메뉴 건너뛰기




Volumn 24, Issue 19, 2012, Pages

The physics of protein-DNA interaction networks in the control of gene expression

Author keywords

[No Author keywords available]

Indexed keywords

CELL-TO-CELL VARIABILITY; CELLULAR PROCESS; CONTROL OF GENE EXPRESSION; DNA BENDING; DNA LOOPING; DOUBLE STRANDED DNA; EXPERIMENTAL TECHNIQUES; GENETIC SYSTEMS; IN-VIVO; INDUCTION PROCESS; INHERENT FLEXIBILITY; LAC OPERON; LAC REPRESSOR; LIVING CELL; LONG RANGE INTERACTIONS; MOLECULAR COMPONENTS; MULTIPLE INTERACTIONS; PHYSICAL INTERACTIONS; PHYSICAL METHODS; PROTEIN-DNA COMPLEXES; PROTEIN-DNA INTERACTIONS; STATISTICAL PHYSICS; TWISTING EFFECT;

EID: 84860207044     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/24/19/193102     Document Type: Review
Times cited : (17)

References (95)
  • 1
    • 79956188503 scopus 로고    scopus 로고
    • Physics approaches to protein interactions and gene regulation
    • 1478-3975 030301
    • Nussinov R, Panchenko A R and Przytycka T 2011 Physics approaches to protein interactions and gene regulation Phys. Biol. 8 030301
    • (2011) Phys. Biol. , vol.8 , Issue.3
    • Nussinov, R.1    Panchenko, A.R.2    Przytycka, T.3
  • 3
    • 33744807717 scopus 로고    scopus 로고
    • DNA looping: The consequences and its control
    • DOI 10.1016/j.sbi.2006.05.008, PII S0959440X06000790
    • Saiz L and Vilar J M G 2006 DNA looping: the consequences and its control Curr. Opin. Struct. Biol. 16 34450 (Pubitemid 43831652)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.3 , pp. 344-350
    • Saiz, L.1    Vilar, J.M.2
  • 4
    • 0024811753 scopus 로고
    • Multipartite genetic control elements: Communication by DNA loop
    • Adhya S 1989 Multipartite genetic control elements: communication by DNA loop Annu. Rev. Genet. 23 22750 (Pubitemid 20033403)
    • (1989) Annual Review of Genetics , vol.23 , pp. 227-250
    • Adhya, S.1
  • 5
    • 15744393452 scopus 로고    scopus 로고
    • DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise
    • DOI 10.1016/j.gde.2005.02.005, Chromosomes and Expression Mechanisms
    • Vilar J M G and Saiz L 2005 DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise Curr. Opin. Genet. Dev. 15 13644 (Pubitemid 40410661)
    • (2005) Current Opinion in Genetics and Development , vol.15 , Issue.2 , pp. 136-144
    • Vilar, J.M.G.1    Saiz, L.2
  • 6
    • 0026624977 scopus 로고
    • DNA looping
    • 10.1146/annurev.bi.61.070192.001215 0066-4154
    • Schleif R 1992 DNA looping Annu. Rev. Biochem. 61 199223
    • (1992) Annu. Rev. Biochem. , vol.61 , Issue.1 , pp. 199-223
    • Schleif, R.1
  • 8
    • 24044540381 scopus 로고    scopus 로고
    • Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking
    • DOI 10.1016/j.molcel.2005.07.018, PII S1097276505015066
    • Wang Q, Carroll J S and Brown M 2005 Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking Mol. Cell 19 63142 (Pubitemid 41219439)
    • (2005) Molecular Cell , vol.19 , Issue.5 , pp. 631-642
    • Wang, Q.1    Carroll, J.S.2    Brown, M.3
  • 9
    • 41649111599 scopus 로고    scopus 로고
    • Progesterone-dependent deoxyribonucleic acid looping between RUSH/SMARCA3 and Egr-1 mediates repression by c-Rel
    • DOI 10.1210/me.2007-0432
    • Hewetson A and Chilton B S 2008 Progesterone-dependent deoxyribonucleic acid looping between RUSH/SMARCA3 and egr-1 mediates repression by c-rel Mol. Endocrinol. 22 81322 (Pubitemid 351482819)
    • (2008) Molecular Endocrinology , vol.22 , Issue.4 , pp. 813-822
