Team:EPF-Lausanne/References

 

 

 

 

References


 * 1) Purcell EB, Crosson S. Photoregulation in prokaryotes.  Curr Opin Microbiol. 2008 Apr;11(2):168-78. Epub 2008 Apr 8. Review. Link
 * 2) Strickland et al. Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences (2008) vol. 105 (31) pp. 10709 [[Media:Light-activated.pdf‎ | Article]]
 * 3) Ávila-Pérez et al. Blue Light Activates the σB-Dependent Stress Response of Bacillus subtilis via YtvA. Journal of bacteriology (2006) [[Media:Blue-light_in_b.subtilis.pdf | Article]]
 * 4) Jaubert et al. Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR. Journal of Biological Chemistry (2004) [[Media:Light_and_Redox_Control_of_Photosynthesis_Gene_Expression.pdf‎ | Article]]
 * 5) Lawson et al. E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure (2004) vol. 12 (6) pp. 1099-1108 Link
 * 6) Cusanovich and Meyer.Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.  Biochemistry, 42, 4759-4770.  (2003) Link
 * 7) Harper et al. Structural basis of a phototropin light switch. Science (2003) Link
 * 8) Baliga et al. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proceedings of the National Academy of Sciences (2002) vol. 99 (23) pp. 14913-14918 [[Media:Coordinate_regulation_of_energy_transduction_modules.pdf‎ | Article]] Supporting information
 * 9) Baliga et al. Genomic and genetic dissection of an archaeal regulon. Proceedings of the National Academy of Sciences (2001) vol. 98 (5) pp. 2521 [[Media: Genomic_and_genetic_dissection_of_an_archaeal_regulon.pdf‎ | Article]]
 * 10) Reedstrom et al. Affinity and specificity of trp repressor-DNA interactions studied with fluorescent oligonucleotides. Journal of Molecular Biology (1997) vol. 273 (3) pp. 572-585
 * 11) Gropp and Betlach. The bat gene of Halobacterium halobium encodes a trans-acting oxygen inducibility factor. Proceedings of the National Academy of Sciences (1994) [[Media:The_bat_gene_of_Halobacterium_halobium.pdf‎ | Article]]
 * 12) Shand and Betlach. Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by light. Journal of bacteriology (1991) [[Media:Expression_of_the_bop_Gene_Cluster.pdf | Article]]
 * 13) Bass et al. Mutant Trp repressors with new DNA-binding specificities. Science (1988) vol. 242 (4876) pp. 240-245, find here
 * 14) Bass et al. DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes &amp; Development (1987) vol. 1 (6) pp. 565-572
 * 15) Giraud et al. Bacteriophytochrome and regulation of the synthesis of the photosynthetic apparatus in Rhodopseudomonas palustris: pitfalls of using laboratory strainsPhotochem.Photobiol.Sci., 2004, 3, 587-591.
 * 16) Allen Introduction to Molecular Dynamics Simulation published in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer(Eds.), John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 23, ISBN3-00-012641-4, pp. 1-28, 2004.  [[Media:Introduction_to_molecular_Dynamics_Simulation.pdf | Article]]
 * 17) Koyama et al. Different role of the Ja Helix in the light-induced activation of the LOV2 domains in various phototropins Biochemistry 2009, 48, 7621-7628 7621.

Media we used
An interesting course on TrpR and Trp operon: TrpR

Biobricks

Characterizes E.Coli Trp repressor, and the Trp operon sequence : Summary of what characterizes E.Coli Trp repressor : [[Media:The_tryptophan_biosynthetic_pathway.pdf|The tryptophan biosynthetic pathway]] One good article : [[Media:RNA-based_regulation_of_genes_of_tryptophan_synthesis_an_degradation.pdf‎|RNA-based regulation of genes of tryptophan synthesis and degradation]] Protein sequence from NCBI [[Media:Sequence_du_Trp_repressor.txt|here‎‎]]

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