메뉴 건너뛰기




Volumn 92, Issue 8, 2007, Pages 2685-2693

A quantitative study of λ-phage SWITCH and its components

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN CRO; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 34147185608     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.097089     Document Type: Article
Times cited : (14)

References (45)
  • 1
    • 4444293086 scopus 로고    scopus 로고
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Ptashne, M. 2004. A Genetic Switch. 3rd. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (2004) A Genetic Switch. 3rd
    • Ptashne, M.1
  • 2
    • 4444256116 scopus 로고    scopus 로고
    • Regulatory circuit design and evolution using phage lambda
    • Atsumi, S., and J. W. Little. 2004. Regulatory circuit design and evolution using phage lambda. Genes Dev. 18:2086-2094.
    • (2004) Genes Dev , vol.18 , pp. 2086-2094
    • Atsumi, S.1    Little, J.W.2
  • 3
    • 0035890132 scopus 로고    scopus 로고
    • Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny
    • Dodd, I. B., A. J. Perkins, D. Tsemitsidis, and J. B. Egan. 2001. Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev. 15:3013-3022.
    • (2001) Genes Dev , vol.15 , pp. 3013-3022
    • Dodd, I.B.1    Perkins, A.J.2    Tsemitsidis, D.3    Egan, J.B.4
  • 5
    • 0033517148 scopus 로고    scopus 로고
    • Robustness of a gene regulatory circuit
    • Little, J. W., D. P. Shepley, and D. W. Wert. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
    • (1999) EMBO J , vol.18 , pp. 4299-4307
    • Little, J.W.1    Shepley, D.P.2    Wert, D.W.3
  • 7
    • 0034703473 scopus 로고    scopus 로고
    • Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding II: Cooperative interactions of cro dimers
    • Darling, P. J., J. M. Holt, and G. K. Ackers. 2000. Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding II: cooperative interactions of cro dimers. J. Mol. Biol. 302:625-638.
    • (2000) J. Mol. Biol , vol.302 , pp. 625-638
    • Darling, P.J.1    Holt, J.M.2    Ackers, G.K.3
  • 8
    • 0001422329 scopus 로고
    • Quantitative model for gene regulation by lambda phage repressor
    • Ackers, G. K., A. D. Johnson, and M. A. Shea. 1982. Quantitative model for gene regulation by lambda phage repressor. Proc. Natl. Acad. Sci. USA. 79:1129-1133.
    • (1982) Proc. Natl. Acad. Sci. USA , vol.79 , pp. 1129-1133
    • Ackers, G.K.1    Johnson, A.D.2    Shea, M.A.3
  • 9
    • 0025122786 scopus 로고
    • Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity
    • Reinitz, J., and J. R. Vaisnys. 1990. Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity. J. Theor. Biol. 145:295-318.
    • (1990) J. Theor. Biol , vol.145 , pp. 295-318
    • Reinitz, J.1    Vaisnys, J.R.2
  • 10
    • 4243911221 scopus 로고    scopus 로고
    • Epigenetics as a first exit problem
    • Aurell, E., and K. Sneppen. 2002. Epigenetics as a first exit problem. Phys. Rev. Lett. 88:048101.
    • (2002) Phys. Rev. Lett , vol.88 , pp. 048101
    • Aurell, E.1    Sneppen, K.2
  • 11
    • 7644234438 scopus 로고    scopus 로고
    • Calculating biological behaviors of epigenetic states in the phage lambda life cycle
    • Zhu, X. M., L. Yin, L. Hood, and P. Ao. 2004. Calculating biological behaviors of epigenetic states in the phage lambda life cycle. Funct. Integr. Genomics. 4:188-195.
    • (2004) Funct. Integr. Genomics , vol.4 , pp. 188-195
    • Zhu, X.M.1    Yin, L.2    Hood, L.3    Ao, P.4
  • 12
    • 5644304343 scopus 로고    scopus 로고
    • Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda
    • Bakk, A., and R. Metzler. 2004. Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda. J. Theor. Biol. 231:525-533.
    • (2004) J. Theor. Biol , vol.231 , pp. 525-533
    • Bakk, A.1    Metzler, R.2
  • 13
    • 1842788224 scopus 로고    scopus 로고
    • In vivo non-specific binding of lambda CI and Cro repressors is significant
    • Bakk, A., and R. Metzler. 2004. In vivo non-specific binding of lambda CI and Cro repressors is significant. FEBS Lett. 563:66-68.
    • (2004) FEBS Lett , vol.563 , pp. 66-68
    • Bakk, A.1    Metzler, R.2
  • 14
    • 0346057952 scopus 로고    scopus 로고
    • Sensitivity of OR in phage lambda
    • Bakk, A., R. Metzler, and K. Sneppen. 2004. Sensitivity of OR in phage lambda. Biophys. J. 86:58-66.
