Team:ESBS-Strasbourg/Project/Reference

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<div class="heading">References</div>
<div class="heading">References</div>
<div class="desc">
<div class="desc">
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<ul>
<ul>
<font>
<font>
-
<li><p ALIGN="LEFT">Baker, T. A., R. T. Sauer, et al. (2005). &quot;Versatile modes of  
+
<li><p ALIGN="LEFT">
-
peptide recognition by the AAA+ adaptor protein SspB.&quot; <u>Nat Struct Mol Biol</u> <b>12</b>(6): 520-5.</p></li>
+
[1] Baker, T. A., R. T. Sauer, et al. </span>
-
<li><p ALIGN="LEFT">Fussenegger, M., M. Tigges, et al. (2009). &quot;A tunable synthetic  
+
<span>(2009).
-
mammalian oscillator.&quot; <u>Nature</u> <b>457</b>(7227):  
+
&quot;Engineering synthetic adaptors and substrates for controlled ClpXP
-
309-12.</p></li>
+
degradation.&quot; <u>J Biol Chem </u><b>284</b>(33): 21848-55.</span></p></li>
-
<li><p ALIGN="LEFT">Goldberg, A. L. (2003). &quot;Protein degradation and protection  
+
<li><p ALIGN="LEFT">
-
against misfolded or damaged proteins.&quot; <u>Nature</u> <b>426</b>(6968):  
+
[2] Baker, T. A., R. T. Sauer, et al. </span>
-
895-9.</p></li>
+
<span>(2009).
-
<li><p ALIGN="LEFT">Gregersen, N., C. B. Pedersen, et al. (2003). &quot;Misfolding,  
+
&quot;Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a
-
degradation, and aggregation of variant proteins. The molecular pathogenesis of  
+
AAA+ protein-unfolding machine.&quot; <u>Cell</u> <b>139</b>(4): 744-56.</span></p></li>
-
short chain acyl-CoA dehydrogenase (SCAD) deficiency.&quot; <u>J Biol Chem</u> <b>278</b>(48): 47449-58.</p></li>
+
<li><p ALIGN="LEFT">
-
<li><p ALIGN="LEFT">Grossman, A. D. and K. L. Griffith (2008). &quot;Inducible protein  
+
[3] Baker, T. A., R. T. Sauer, et al. </span>
-
degradation in Bacillus subtilis using heterologous peptide tags and adaptor  
+
<span>(2010).
-
proteins to target substrates to the protease ClpXP.&quot; <u>Mol Microbiol</u> <b>70</b>(4): 1012-25.</p></li>
+
&quot;Control of substrate gating and translocation into ClpP by channel residues and
-
<li><p ALIGN="LEFT">Houry, W. A., U. A. Wojtyra, et al. (2003). &quot;The N-terminal zinc  
+
ClpX binding.&quot; <u>J Mol Biol</u> <b>399</b>(5): 707-18.</span></p></li>
-
binding domain of ClpX is a dimerization domain that modulates the chaperone  
+
<p>
-
function.&quot; <u>J Biol Chem</u> <b>278</b>(49): 48981-90.</p></li>
+
<li><p ALIGN="LEFT">[4] Baker,
-
<li><p ALIGN="LEFT">Hughes, J., F. T. Landgraf, et al. (2001). &quot;Recombinant  
+
T. A., R. T. Sauer, et al. (2005). &quot;Versatile modes of peptide recognition by  
-
holophytochrome in Escherichia coli.&quot; <u>FEBS Lett</u> <b>508</b>(3):  
+
the AAA+ adaptor protein SspB.&quot; <u>Nat Struct Mol Biol</u> <b>12</b>(6): 520-5.</span></p></li>
-
459-62.</p></li>
+
<p>
-
<li><p ALIGN="LEFT">Kohchi, T., K. Mukougawa, et al. (2006). &quot;Metabolic engineering  
+
<li><p ALIGN="LEFT">[5] Baker,
-
to produce phytochromes with phytochromobilin, phycocyanobilin, or  
+
T. A., R. T. Sauer, et al. (2005). &quot;Rebuilt AAA + motors reveal operating
-
phycoerythrobilin chromophore in Escherichia coli.&quot; <u>FEBS Lett</u> <b>580</b>(5): 1333-8.</p></li>
+
principles for ATP-fuelled machines.&quot; </span><u>
-
<li><p ALIGN="LEFT">Maurizi, M. R., R. Grimaud, et al. (1998). &quot;Enzymatic and  
+
<span>
-
structural similarities between the Escherichia coli ATP-dependent proteases,  
+
Nature</span></u><span>
-
ClpXP and ClpAP.&quot; <u>J Biol Chem</u> <b>273</b>(20):  
+
<b>437</b>(7062): 1115-20.</span></p></li>
-
12476-81.</p></li>
+
<li><p ALIGN="LEFT">
-
<li><p ALIGN="LEFT">Moffat, K. and A. Moglich (2010). &quot;Engineered photoreceptors as  
+
[6] Baker, T. A., R. T. Sauer, et al. </span>
-
novel optogenetic tools.&quot; <u>Photochem Photobiol Sci</u> <b>9</b>(10):  
+
<span>(2006).
