-
1
-
-
0030612613
-
Phage Ø29 Protein p6 is in a monomer-dimer equilibrium that shifts to higher association states at the millimolar concentrations found in vivo
-
Abril A.M., Salas M., Andreu J.M., Hermoso J.M., Rivas G. Phage Ø29 Protein p6 is in a monomer-dimer equilibrium that shifts to higher association states at the millimolar concentrations found in vivo. Biochemistry 1997, 36:11901-11908.
-
(1997)
Biochemistry
, vol.36
, pp. 11901-11908
-
-
Abril, A.M.1
Salas, M.2
Andreu, J.M.3
Hermoso, J.M.4
Rivas, G.5
-
2
-
-
9144232912
-
the universal protein knowledgebase
-
Nucleic Acids Res. 32, D115-D119, ID:Q9H0H5. (UniProt ID:Q9H0H5, accessed 15 June 2011) Uniprot
-
Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O'Donovan, C., Redaschi, N., Yeh, L.S.L., 2004. Uniprot: the universal protein knowledgebase. Nucleic Acids Res. 32, D115-D119, ID:Q9H0H5. (UniProt ID:Q9H0H5, accessed 15 June 2011). http://www.uniprot.org/uniprot/P0.
-
(2004)
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O'Donovan, C.13
Redaschi, N.14
Yeh, L.S.L.15
-
3
-
-
0015458929
-
DNA replication during development of competence in Bacillus subtilis
-
Barlati S. DNA replication during development of competence in Bacillus subtilis. Mol. Gen. Genet. 1972, 118:327-333.
-
(1972)
Mol. Gen. Genet.
, vol.118
, pp. 327-333
-
-
Barlati, S.1
-
4
-
-
17544365656
-
Kinetic and thermodynamic analysis of the interaction between TRAP (trp RNA-binding Attenuation Protein) of Bacillus subtilis and trp leader RNA
-
Baumann C., Otridge J., Gollnick P. Kinetic and thermodynamic analysis of the interaction between TRAP (trp RNA-binding Attenuation Protein) of Bacillus subtilis and trp leader RNA. J. Biol. Chem. 1996, 271:12269-12274.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 12269-12274
-
-
Baumann, C.1
Otridge, J.2
Gollnick, P.3
-
5
-
-
0034212551
-
Engineering stability in gene networks by auto regulation
-
Becskei A., Serrano L. Engineering stability in gene networks by auto regulation. Nature 2000, 405:590-593.
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
6
-
-
34247617729
-
Multiple feedback loop design in the tryptophan regulatory network of Escherichia coli suggests a paradigm for robust regulation of processes in series
-
Bhartiya S., Chaudhray N., Venkatesh K.V., Doyle F.J. Multiple feedback loop design in the tryptophan regulatory network of Escherichia coli suggests a paradigm for robust regulation of processes in series. J. R. Soc. Interface 2006, 3:383-391.
-
(2006)
J. R. Soc. Interface
, vol.3
, pp. 383-391
-
-
Bhartiya, S.1
Chaudhray, N.2
Venkatesh, K.V.3
Doyle, F.J.4
-
7
-
-
0018449390
-
A specific method for determination of free tryptophan and endogenous tryptophan in Escherichia coli
-
Bliss R.D. A specific method for determination of free tryptophan and endogenous tryptophan in Escherichia coli. Anal. Biochem. 1979, 93:390-398.
-
(1979)
Anal. Biochem.
, vol.93
, pp. 390-398
-
-
Bliss, R.D.1
-
8
-
-
0019974626
-
Role of feedback inhibition in stabilizing the classical operon
-
Bliss R.D., Painter P.R., Marr A.G. Role of feedback inhibition in stabilizing the classical operon. J. Theor. Biol. 1982, 97:177-193.
-
(1982)
J. Theor. Biol.
, vol.97
, pp. 177-193
-
-
Bliss, R.D.1
Painter, P.R.2
Marr, A.G.3
-
9
-
-
0000640710
-
Modulation of chemical composition and other parameters of the cell by growth rate
-
American Society of Microbiology, Washington, DC
-
Bremmer H., Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth rate. Escherichia coli and Salmonella thyphymurium: Cellular and Molecular Biology 1996, 2:1553-1569. American Society of Microbiology, Washington, DC.
-
(1996)
Escherichia coli and Salmonella thyphymurium: Cellular and Molecular Biology
, vol.2
, pp. 1553-1569
-
-
Bremmer, H.1
Dennis, P.P.2
-
10
-
-
0022539786
-
Growth kinetics of individual Bacillus subtilis cells and correlation with nucleoid extension
-
Burdett I.D.J., Kirkwood T.B.L., Whalley J.B. Growth kinetics of individual Bacillus subtilis cells and correlation with nucleoid extension. J. Bacteriol. 1986, 167:219-230.