    • Hewetson, A.1    Chilton, B.S.2
  • 10
    • 0021188333 scopus 로고
    • An operator at -280 base pairs that is required for repression of araBAD operon promoter: Addition of DNA helical turns between the operator and promoter cyclically hinders repression
    • DOI 10.1073/pnas.81.16.5017
    • Dunn T M et al 1984 An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression Proc. Natl Acad. Sci. USA 81 501720 (Pubitemid 14008872)
    • (1984) Proceedings of the National Academy of Sciences of the United States of America , vol.81 , Issue.16 , pp. 5017-5020
    • Dunn, T.M.1    Hahn, S.2    Ogden, S.3    Schleif, R.F.4
  • 12
    • 0036923833 scopus 로고    scopus 로고
    • Looping and interaction between hypersensitive sites in the active β-globin locus
    • DOI 10.1016/S1097-2765(02)00781-5
    • Tolhuis B et al 2002 Looping and interaction between hypersensitive sites in the active beta-globin locus Mol. Cell 10 145365 (Pubitemid 36050885)
    • (2002) Molecular Cell , vol.10 , Issue.6 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.-J.2    Splinter, E.3    Grosveld, F.4    De Laat, W.5
  • 13
    • 0019769520 scopus 로고
    • The SV40 72 base repair has a striking effect on gene expression both in SV40 and other chimeric recombinants
    • Moreau P et al 1981 The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants Nucleic Acids Res. 9 604768 (Pubitemid 12133112)
    • (1981) Nucleic Acids Research , vol.9 , Issue.22 , pp. 6047-6068
    • Moreau, P.1    Hen, R.2    Wasylyk, B.3
  • 14
    • 73949116253 scopus 로고    scopus 로고
    • Transcription factors mediate long-range enhancer-promoter interactions
    • 10.1073/pnas.0902454106 0027-8424
    • Nolis I K et al 2009 Transcription factors mediate long-range enhancer-promoter interactions Proc. Natl Acad. Sci. USA 106 202227
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.48 , pp. 20222-20227
    • Nolis, I.K.1
  • 15
    • 77957139539 scopus 로고    scopus 로고
    • Mediator and cohesin connect gene expression and chromatin architecture
    • 10.1038/nature09380 0028-0836
    • Kagey M H et al 2010 Mediator and cohesin connect gene expression and chromatin architecture Nature 467 4305
    • (2010) Nature , vol.467 , Issue.7314 , pp. 430-435
    • Kagey, M.H.1
  • 16
    • 54849422001 scopus 로고    scopus 로고
    • Long-range enhancer associated with chromatin looping allows AP-1 regulation of the peptidylarginine deiminase 3 gene in differentiated keratinocyte
    • 10.1371/journal.pone.0003408 1932-6203
    • Chavanas S et al 2008 Long-range enhancer associated with chromatin looping allows AP-1 regulation of the peptidylarginine deiminase 3 gene in differentiated keratinocyte PLoS ONE 3 e3408
    • (2008) PLoS ONE , vol.3 , Issue.10 , pp. 3408
    • Chavanas, S.1
  • 17
    • 80053190826 scopus 로고    scopus 로고
    • Evidence for a complex of transcription factor IIB (TFIIB) with poly(A) polymerase and cleavage factor 1 subunits required for gene looping
    • 10.1074/jbc.M110.193870 0021-9258
    • Medler S et al 2011 Evidence for a complex of transcription factor IIB (TFIIB) with poly(A) polymerase and cleavage factor 1 subunits required for gene looping J. Biol. Chem. 286 3370918
    • (2011) J. Biol. Chem. , vol.286 , Issue.39 , pp. 33709-33718
    • Medler, S.1
  • 18
    • 35148880383 scopus 로고    scopus 로고
    • Direct visualization of the binding of c-Myc/Max heterodimeric b-HLH-LZ to E-box sequences on the hTERT promoter
