1    Shortle, D.2
  • 16
    • 77958510026 scopus 로고    scopus 로고
    • Modeling intrinsically disordered proteins with Bayesian statistics
    • C.K. Fisher, A. Huang, and C.M. Stultz Modeling intrinsically disordered proteins with Bayesian statistics J. Am. Chem. Soc. 132 2010 14919 14927
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 14919-14927
    • Fisher, C.K.1    Huang, A.2    Stultz, C.M.3
  • 17
    • 0034628913 scopus 로고    scopus 로고
    • Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
    • K.B. Wong, and J. Clarke V. Daggett Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding J. Mol. Biol. 296 2000 1257 1282
    • (2000) J. Mol. Biol. , vol.296 , pp. 1257-1282
    • Wong, K.B.1    Clarke, J.2    Daggett, V.3
  • 19
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
    • D. Hamelberg, J. Mongan, and J.A. McCammon Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J. Chem. Phys. 120 2004 11919 11929
    • (2004) J. Chem. Phys. , vol.120 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 23
    • 79953011717 scopus 로고    scopus 로고
    • On easy implementation of a variant of the replica exchange with solute tempering in GROMACS
    • T. Terakawa, T. Kameda, and S. Takada On easy implementation of a variant of the replica exchange with solute tempering in GROMACS J. Comput. Chem. 32 2011 1228 1234
    • (2011) J. Comput. Chem. , vol.32 , pp. 1228-1234
    • Terakawa, T.1    Kameda, T.2    Takada, S.3
  • 24
    • 0042783950 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • D. Reith, M. Pütz, and F. Müller-Plathe Deriving effective mesoscale potentials from atomistic simulations J. Comput. Chem. 24 2003 1624 1636
    • (2003) J. Comput. Chem. , vol.24 , pp. 1624-1636
    • Reith, D.1    Pütz, M.2    Müller-Plathe, F.3
  • 26
    • 47649096991 scopus 로고    scopus 로고
    • Structural biology of the tumor suppressor p53
    • A.C. Joerger, and A.R. Fersht Structural biology of the tumor suppressor p53 Annu. Rev. Biochem. 77 2008 557 582
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 557-582
    • Joerger, A.C.1    Fersht, A.R.2
  • 28
    • 0030575937 scopus 로고    scopus 로고
    • Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain
    • DOI 10.1126/science.274.5289.948
    • P.H. Kussie, and S. Gorina N.P. Pavletich Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain Science 274 1996 948 953 (Pubitemid 26398409)
    • (1996) Science , vol.274 , Issue.5289 , pp. 948-953
    • Kussie, P.H.1    Gorina, S.2    Marechal, V.3    Elenbaas, B.4    Moreau, J.5    Levine, A.J.6    Pavletich, N.P.7
  • 30
    • 33745214419 scopus 로고    scopus 로고
    • Structure of the Tfb1/p53 complex: Insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53
    • P. Di Lello, and L.M. Jenkins J.G. Omichinski Structure of the Tfb1/p53 complex: insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53 Mol. Cell 22 2006 731 740
    • (2006) Mol. Cell , vol.22 , pp. 731-740
    • Di Lello, P.1    Jenkins, L.M.2    Omichinski, J.G.3
  • 34
    • 0026643094 scopus 로고
    • The nature of folded states of globular proteins
    • J.D. Honeycutt, and D. Thirumalai The nature of folded states of globular proteins Biopolymers 32 1992 695 709
    • (1992) Biopolymers , vol.32 , pp. 695-709
    • Honeycutt, J.D.1    Thirumalai, D.2
  • 35
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • DOI 10.1021/ja9621760, PII S0002786396021762
    • W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236 (Pubitemid 26399746)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 36
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • DOI 10.1021/jp003919d
    • G.A. Kaminski, and R.A. Friesner W.L. Jorgensen Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 105 2001 6474 6487 (Pubitemid 35339015)
    • (2001) Journal of Physical Chemistry B , vol.105 , Issue.28 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 37
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Klein, M.L.3
  • 38
  • 39
    • 38749123962 scopus 로고    scopus 로고
    • P-LINCS: A parallel linear constraint solver for molecular simulation
    • B. Hess P-LINCS: a parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 4 2008 116 122
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 116-122
    • Hess, B.1
  • 40
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • S. Miyamoto, and P.A. Kollman SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13 1992 952 962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 41
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, and C. Kutzner E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Lindahl, E.3
  • 42
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 43
    • 34249821932 scopus 로고    scopus 로고
    • Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
    • DOI 10.1002/jcc.20624
    • D. Gront, S. Kmiecik, and A. Kolinski Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from α-carbon coordinates J. Comput. Chem. 28 2007 1593 1597 (Pubitemid 46853797)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.9 , pp. 1593-1597
    • Gront, D.1    Kmiecik, S.2    Kolinski, A.3
  • 44
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • G.G. Krivov, M.V. Shapovalov, and R.L. Dunbrack Jr. Improved prediction of protein side-chain conformations with SCWRL4 Proteins 77 2009 778 795
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack Jr., R.L.3
  • 45
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR [11]
    • DOI 10.1021/ja0000908
    • M. Zweckstetter, and A. Bax Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR J. Am. Chem. Soc. 122 2000 3791 3792 (Pubitemid 30233459)
    • (2000) Journal of the American Chemical Society , vol.122 , Issue.15 , pp. 3791-3792
    • Zweckstetter, M.1    Bax, A.2
  • 46
    • 0029185933 scopus 로고
    • CRYSOL - A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • DOI 10.1107/S0021889895007047
    • D. Svergun, C. Barberato, and M.H.J. Koch CRYSOL - a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Cryst. 28 1995 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
  • 47
    • 23144444979 scopus 로고    scopus 로고
    • Protein structure prediction servers at University College London
    • K. Bryson, and L.J. McGuffin D.T. Jones Protein structure prediction servers at University College London Nucleic Acids Res. 33 2005 W36 W38
    • (2005) Nucleic Acids Res. , vol.33
    • Bryson, K.1    McGuffin, L.J.2    Jones, D.T.3
  • 48
    • 77955487466 scopus 로고    scopus 로고
    • Multiscale coarse-graining of the protein energy landscape
    • R.D. Hills Jr., L. Lu, and G.A. Voth Multiscale coarse-graining of the protein energy landscape PLOS Comput. Biol. 6 2010 e1000827
    • (2010) PLOS Comput. Biol. , vol.6 , pp. 1000827
    • Hills Jr., R.D.1    Lu, L.2    Voth, G.A.3
  • 49
    • 77952478054 scopus 로고    scopus 로고
    • Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data
    • R. DeVane, and M.L. Klein P.B. Moore Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data J. Phys. Chem. B 114 2010 6386 6393
    • (2010) J. Phys. Chem. B , vol.114 , pp. 6386-6393
    • Devane, R.1    Klein, M.L.2    Moore, P.B.3
  • 50
    • 77954928439 scopus 로고    scopus 로고
    • Comparison between molecular dynamic based and knowledge based potentials for protein side chains
    • M.R. Betancourt Comparison between molecular dynamic based and knowledge based potentials for protein side chains J. Comput. Biol. 17 2010 943 952
    • (2010) J. Comput. Biol. , vol.17 , pp. 943-952
    • Betancourt, M.R.1
  • 51
    • 79959215991 scopus 로고    scopus 로고
    • CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work
    • H. Kenzaki, and N. Koga S. Takada CafeMol: a coarse-grained biomolecular simulator for simulating proteins at work J. Chem. Theory Comput. 7 2011 1979 1989
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1979-1989
    • Kenzaki, H.1    Koga, N.2    Takada, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.