    • (2004) Biophys. J , vol.86 , pp. 58-66
    • Bakk, A.1    Metzler, R.2    Sneppen, K.3
  • 15
    • 0346688719 scopus 로고    scopus 로고
    • Why the lysogenic state of phage lambda is so stable: A mathematical modeling approach
    • Santillan, M., and M. C. Mackey. 2004. Why the lysogenic state of phage lambda is so stable: a mathematical modeling approach. Biophys. J. 86:75-84.
    • (2004) Biophys. J , vol.86 , pp. 75-84
    • Santillan, M.1    Mackey, M.C.2
  • 16
    • 0344630293 scopus 로고    scopus 로고
    • On the relation between fluctuation and response in biological systems
    • Sato, K., Y. Ito, T. Yomo, and K. Kaneko. 2003. On the relation between fluctuation and response in biological systems. Proc. Natl. Acad. Sci. USA. 100:14086-14090.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 14086-14090
    • Sato, K.1    Ito, Y.2    Yomo, T.3    Kaneko, K.4
  • 17
    • 15744396343 scopus 로고    scopus 로고
    • Revisited gene regulation in bacteriophage lambda
    • Dodd, I. B., K. E. Shearwin, and J. B. Egan. 2005. Revisited gene regulation in bacteriophage lambda. Curr. Opin. Genet. Dev. 15:145-152.
    • (2005) Curr. Opin. Genet. Dev , vol.15 , pp. 145-152
    • Dodd, I.B.1    Shearwin, K.E.2    Egan, J.B.3
  • 18
    • 15744393452 scopus 로고    scopus 로고
    • DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise
    • Vilar, J. M., and L. Saiz. 2005. DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr. Opin. Genet. Dev. 15:136-144.
    • (2005) Curr. Opin. Genet. Dev , vol.15 , pp. 136-144
    • Vilar, J.M.1    Saiz, L.2
  • 19
    • 0019887628 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
    • Berg, O. G., R. B. Winter, and P. H. von Hippel. 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    Winter, R.B.2    von Hippel, P.H.3
  • 20
    • 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., O. G. Berg, and P. H. von Hippel. 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    Berg, O.G.2    von Hippel, P.H.3
  • 21
    • 0032986554 scopus 로고    scopus 로고
    • One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements
    • Shimamoto, N. 1999. One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements. J. Biol. Chem. 274:15293-15296.
    • (1999) J. Biol. Chem , vol.274 , pp. 15293-15296
    • Shimamoto, N.1
  • 22
    • 18044403216 scopus 로고    scopus 로고
    • Dynamics of DNA-protein interaction deduced from in vitro DNA evolution
    • Dubertret, B., S. Liu, Q. Ouyang, and A. Libchaber. 2001. Dynamics of DNA-protein interaction deduced from in vitro DNA evolution. Phys. Rev. Lett. 86:6022-6025.
    • (2001) Phys. Rev. Lett , vol.86 , pp. 6022-6025
    • Dubertret, B.1    Liu, S.2    Ouyang, Q.3    Libchaber, A.4
  • 23
    • 0037451299 scopus 로고    scopus 로고
    • Protein motion from non-specific to specific DNA by three-dimensional routes aided by super-coiling
    • Gowers, D. M., and S. E. Halford. 2003. Protein motion from non-specific to specific DNA by three-dimensional routes aided by super-coiling. EMBO J. 22:1410-1418.
    • (2003) EMBO J , vol.22 , pp. 1410-1418
    • Gowers, D.M.1    Halford, S.E.2
  • 24
    • 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., G. G. Wilson, and S. E. Halford. 2005. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. USA. 102:15883-15888.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15883-15888
    • Gowers, D.M.1    Wilson, G.G.2    Halford, S.E.3
  • 26
  • 27
    • 30344463841 scopus 로고    scopus 로고
    • Optimal target search on a fast-folding polymer chain with volume exchange
    • Lomholt, M. A., T. Ambjornsson, and R. Metzler. 2005. Optimal target search on a fast-folding polymer chain with volume exchange. Phys. Rev. Lett. 95:260603.
    • (2005) Phys. Rev. Lett , vol.95 , pp. 260603
    • Lomholt, M.A.1    Ambjornsson, T.2    Metzler, R.3
  • 28
    • 21244475671 scopus 로고    scopus 로고
    • A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: Dependence on DNA length and presence of obstacles
    • Zhou, H. X. 2005. A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles. Biophys. J. 88:1608-1615.
    • (2005) Biophys. J , vol.88 , pp. 1608-1615
    • Zhou, H.X.1
  • 29
    • 4444236055 scopus 로고    scopus 로고
    • Kinetics of target site localization of a protein on DNA: A stochastic approach
    • Coppey, M., O. Benichou, R. Voituriez, and M. Moreau. 2004. Kinetics of target site localization of a protein on DNA: a stochastic approach. Biophys. J. 87:1640-1649.
    • (2004) Biophys. J , vol.87 , pp. 1640-1649
    • Coppey, M.1    Benichou, O.2    Voituriez, R.3    Moreau, M.4
  • 30
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
    • Slutsky, M., and L. A. Mirny. 2004. Kinetics of protein-DNA interaction: 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
  • 31
    • 33645816459 scopus 로고    scopus 로고
    • How proteins search for their specific sites on DNA: The role of DNA conformation
    • Hu, T., A. Y. Grosberg, and B. I. Shklovskii. 2006. How proteins search for their specific sites on DNA: the role of DNA conformation. Biophys. J. 90:2731-2744.