    • DOI 10.1021/bi700076m
    • Lebel R et al 2007 Direct visualization of the binding of c-Myc/Max heterodimeric b-HLH-LZ to E-box sequences on the hTERT promoter Biochemistry 46 1027986 (Pubitemid 350067621)
    • (2007) Biochemistry , vol.46 , Issue.36 , pp. 10279-10286
    • Lebel, R.1    McDuff, F.-O.2    Lavigne, P.3    Grandbois, M.4
  • 20
    • 80053355340 scopus 로고    scopus 로고
    • A dynamic model of transcriptional imprinting derived from the vitellogenesis memory effect
    • 10.1016/j.bpj.2011.07.004 0006-3495
    • Nicol-Benoit F et al 2011 A dynamic model of transcriptional imprinting derived from the vitellogenesis memory effect Biophys. J. 101 155768
    • (2011) Biophys. J. , vol.101 , Issue.7 , pp. 1557-1568
    • Nicol-Benoit, F.1
  • 21
    • 4644252538 scopus 로고    scopus 로고
    • One nucleotide in a κB site can determine cofactor specificity for NF-κB dimers
    • DOI 10.1016/j.cell.2004.08.007, PII S0092867404007445
    • Leung T H, Hoffmann A and Baltimore D 2004 One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers Cell 118 45364 (Pubitemid 39485665)
    • (2004) Cell , vol.118 , Issue.4 , pp. 453-464
    • Leung, T.H.1    Hoffmann, A.2    Baltimore, D.3
  • 22
    • 0028606859 scopus 로고
    • P53 oligomerization and DNA looping are linked with transcriptional activation
    • 0261-4189
    • Stenger J E et al 1994 P53 oligomerization and DNA looping are linked with transcriptional activation Embo J. 13 601120
    • (1994) Embo J. , vol.13 , pp. 6011-6020
    • Stenger, J.E.1
  • 23
    • 33745188049 scopus 로고    scopus 로고
    • Multiprotein DNA looping
    • 10.1103/PhysRevLett.96.238103 0031-9007 238103
    • Vilar J M G and Saiz L 2006 Multiprotein DNA looping Phys. Rev. Lett. 96 238103
    • (2006) Phys. Rev. Lett. , vol.96 , Issue.23
    • Vilar, J.M.G.1    Saiz, L.2
  • 24
    • 39449115716 scopus 로고    scopus 로고
    • Ab initio thermodynamic modeling of distal multisite transcription regulation
    • DOI 10.1093/nar/gkm1034
    • Saiz L and Vilar J M G 2008 Ab initio thermodynamic modeling of distal multisite transcription regulation Nucleic Acids Res. 36 72631 (Pubitemid 351267230)
    • (2008) Nucleic Acids Research , vol.36 , Issue.3 , pp. 726-731
    • Saiz, L.1    Vilar, J.M.G.2
  • 25
    • 20444387232 scopus 로고    scopus 로고
    • A gamut of loops: Meandering DNA
    • DOI 10.1016/j.tibs.2005.04.009, PII S0968000405001179, Celebrating 50 Years of the IUBMB
    • Semsey S, Virnik K and Adhya S 2005 A gamut of loops: meandering DNA Trends Biochem. Sci. 30 33441 (Pubitemid 40799052)
    • (2005) Trends in Biochemical Sciences , vol.30 , Issue.6 , pp. 334-341
    • Semsey, S.1    Virnik, K.2    Adhya, S.3
  • 26
    • 33744821974 scopus 로고    scopus 로고
    • Stochastic dynamics of macromolecular-assembly networks
    • DOI 10.1038/msb4100061, PII M4100061, msb4100061
    • Saiz L and Vilar J M G 2006 Stochastic dynamics of macromolecular- assembly networks Mol. Syst. Biol. 2 0024 (Pubitemid 43948167)
    • (2006) Molecular Systems Biology , vol.2 , pp. 0024
    • Saiz, L.1    Vilar, J.M.G.2
  • 27
    • 2942588906 scopus 로고    scopus 로고
    • Mathematical and computational models of immune-receptor signalling
    • Goldstein B, Faeder J R and Hlavacek W S 2004 Mathematical and computational models of immune-receptor signalling Nature Rev. Immunol. 4 44556 (Pubitemid 38745556)
