메뉴 건너뛰기




Volumn 28, Issue 11, 2012, Pages 1517-1524

A comprehensive computational model of facilitated diffusion in prokaryotes

Author keywords

[No Author keywords available]

Indexed keywords

PROKARYOTA;

EID: 84861756737     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts178     Document Type: Article
Times cited : (19)

References (28)
  • 1
    • 77950833499 scopus 로고    scopus 로고
    • Detailed simulations of cell biology with smoldyn 2
    • Andrews, S.S. et al. (2010) Detailed simulations of cell biology with smoldyn 2.1. PLoS Comput. Biol., 6, e1000705.
    • (2010) 1. PLoS Comput. Biol. , vol.6
    • Andrews, S.S.1
  • 2
    • 72449204595 scopus 로고    scopus 로고
    • Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin
    • Bancaud, A. et al. (2009) Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J., 28, 3785-3798.
    • (2009) EMBO J , vol.28 , pp. 3785-3798
    • Bancaud, A.1
  • 3
    • 7744241509 scopus 로고    scopus 로고
    • A model of sequence-dependent protein diffusion along DNA
    • Barbi, M. et al. (2004) A model of sequence-dependent protein diffusion along DNA. J. Biol. Phys., 30, 203-226.
    • (2004) J. Biol. Phys. , vol.30 , pp. 203-226
    • Barbi, M.1
  • 5
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins statistical-mechanical theory and application to operators and promoters
    • Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
    • (1987) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 6
    • 0019887628 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids 1. models and theory
    • Berg, O.G. et al. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. models and theory. Biochemistry, 20, 6929-6948.
    • (1981) Biochemistry , vol.20 , pp. 6929-6948
    • Berg, O.G.1
  • 7
    • 33645807371 scopus 로고    scopus 로고
    • A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
    • Blainey, P.C. et al. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. PNAS, 103, 5752-5757.
    • (2006) PNAS , vol.103 , pp. 5752-5757
    • Blainey, P.C.1
  • 8
    • 61449155349 scopus 로고    scopus 로고
    • Models of transcription factor binding: sensitivity of activation functions to model assumptions
    • Chu, D. et al. (2009) Models of transcription factor binding: sensitivity of activation functions to model assumptions. J. Theor. Biol., 257, 419-429.
    • (2009) J. Theor. Biol. , vol.257 , pp. 419-429
    • Chu, D.1
  • 9
    • 77949397232 scopus 로고    scopus 로고
    • Facilitated search of proteins on DNA: correlations are important
    • Das, R.K. and Kolomeisky, A.B. (2010) Facilitated search of proteins on DNA: correlations are important. Phys. Chem. Chem. Phys., 12, 2999-3004.
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 2999-3004
    • Das, R.K.1    Kolomeisky, A.B.2
  • 10
    • 79952494759 scopus 로고    scopus 로고
    • Protein sliding and hopping kinetics on DNA
    • DeSantis, M.C. et al. (2011) Protein sliding and hopping kinetics on DNA. Phys. Rev. E, 83, 021907.
    • (2011) Phys. Rev. E , vol.83 , pp. 021907
    • DeSantis, M.C.1
  • 11
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single-molecule level in a living cell
    • Elf, J. et al. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science, 316, 1191-1194.
    • (2007) Science , vol.316 , pp. 1191-1194
    • Elf, J.1
  • 12
    • 33646945653 scopus 로고    scopus 로고
    • Strong physical constraints on sequence-specific target location by proteins on DNA molecules
    • Flyvbjerg, H. et al. (2006) Strong physical constraints on sequence-specific target location by proteins on DNA molecules. Nucleic Acids Res., 34, 2550-2557.
    • (2006) Nucleic Acids Res , vol.34 , pp. 2550-2557
    • Flyvbjerg, H.1
  • 13
    • 0037126028 scopus 로고    scopus 로고
    • Physical constraints and functional characteristics of transcription factor-DNA interaction
    • Gerland, U. et al. (2002) Physical constraints and functional characteristics of transcription factor-DNA interaction. PNAS, 99, 12015-12020.
    • (2002) PNAS , vol.99 , pp. 12015-12020
    • Gerland, U.1
  • 14
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.T. (1977) Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81, 2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 15
    • 27644460480 scopus 로고    scopus 로고
    • Measurement of the contributions of 1d and 3d pathways to the translocation of a protein along DNA