-
(1986)
J. Bacteriol.
, vol.167
, pp. 219-230
-
-
Burdett, I.D.J.1
Kirkwood, T.B.L.2
Whalley, J.B.3
-
11
-
-
0025781628
-
Identification of amino acid residues involved in feedback regulation of the anthranilate synthase complex from Salmonella typhimurium
-
Caligiuri M.G., Bauerle R. Identification of amino acid residues involved in feedback regulation of the anthranilate synthase complex from Salmonella typhimurium. J. Biol. Chem. 1991, 266:8328-8335.
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 8328-8335
-
-
Caligiuri, M.G.1
Bauerle, R.2
-
12
-
-
18144386494
-
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
-
Cao Y, Gillespie D., Petzold L. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems. J. Comput. Phys. 2005, 206:395-411.
-
(2005)
J. Comput. Phys.
, vol.206
, pp. 395-411
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
13
-
-
0037477478
-
Tandem transcription and translation regulatory sensing of uncharged tryptophan tRNA
-
Chen G., Yanofsky C. Tandem transcription and translation regulatory sensing of uncharged tryptophan tRNA. Science 2003, 301:211-213.
-
(2003)
Science
, vol.301
, pp. 211-213
-
-
Chen, G.1
Yanofsky, C.2
-
14
-
-
40849126491
-
Alanine scanning mutagenesis of Anti-TRAP (AT) reveals residues involved in binding to TRAP
-
Chen Y., Gollnick P. Alanine scanning mutagenesis of Anti-TRAP (AT) reveals residues involved in binding to TRAP. J. Mol. Biol. 2008, 377:1529-1543.
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 1529-1543
-
-
Chen, Y.1
Gollnick, P.2
-
15
-
-
52949112270
-
Modeling molecular interaction Networks with nonlinear ordinary differential equations
-
Szallasi, Z., Stelling, J., Periwal, V. (Eds.), System Modeling in Cellular Biology: From concepts to Nuts and Bolts, London, England
-
Conrad, E.D., Tyson, J.J., 2006. Modeling molecular interaction Networks with nonlinear ordinary differential equations. In: Szallasi, Z., Stelling, J., Periwal, V. (Eds.), System Modeling in Cellular Biology: From concepts to Nuts and Bolts, London, England, pp. 97-123.
-
(2006)
, pp. 97-123
-
-
Conrad, E.D.1
Tyson, J.J.2
-
17
-
-
33846108256
-
Noise in transcription negative feedback loops: simulation and experimental analysis
-
Dublanche Y., Michalodimitrakis K., Kummerer N., Foglierini M., Serrano L. Noise in transcription negative feedback loops: simulation and experimental analysis. Mol. Syst. Biol. 2006, 2:1-12.
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 1-12
-
-
Dublanche, Y.1
Michalodimitrakis, K.2
Kummerer, N.3
Foglierini, M.4
Serrano, L.5
-
18
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1997, 81:2340-2361.
-
(1997)
J. Phys. Chem.
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
19
-
-
29144475324
-
Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis
-
Gollnick P., Babitzke P., Antson A., Yanofsky C. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu. Rev. Genet. 2005, 39:47-68.
-
(2005)
Annu. Rev. Genet.
, vol.39
, pp. 47-68
-
-
Gollnick, P.1
Babitzke, P.2
Antson, A.3
Yanofsky, C.4
-
20
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
Haseltine E.L., Rawlings J.B. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys. 2002, 117:6959-6969.
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 6959-6969
-
-
Haseltine, E.L.1
Rawlings, J.B.2
-
21
-
-
77149169402
-
Cycling expression and cooperative operator interaction in the trp operon of Escherichia coli
-
Hernández-Valdéz A., Santillán M., Zeron E.S. Cycling expression and cooperative operator interaction in the trp operon of Escherichia coli. J. Theor. Biol. 2010, 263:340-352.
-
(2010)
J. Theor. Biol.
, vol.263
, pp. 340-352
-
-
Hernández-Valdéz, A.1
Santillán, M.2
Zeron, E.S.3
-
22
-
-
19544379881
-
Stochasticity in gene expression: from theories to phenotypes
-
Kaern M., Elston T.C., Blake W.J., Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 2005, 6:451-464.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 451-464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
23
-
-
3242782478
-
Cellular levels of trp RNA-binding attenuation protein in Bacillus subtilis
-
McCabe B.C., Gollnick P. Cellular levels of trp RNA-binding attenuation protein in Bacillus subtilis. J. Bacteriol. 2004, 186:5157-5159.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 5157-5159
-
-
McCabe, B.C.1
Gollnick, P.2
-
24
-
-
0017400285
-
Age and evolution of bacteria
-
Müller H.E. Age and evolution of bacteria. Cell. Mol. Life Sci. 1977, 33:979-984.