    • (2004) Nature Reviews Immunology , vol.4 , Issue.6 , pp. 445-456
    • Goldstein, B.1    Faeder, J.R.2    Hlavacek, W.S.3
  • 28
    • 33747366698 scopus 로고    scopus 로고
    • Rules for modeling signal-transduction systems
    • 10.1126/stke.3442006re6 1525-8882
    • Hlavacek W S et al 2006 Rules for modeling signal-transduction systems Sci. STKE 2006 re6
    • (2006) Sci. STKE , vol.2006 , Issue.344 , pp. 6
    • Hlavacek, W.S.1
  • 29
    • 78649682240 scopus 로고    scopus 로고
    • Scalable rule-based modelling of allosteric proteins and biochemical networks
    • 10.1371/journal.pcbi.1000975 1553-7358 e1000975
    • Ollivier J F, Shahrezaei V and Swain P S 2010 Scalable rule-based modelling of allosteric proteins and biochemical networks PLoS Comput. Biol. 6 e1000975
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.11
    • Ollivier, J.F.1    Shahrezaei, V.2    Swain, P.S.3
  • 32
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • DOI 10.1038/35002125
    • Elowitz M B and Leibler S 2000 A synthetic oscillatory network of transcriptional regulators Nature 403 3358 (Pubitemid 30062393)
    • (2000) Nature , vol.403 , Issue.6767 , pp. 335-338
    • Elowitz, M.B.1    Leibier, S.2
  • 33
    • 77955443147 scopus 로고    scopus 로고
    • CplexA: A mathematica package to study macromolecular-assembly control of gene expression
    • 10.1093/bioinformatics/btq328 1367-4803
    • Vilar J M G and Saiz L 2010 CplexA: a mathematica package to study macromolecular-assembly control of gene expression Bioinformatics 26 20601
    • (2010) Bioinformatics , vol.26 , Issue.16 , pp. 2060-2061
    • Vilar, J.M.G.1    Saiz, L.2
  • 34
    • 0042622638 scopus 로고    scopus 로고
    • DNA looping and physical constraints on transcription regulation
    • DOI 10.1016/S0022-2836(03)00764-2
    • Vilar J M G and Leibler S 2003 DNA looping and physical constraints on transcription regulation J. Mol. Biol. 331 9819 (Pubitemid 36969959)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.5 , pp. 981-989
    • Vilar, J.M.G.1    Leibler, S.2
  • 35
    • 54049095551 scopus 로고    scopus 로고
    • Proteinprotein/DNA interaction networks: Versatile macromolecular structures for the control of gene expression
    • 10.1049/iet-syb:20080091 1751-8849
    • Saiz L and Vilar J M G 2008 Proteinprotein/DNA interaction networks: versatile macromolecular structures for the control of gene expression IET Syst. Biol. 2 24755
    • (2008) IET Syst. Biol. , vol.2 , Issue.5 , pp. 247-255
    • Saiz, L.1    Vilar, J.M.G.2
  • 37
    • 55849089592 scopus 로고    scopus 로고
    • Multilevel deconstruction of the in vivo behavior of looped DNAprotein complexes
    • 10.1371/journal.pone.0000355 1932-6203
    • Saiz L and Vilar J M G 2007 Multilevel deconstruction of the in vivo behavior of looped DNAprotein complexes PLoS ONE 2 e355
    • (2007) PLoS ONE , vol.2 , Issue.4 , pp. 355
    • Saiz, L.1    Vilar, J.M.G.2
  • 38
    • 0029938053 scopus 로고    scopus 로고
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
    • 10.1126/science.271.5253.1247 0036-8075
    • Lewis M et al 1996 Crystal structure of the lactose operon repressor and its complexes with DNA and inducer Science 271 124754
    • (1996) Science , vol.271 , Issue.5253 , pp. 1247-1254
    • Lewis, M.1
  • 42
    • 0022429106 scopus 로고
    • The or control system of bacteriophage lambda. A physicalchemical model for gene regulation
    • 10.1016/0022-2836(85)90086-5 0022-2836