    • Gowers, D.M. et al. (2005) Measurement of the contributions of 1d and 3d pathways to the translocation of a protein along DNA. PNAS, 102, 15883-15888.
    • (2005) PNAS , vol.102 , pp. 15883-15888
    • Gowers, D.M.1
  • 16
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • Halford, S.E. and Marko, J.F. (2004)How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res., 32, 3040-3052.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 17
    • 63849284078 scopus 로고    scopus 로고
    • Effects of macromolecular crowding and DNA looping on gene regulation kinetics
    • Li, G.-W. et al. (2009) Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nat. Phys., 5, 294-297.
    • (2009) Nat. Phys. , vol.5 , pp. 294-297
    • Li, G.-W.1
  • 18
    • 66249106717 scopus 로고    scopus 로고
    • Facilitated diffusion with DNA coiling
    • Lomholt, M.A. et al. (2009) Facilitated diffusion with DNA coiling. PNAS, 106, 8204-8208.
    • (2009) PNAS , vol.106 , pp. 8204-8208
    • Lomholt, M.A.1
  • 19
    • 72149127671 scopus 로고    scopus 로고
    • How a protein searches for its site on DNA: the mechanism of facilitated diffusion
    • Mirny, L. et al. (2009) How a protein searches for its site on DNA: the mechanism of facilitated diffusion. J. Phys. A Math. Theor., 42, 434013.
    • (2009) J. Phys. A Math. Theor. , vol.42 , pp. 434013
    • Mirny, L.1
  • 20
    • 0014945567 scopus 로고
    • The lac represser-operator interaction: iii. kinetic studies
    • Riggs, A.D. et al. (1970) The lac represser-operator interaction: iii. kinetic studies. J. Mol. Biol., 53, 401-417.
    • (1970) J. Mol. Biol. , vol.53 , pp. 401-417
    • Riggs, A.D.1
  • 21
    • 31544443526 scopus 로고    scopus 로고
    • Escherichia coli k-12: a cooperatively developed annotation snapshot - 2005
    • Riley, M. et al. (2006) Escherichia coli k-12: a cooperatively developed annotation snapshot - 2005. Nucleic Acids Res., 34, 1-9.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1-9
    • Riley, M.1
  • 22
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of protein-DNAinteraction: facilitated target location in sequence-dependent potential
    • Slutsky, M. and Mirny, L.A. (2004) Kinetics of protein-DNAinteraction: facilitated target location in sequence-dependent potential. Biophys. J., 87, 4021-4035.
    • (2004) Biophys. J. , vol.87 , pp. 4021-4035
    • Slutsky, M.1    Mirny, L.A.2
  • 23
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 24
    • 33845442827 scopus 로고    scopus 로고
    • Diffusion of transcription factors can drastically enhance the noise in gene expression
    • van Zon, J.S. et al. (2006) Diffusion of transcription factors can drastically enhance the noise in gene expression. Biophys. J., 91, 4350-4367.
    • (2006) Biophys. J. , vol.91 , pp. 4350-4367
    • van Zon, J.S.1
  • 25
    • 36749088055 scopus 로고    scopus 로고
    • Modeling DNA-binding of escherichia coli σ70 exhibits a characteristic energy landscape around strong promoters
    • Weindl, J. et al. (2007) Modeling DNA-binding of escherichia coli σ70 exhibits a characteristic energy landscape around strong promoters. Nucleic Acids Res., 35, 7003-7010.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7003-7010
    • Weindl, J.1
  • 26
    • 0019867850 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids 3. the escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions
    • Winter, R.B. et al. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. the escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry, 20, 6961-6977.
    • (1981) Biochemistry , vol.20 , pp. 6961-6977
    • Winter, R.B.1
  • 27
    • 46349108554 scopus 로고    scopus 로고
    • Spatial effects on the speed and reliability of protein-DNA search
    • Wunderlich, Z. and Mirny, L.A. (2008) Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res., 36, 3570-3578.
    • (2008) Nucleic Acids Res , vol.36 , pp. 3570-3578
    • Wunderlich, Z.1    Mirny, L.A.2
  • 28
    • 84860495813 scopus 로고    scopus 로고
    • GRiP: a computational tool to simulate transcription factor binding in prokaryotes
    • Zabet, N.R. and Adryan, B. (2012) GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics.
    • (2012) Bioinformatics
    • Zabet, N.R.1    Adryan, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.