-
(1977)
Cell. Mol. Life Sci.
, vol.33
, pp. 979-984
-
-
Müller, H.E.1
-
25
-
-
79952657402
-
Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system
-
Nguyen L.K., Kulasiri D. Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system. IET Syst. Biol. 2011, 5:145-156.
-
(2011)
IET Syst. Biol.
, vol.5
, pp. 145-156
-
-
Nguyen, L.K.1
Kulasiri, D.2
-
26
-
-
0035166979
-
The comprehensive microbial resource
-
(accessed 15 June 2011)
-
Peterson J.D., Umayam L.A., Dickinson T.M., Hickey E.K., White O. The comprehensive microbial resource. Nucleic Acids Res. 2001, 29:123-125. (accessed 15 June 2011).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.M.3
Hickey, E.K.4
White, O.5
-
27
-
-
0033787132
-
Ancient adaptation of the active site of tryptophanyl-tRNA synthetase for tryptophan binding
-
Praetorius-Ibba M., Stange-Thomann N., Kitabatake M., Ali K., Söll I., Carter C.W., Ibba M., Söll D. Ancient adaptation of the active site of tryptophanyl-tRNA synthetase for tryptophan binding. Biochemistry 2000, 39:13136-13143.
-
(2000)
Biochemistry
, vol.39
, pp. 13136-13143
-
-
Praetorius-Ibba, M.1
Stange-Thomann, N.2
Kitabatake, M.3
Ali, K.4
Söll, I.5
Carter, C.W.6
Ibba, M.7
Söll, D.8
-
28
-
-
25444468618
-
Noise in gene expression: origins, consequences, and control
-
Raser J.M., O'Shea E.K. Noise in gene expression: origins, consequences, and control. Science 2005, 309:2010-2013.
-
(2005)
Science
, vol.309
, pp. 2010-2013
-
-
Raser, J.M.1
O'Shea, E.K.2
-
29
-
-
77149174828
-
On the use of the Hill functions in mathematical models of gene regulatory networks
-
Santillán M. On the use of the Hill functions in mathematical models of gene regulatory networks. Math. Model. Nat. Phenom. 2008, 3:85-97.
-
(2008)
Math. Model. Nat. Phenom.
, vol.3
, pp. 85-97
-
-
Santillán, M.1
-
30
-
-
4544334943
-
Dynamic influence of feedback enzyme inhibition and transcription attenuation on the tryptophan operon response to nutritional shifts
-
Santillán M., Zeron E.S. Dynamic influence of feedback enzyme inhibition and transcription attenuation on the tryptophan operon response to nutritional shifts. J. Theor. Biol. 2004, 231:287-298.
-
(2004)
J. Theor. Biol.
, vol.231
, pp. 287-298
-
-
Santillán, M.1
Zeron, E.S.2
-
31
-
-
0029781898
-
Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis
-
Sauer U., Hatzimanikatis V., Hohmann H.P., Manneberg M., van Loon A.P., Bailey J.E. Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis. Appl. Environ. Microbiol. 1996, 62:3687-3696.
-
(1996)
Appl. Environ. Microbiol.
, vol.62
, pp. 3687-3696
-
-
Sauer, U.1
Hatzimanikatis, V.2
Hohmann, H.P.3
Manneberg, M.4
van Loon, A.P.5
Bailey, J.E.6
-
32
-
-
56249130793
-
Analytical distributions for stochastic gene expression
-
Shahrezaei V., Swain P.S. Analytical distributions for stochastic gene expression. Proc. Natl. Acad. Sci. USA 2008, 105:17256-17261.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 17256-17261
-
-
Shahrezaei, V.1
Swain, P.S.2
-
33
-
-
29144481616
-
Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction
-
Shevtsov M.B., Chen Y., Gollnick P., Antson A.A. Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction. Proc. Natl. Acad. Sci. 2005, 102:17600-17605.
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 17600-17605
-
-
Shevtsov, M.B.1
Chen, Y.2
Gollnick, P.3
Antson, A.A.4
-
34
-
-
0024278213
-
Theoretical study of tryptophan operon: applications in microbial technology
-
Sinha S. Theoretical study of tryptophan operon: applications in microbial technology. Biotechnol. Bioeng. 1988, 31:117-124.