    • Shea M A and Ackers G K 1985 The OR control system of bacteriophage lambda. A physicalchemical model for gene regulation J. Mol. Biol. 181 21130
    • (1985) J. Mol. Biol. , vol.181 , Issue.2 , pp. 211-230
    • Shea, M.A.1    Ackers, G.K.2
  • 43
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
    • Arkin A, Ross J and McAdams H H 1998 Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells Genetics 149 163348 (Pubitemid 28375939)
    • (1998) Genetics , vol.149 , Issue.4 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 46
    • 80052446671 scopus 로고    scopus 로고
    • Control of gene expression by modulated self-assembly
    • 10.1093/nar/gkr272 0305-1048
    • Vilar J M G and Saiz L 2011 Control of gene expression by modulated self-assembly Nucleic Acids Res. 39 685463
    • (2011) Nucleic Acids Res. , vol.39 , Issue.16 , pp. 6854-6863
    • Vilar, J.M.G.1    Saiz, L.2
  • 47
    • 79961190459 scopus 로고    scopus 로고
    • Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers
    • 1478-3975 044001
    • Teif V B and Rippe K 2011 Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers Phys. Biol. 8 044001
    • (2011) Phys. Biol. , vol.8 , Issue.4 , pp. 044001
    • Teif, V.B.1    Rippe, K.2
  • 48
    • 68049083831 scopus 로고    scopus 로고
    • Incorporating nucleosomes into thermodynamic models of transcription regulation
    • 10.1101/gr.088260.108 1088-9051
    • Raveh-Sadka T, Levo M and Segal E 2009 Incorporating nucleosomes into thermodynamic models of transcription regulation Genome Res. 19 148096
    • (2009) Genome Res. , vol.19 , Issue.8 , pp. 1480-1496
    • Raveh-Sadka, T.1    Levo, M.2    Segal, E.3
  • 49
    • 77955502318 scopus 로고    scopus 로고
    • Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate
    • 10.1371/journal.pcbi.1000771 1553-7358
    • Narula J et al 2010 Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate PLoS Comput. Biol. 6 e1000771
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.5 , pp. 1000771
    • Narula, J.1
  • 50
    • 58149354385 scopus 로고    scopus 로고
    • Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    • 10.1038/nature07521 0028-0836
    • Gertz J, Siggia E D and Cohen B A 2009 Analysis of combinatorial cis-regulation in synthetic and genomic promoters Nature 457 2158
    • (2009) Nature , vol.457 , Issue.7226 , pp. 215-218
    • Gertz, J.1    Siggia, E.D.2    Cohen, B.A.3
  • 51
    • 55549113874 scopus 로고    scopus 로고
    • A quantitative model of transcription factor-activated gene expression
    • 10.1038/nsmb.1500 1545-9993
    • Kim H D and OShea E K 2008 A quantitative model of transcription factor-activated gene expression Nature Struct. Mol. Biol. 15 11928
    • (2008) Nature Struct. Mol. Biol. , vol.15 , Issue.11 , pp. 1192-1198
    • Kim, H.D.1    Oshea, E.K.2
  • 52
    • 3042651100 scopus 로고    scopus 로고
    • Conformational spread: The propagation of allosteric states in large multiprotein complexes
    • DOI 10.1146/annurev.biophys.33.110502.132703
    • Bray D and Duke T 2004 Conformational spread: the propagation of allosteric states in large multiprotein complexes Annu. Rev. Biophys. Biomol. Struct. 33 5373 (Pubitemid 38829951)
    • (2004) Annual Review of Biophysics and Biomolecular Structure , vol.33 , pp. 53-73
    • Bray, D.1    Duke, T.2
  • 54
    • 0027209703 scopus 로고
    • Transition modes in Ising networks: An approximate theory for macromolecular recognition