    • (2006) Biophys. J , vol.90 , pp. 2731-2744
    • Hu, T.1    Grosberg, A.Y.2    Shklovskii, B.I.3
  • 32
    • 0024531901 scopus 로고
    • Facilitated target location in biological systems
    • von Hippel, P. H., and O. G. Berg. 1989. Facilitated target location in biological systems. J. Biol. Chem. 264:675-678.
    • (1989) J. Biol. Chem , vol.264 , pp. 675-678
    • von Hippel, P.H.1    Berg, O.G.2
  • 33
    • 2042475515 scopus 로고
    • Nonspecific DNA binding of genome regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli Lac repressor in vivo
    • Huang, Y. K., A. Revzin, A. P. Butler, P. O'Conner, D. W. Noble, and P. H. Von Hippel. 1977. Nonspecific DNA binding of genome regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli Lac repressor in vivo. Proc. Natl. Acad. Sci. USA. 74:4228-4232.
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , pp. 4228-4232
    • Huang, Y.K.1    Revzin, A.2    Butler, A.P.3    O'Conner, P.4    Noble, D.W.5    Von Hippel, P.H.6
  • 34
    • 0031453895 scopus 로고    scopus 로고
    • The role of DNA bending in Cro protein-DNA interactions
    • Gromiha, M. M., M. G. Munteanu, I. Simon, and S. Pongor. 1997. The role of DNA bending in Cro protein-DNA interactions. Biophys. Chem. 69:153-160.
    • (1997) Biophys. Chem , vol.69 , pp. 153-160
    • Gromiha, M.M.1    Munteanu, M.G.2    Simon, I.3    Pongor, S.4
  • 35
    • 0036013781 scopus 로고    scopus 로고
    • Is there a code for protein-DNA recognition? Probab(ilistical)ly
    • Benos, P. V., A. S. Lapedes, and G. D. Stormo. 2002. Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays. 24:466-475.
    • (2002) Bioessays , vol.24 , pp. 466-475
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 36
    • 33744821974 scopus 로고    scopus 로고
    • Saiz, L., and J. M. Vilar. 2006. Stochastic dynamics of macromolecular-assembly networks. Mol. Syst. Biol. 2:2006.0024 (Epub ahead of print).
    • Saiz, L., and J. M. Vilar. 2006. Stochastic dynamics of macromolecular-assembly networks. Mol. Syst. Biol. 2:2006.0024 (Epub ahead of print).
  • 37
    • 1842607238 scopus 로고    scopus 로고
    • Secondary structure switching in Cro protein evolution
    • Newlove, T., J. H. Konieczka, and M. H. Cordes. 2004. Secondary structure switching in Cro protein evolution. Structure. 12:569-581.
    • (2004) Structure , vol.12 , pp. 569-581
    • Newlove, T.1    Konieczka, J.H.2    Cordes, M.H.3
  • 38
    • 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
  • 39
    • 22144443131 scopus 로고    scopus 로고
    • Nonlinear protein degradation and the function of genetic circuits
    • Buchler, N. E., U. Gerland, and T. Hwa. 2005. Nonlinear protein degradation and the function of genetic circuits. Proc. Natl. Acad. Sci. USA. 102:9559-9564.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 9559-9564
    • Buchler, N.E.1    Gerland, U.2    Hwa, T.3
  • 40
    • 0014945080 scopus 로고
    • Immunity phase-shift in defective lysogens: Non-mutational hereditary change of early regulation of lambda prophage
    • Neubauer, Z., and E. Calef. 1970. Immunity phase-shift in defective lysogens: non-mutational hereditary change of early regulation of lambda prophage. J. Mol. Biol. 51:1-13.
    • (1970) J. Mol. Biol , vol.51 , pp. 1-13
    • Neubauer, Z.1    Calef, E.2
  • 41
    • 0017649239 scopus 로고
    • The essential role of the cro gene in lytic development by bacteriophage lambda
    • Folkmanis, A., W. Maltzman, P. Mellon, A. Skalka, and H. Echols. 1977. The essential role of the cro gene in lytic development by bacteriophage lambda. Virology. 81:352-362.
    • (1977) Virology , vol.81 , pp. 352-362
    • Folkmanis, A.1    Maltzman, W.2    Mellon, P.3    Skalka, A.4    Echols, H.5
  • 44
    • 0037418253 scopus 로고    scopus 로고
    • Retroevolution of lambda Cro toward a stable monomer
    • LeFevre, K. R., and M. H. Cordes. 2003. Retroevolution of lambda Cro toward a stable monomer. Proc. Natl. Acad. Sci. USA. 100:2345-2350.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 2345-2350
    • LeFevre, K.R.1    Cordes, M.H.2
  • 45
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
    • Arkin, A., J. Ross, and H. H. McAdams. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 149:1633-1648.
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.