-
(1988)
Biotechnol. Bioeng.
, vol.31
, pp. 117-124
-
-
Sinha, S.1
-
36
-
-
0032753202
-
Free energy calculations of Watson-Crick base pairing in aqueous solution
-
Stofer E., Chipot C, Lavery R. Free energy calculations of Watson-Crick base pairing in aqueous solution. J. Am. Chem. Soc. 1999, 121:9503-9508.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 9503-9508
-
-
Stofer, E.1
Chipot, C.2
Lavery, R.3
-
37
-
-
0345863934
-
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
-
(accessed 14 June 2011)
-
Sundararaj S., Guo A., Habibi-Nazhad B., Rouani M., Stothard P., Ellison M M., David S., Wishart D.S. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2003, 32:D293-D295. (accessed 14 June 2011).
-
(2003)
Nucleic Acids Res.
, vol.32
-
-
Sundararaj, S.1
Guo, A.2
Habibi-Nazhad, B.3
Rouani, M.4
Stothard, P.5
Ellison M, M.6
David, S.7
Wishart, D.S.8
-
38
-
-
0035902599
-
Intrinsic noise in gene regulatory networks
-
Thattai M., Oudenaarden A.V. Intrinsic noise in gene regulatory networks. PNAS 2001, 98:8614-8619.
-
(2001)
PNAS
, vol.98
, pp. 8614-8619
-
-
Thattai, M.1
Oudenaarden, A.V.2
-
39
-
-
0035860533
-
Inhibition of the B. subtilis regulatory protein TRAP by the TRAP-Inhibitory protein, AT,
-
Valbuzzi A., Yanofsky C. Inhibition of the B. subtilis regulatory protein TRAP by the TRAP-Inhibitory protein, AT,. Science 2001, 293:2057-2059.
-
(2001)
Science
, vol.293
, pp. 2057-2059
-
-
Valbuzzi, A.1
Yanofsky, C.2
-
40
-
-
0141454823
-
Ancient origin of the tryptophan operon and the dynamics of evolutionary change
-
Xie G., Keyhani N.O., Bonner C.A., Jensen R.A. Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol. Mol. Biol. Rev. 2003, 67:303-342.
-
(2003)
Microbiol. Mol. Biol. Rev.
, vol.67
, pp. 303-342
-
-
Xie, G.1
Keyhani, N.O.2
Bonner, C.A.3
Jensen, R.A.4
-
41
-
-
0034811041
-
Expression of the Bacillus subtilis trpEDCFBA Operon is influenced by translational coupling and Rho termination factor
-
Yakhnin H., Babiarz J.E., Yakhnin A.V, Babitzke P. Expression of the Bacillus subtilis trpEDCFBA Operon is influenced by translational coupling and Rho termination factor. J. Bacteriol. 2001, 183:5918-5926.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 5918-5926
-
-
Yakhnin, H.1
Babiarz, J.E.2
Yakhnin, A.V.3
Babitzke, P.4
-
42
-
-
14644440509
-
Effects of tryptophan starvation on levels of the trp RNA-binding attenuation protein (TRAP) and Anti-TRAP regulatory protein and their influence on trp operon expression in Bacillus subtilis
-
Yang W.J, Yanofsky C. Effects of tryptophan starvation on levels of the trp RNA-binding attenuation protein (TRAP) and Anti-TRAP regulatory protein and their influence on trp operon expression in Bacillus subtilis. J. Bacteriol. 2005, 187:1884-1891.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 1884-1891
-
-
Yang, W.J.1
Yanofsky, C.2
-
43
-
-
3242668172
-
The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis
-
Yanofsky C. The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis. Trends Genet. 2004, 20:367-374.
-
(2004)
Trends Genet.
, vol.20
, pp. 367-374
-
-
Yanofsky, C.1
-
44
-
-
34447528966
-
RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria
-
Yanofsky C. RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria. RNA 2007, 13:1141-1154.
-
(2007)
RNA
, vol.13
, pp. 1141-1154
-
-
Yanofsky, C.1
-
45
-
-
77951652447
-
Distributions for negative-feedback-regulated stochastic gene expression: dimension reduction and numerical solution of the chemical master equation
-
Zeron E.S., Santillán M. Distributions for negative-feedback-regulated stochastic gene expression: dimension reduction and numerical solution of the chemical master equation. J. Theor. Biol. 2010, 264:377-385.
-
(2010)
J. Theor. Biol.
, vol.264
, pp. 377-385
-
-
Zeron, E.S.1
Santillán, M.2
|