    • Keating S and Di Cera E 1993 Transition modes in Ising networks: an approximate theory for macromolecular recognition Biophys. J. 65 25369 (Pubitemid 23206059)
    • (1993) Biophysical Journal , vol.65 , Issue.1 , pp. 253-269
    • Keating, S.1    Di Cera, E.2
  • 55
    • 23244465153 scopus 로고    scopus 로고
    • Signaling through receptors and scaffolds: Independent interactions reduce combinatorial complexity
    • DOI 10.1529/biophysj.105.060533
    • Borisov N M et al 2005 Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity Biophys. J. 89 95166 (Pubitemid 41098981)
    • (2005) Biophysical Journal , vol.89 , Issue.2 , pp. 951-966
    • Borisov, N.M.1    Markevich, N.I.2    Hoek, J.B.3    Kholodenko, B.N.4
  • 56
    • 0032492852 scopus 로고    scopus 로고
    • Receptor clustering as a cellular mechanism to control sensitivity
    • DOI 10.1038/30018
    • Bray D, Levin M D and Morton-Firth C J 1998 Receptor clustering as a cellular mechanism to control sensitivity Nature 393 858 (Pubitemid 28240260)
    • (1998) Nature , vol.393 , Issue.6680 , pp. 85-88
    • Bray, D.1    Levin, M.D.2    Morton-Firth, C.J.3
  • 58
    • 0037816259 scopus 로고    scopus 로고
    • Quantitative modeling of sensitivity in bacterial chemotaxis: The role of coupling among different chemoreceptor species
    • DOI 10.1073/pnas.1330839100
    • Mello B A and Tu Y 2003 Quantitative modeling of sensitivity in bacterial chemotaxis: the role of coupling among different chemoreceptor species Proc. Natl Acad. Sci. USA 100 82238 (Pubitemid 36842526)
    • (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , Issue.14 , pp. 8223-8228
    • Mello, B.A.1    Tu, Y.2
  • 59
    • 84857131710 scopus 로고    scopus 로고
    • Optimizing ring assembly reveals the strength of weak interactions
    • 10.1073/pnas.1113095109 0027-8424
    • Deeds E J, Bachman J A and Fontana W 2012 Optimizing ring assembly reveals the strength of weak interactions Proc. Natl Acad. Sci. USA 109 234853
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , Issue.7 , pp. 2348-2353
    • Deeds, E.J.1    Bachman, J.A.2    Fontana, W.3
  • 60
    • 80051726307 scopus 로고    scopus 로고
    • Theoretical assessment of the oligolysine model for ionic interactions in proteinDNA complexes
    • 10.1021/jp204915y 1520-6106 B
    • Fenley M O, Russo C and Manning G S 2011 Theoretical assessment of the oligolysine model for ionic interactions in proteinDNA complexes J. Phys. Chem. B 115 986472
    • (2011) J. Phys. Chem. , vol.115 , Issue.32 , pp. 9864-9872
    • Fenley, M.O.1    Russo, C.2    Manning, G.S.3
  • 61
    • 65249101772 scopus 로고    scopus 로고
    • Positively charged residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups
    • 10.1021/jp810009s 1520-6106 B
    • Cherstvy A G 2009 Positively charged residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups J. Phys. Chem. B 113 42427
    • (2009) J. Phys. Chem. , vol.113 , Issue.13 , pp. 4242-4247
    • Cherstvy, A.G.1
  • 62
    • 79151474415 scopus 로고    scopus 로고
    • Looping charged elastic rods: Applications to protein-induced DNA loop formation
    • 10.1007/s00249-010-0628-5 0175-7571
    • Cherstvy A G 2011 Looping charged elastic rods: applications to protein-induced DNA loop formation Eur. Biophys. J. 40 6980
    • (2011) Eur. Biophys. J. , vol.40 , Issue.1 , pp. 69-80
    • Cherstvy, A.G.1
  • 65
    • 0025343547 scopus 로고
    • The three operators of the lac operon cooperate in repression
    • 0261-4189
    • Oehler S et al 1990 The three operators of the lac operon cooperate in repression Embo J. 9 9739
    • (1990) Embo J. , vol.9 , pp. 973-979
    • Oehler, S.1
  • 68
    • 0002296942 scopus 로고
    • New algorithm for Monte-Carlo simulation of ising spin systems
    • 10.1016/0021-9991(75)90060-1 0021-9991
    • Bortz A B, Kalos M H and Lebowitz J L 1975 New algorithm for Monte-Carlo simulation of ising spin systems J. Comput. Phys. 17 108
    • (1975) J. Comput. Phys. , vol.17 , Issue.1 , pp. 10-18
    • Bortz, A.B.1    Kalos, M.H.2    Lebowitz, J.L.3
  • 69
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • DOI 10.1016/0021-9991(76)90041-3
    • Gillespie D T 1976 General method for numerically simulating stochastic time evolution of coupled chemical-reactions J. Comput. Phys. 22 40334 (Pubitemid 8008311)
    • (1976) Journal of Computational Physics , vol.22 , Issue.4 , pp. 403-434
    • Gillepsie, D.T.1
  • 70
    • 8844270181 scopus 로고    scopus 로고
    • Making the right choice - Long-range chromosomal interactions in development
    • DOI 10.1016/j.cell.2004.11.029, PII S0092867404010955
    • Broach J R 2004 Making the right choicelong-range chromosomal interactions in development Cell 119 5836 (Pubitemid 39535745)
    • (2004) Cell , vol.119 , Issue.5 , pp. 583-586
    • Broach, J.R.1
  • 72
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • DOI 10.1126/science.1070919
    • Elowitz M B et al 2002 Stochastic gene expression in a single cell Science 297 11836 (Pubitemid 36193353)
    • (2002) Science , vol.297 , Issue.5584 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 73
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • DOI 10.1038/nature02257
    • Paulsson J 2004 Summing up the noise in gene networks Nature 427 4158 (Pubitemid 38168488)
    • (2004) Nature , vol.427 , Issue.6973 , pp. 415-418
    • Paulsson, J.1
  • 74
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single-molecule level in a living cell
    • DOI 10.1126/science.1141967
    • Elf J, Li G W and Xie X S 2007 Probing transcription factor dynamics at the single-molecule level in a living cell Science 316 11914 (Pubitemid 46877481)
    • (2007) Science , vol.316 , Issue.5828 , pp. 1191-1194
    • Elf, J.1    Li, G.-W.2    Xie, X.S.3
  • 75
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • DOI 10.1126/science.1098641
    • Raser J M and OShea E K 2004 Control of stochasticity in eukaryotic gene expression Science 304 18114 (Pubitemid 38787899)
    • (2004) Science , vol.304 , Issue.5678 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 77
    • 78049281957 scopus 로고    scopus 로고
    • Accurate prediction of gene expression by integration of DNA sequence statistics with detailed modeling of transcription regulation
    • 10.1016/j.bpj.2010.08.006 0006-3495
    • Vilar J M G 2010 Accurate prediction of gene expression by integration of DNA sequence statistics with detailed modeling of transcription regulation Biophys. J. 99 240813
    • (2010) Biophys. J. , vol.99 , Issue.8 , pp. 2408-2413
    • Vilar, J.M.G.1
  • 79
    • 0035478585 scopus 로고    scopus 로고
    • Macromolecular crowding: Obvious but underappreciated
    • DOI 10.1016/S0968-0004(01)01938-7, PII S0968000401019387
    • Ellis R J 2001 Macromolecular crowding: obvious but underappreciated Trends Biochem. Sci. 26 597604 (Pubitemid 32925190)
    • (2001) Trends in Biochemical Sciences , vol.26 , Issue.10 , pp. 597-604
    • Ellis R.John1
  • 80
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • 10.1006/jmbi.1996.0143 0022-2836
    • Muller J, Oehler S and Muller-Hill B 1996 Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator J. Mol. Biol. 257 219
    • (1996) J. Mol. Biol. , vol.257 , Issue.1 , pp. 21-29
    • Muller, J.1    Oehler, S.2    Muller-Hill, B.3
  • 81
    • 0004211673 scopus 로고    scopus 로고
    • Ptashne M and Gann A 2002 Genes and Signals vol 16 (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press) p 192
    • (2002) Genes and Signals , vol.16 , pp. 192
    • Ptashne, M.1    Gann, A.2
  • 83
    • 19544379865 scopus 로고    scopus 로고
    • Localized single-stranded bubble mechanism for cyclization of short double helix DNA
    • 10.1103/PhysRevLett.93.108108 0031-9007 108108
    • Yan J and Marko J F 2004 Localized single-stranded bubble mechanism for cyclization of short double helix DNA Phys. Rev. Lett. 93 108108
    • (2004) Phys. Rev. Lett. , vol.93 , Issue.10
    • Yan, J.1    Marko, J.F.2
  • 87
    • 33645991551 scopus 로고    scopus 로고
    • Statistical-mechanical theory of DNA looping
    • 10.1529/biophysj.105.070490 0006-3495
    • Zhang Y et al 2006 Statistical-mechanical theory of DNA looping Biophys. J. 90 190312
    • (2006) Biophys. J. , vol.90 , Issue.6 , pp. 1903-1912
    • Zhang, Y.1
  • 89
    • 19444387811 scopus 로고    scopus 로고
    • Bacterial repression loops require enhanced DNA flexibility
    • DOI 10.1016/j.jmb.2005.04.035, PII S0022283605004559
    • Becker N A, Kahn J D and Maher L J 3rd 2005 Bacterial repression loops require enhanced DNA flexibility J. Mol. Biol. 349 71630 (Pubitemid 40725950)
    • (2005) Journal of Molecular Biology , vol.349 , Issue.4 , pp. 716-730
    • Becker, N.A.1    Kahn, J.D.2    Maher III, L.J.3
  • 90
    • 54749084305 scopus 로고    scopus 로고
    • Interconvertible lac repressorDNA loops revealed by single-molecule experiments
    • 10.1371/journal.pbio.0060232 1544-9173
    • Wong O K et al 2008 Interconvertible lac repressorDNA loops revealed by single-molecule experiments PLoS Biol. 6 e232
    • (2008) PLoS Biol. , vol.6 , Issue.9 , pp. 232
    • Wong, O.K.1
  • 91
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • DOI 10.1016/S1097-2765(04)00210-2, PII S1097276504002102
    • Cloutier T E and Widom J 2004 Spontaneous sharp bending of double-stranded DNA Mol. Cell 14 35562 (Pubitemid 38591406)
    • (2004) Molecular Cell , vol.14 , Issue.3 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 93
    • 0033552946 scopus 로고    scopus 로고
    • Robustness in bacterial chemotaxis
    • DOI 10.1038/16483
    • Alon U et al 1999 Robustness in bacterial chemotaxis Nature 397 16871 (Pubitemid 29050922)
    • (1999) Nature , vol.397 , Issue.6715 , pp. 168-171
    • Alon, U.1    Surette, M.G.2    Barkai, N.3    Leibler, S.4
  • 94
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • 10.1038/35011540 0028-0836
    • Hartwell L H et al 1999 From molecular to modular cell biology Nature 402 C4752
    • (1999) Nature , vol.402 , Issue.SUPPL.
    • Hartwell, L.H.1
  • 95
    • 0015231849 scopus 로고
    • Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems
    • 10.1038/229542a0 0028-0836
    • Savageau M A 1971 Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems Nature 229 5424
    • (1971) Nature , vol.229 , Issue.5286 , pp. 542-544
    • Savageau, M.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.