-
1286-300.</p></li>
+
&quot;Engineering controllable protein degradation.&quot; <u>Mol Cell</u> <b>22</b>(5):
-
<li><p ALIGN="LEFT">Moroder, L. and C. Renner (2006). &quot;Azobenzene as conformational  
+
701-7.</span></p></li>
-
switch in model peptides.&quot; <u>Chembiochem</u> <b>7</b>(6):  
+
<li><p ALIGN="LEFT">
-
868-78.</p></li>
+
[7] Baker, T. A., R. T. Sauer, et al. </span>
-
<li><p ALIGN="LEFT">Morrison, D. A. and S. Ahlawat (2009). &quot;ClpXP degrades SsrA-tagged  
+
<span>(2007).
-
proteins in Streptococcus pneumoniae.&quot; <u>J Bacteriol</u> <b>
+
&quot;Altered tethering of the SspB adaptor to the ClpXP protease causes changes in
-
191</b>(8): 2894-8.</p></li>
+
substrate delivery.&quot; <u>J Biol Chem</u> <b>282</b>(15): 11465-73.</span></p></li>
-
<li><p ALIGN="LEFT">Quail, P. H., R. Khanna, et al. (2004). &quot;A novel molecular
+
<li><p ALIGN="LEFT">
-
recognition motif necessary for targeting photoactivated phytochrome signaling
+
[8] Deisseroth, K., F. Zhang, et al. </span>
-
to specific basic helix-loop-helix transcription factors.&quot; <u>Plant Cell</u> <b>16</b>(11): 3033-44.</p></li>
+
<span>(2006).
-
<li><p ALIGN="LEFT">Rosen, M. K., D. W. Leung, et al. (2008). &quot;Genetically encoded
+
&quot;Channelrhodopsin-2 and optical control of excitable cells.&quot; <u>Nat Methods</u>
-
photoswitching of assembly through the Cdc42-WASP-Arp2/3 complex pathway.&quot;  
+
<b>3</b>(10): 785-92.</span></p></li>
-
<u>Proc Natl Acad Sci U S A</u> <b>105</b>(35): 12797-802.</p></li>
+
<p>
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2009). &quot;Engineering synthetic
+
<li><p ALIGN="LEFT">[9]
-
adaptors and substrates for controlled ClpXP degradation.&quot; <u>J Biol Chem</u> <b>284</b>(33): 21848-55.</p></li>
+
Fussenegger, M., M. Tigges, et al. (2009). &quot;A tunable synthetic mammalian  
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2009). &quot;Structures of
+
oscillator.&quot; <u>Nature</u> <b>457</b>(7227): 309-12.</span></p></li>
-
asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+
+
<p>
-
protein-unfolding machine.&quot; <u>Cell</u> <b>139</b>(4):  
+
<li><p ALIGN="LEFT">[10]
-
744-56.</p></li>
+
Goldberg, A. L. (2003). &quot;Protein degradation and protection against misfolded or  
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2010). &quot;Control of substrate
+
damaged proteins.&quot; </span><u>
-
gating and translocation into ClpP by channel residues and ClpX binding.&quot;  
+
<span>
-
<u>J Mol Biol</u> <b>39 </b>(5): 707-18.</p></li>
+
Nature</span></u><span>
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2005). &quot;Rebuilt AAA + motors
+
<b>426</b>(6968): 895-9.</span></p></li>
-
reveal operating principles for ATP-fuelled machines.&quot; <u>Nature</u> <b>437</b>(7062): 1115-20.</p></li>
+
<p>
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2006). &quot;Engineering
+
<span>[11] Gregersen, N., C. B.  
-
controllable protein degradation.&quot; <u>Mol Cell</u> <b>22</b>(5):  
+
Pedersen, et al. </span>
-
701-7.</font></p></li>
+
<span>(2003).  
-
<font>
+
&quot;Misfolding, degradation, and aggregation of variant proteins. The molecular  
-
<li><p ALIGN="LEFT">Sauer, R. T., T. A. Baker, et al. (2007). &quot;Altered tethering of
+
pathogenesis of short chain acyl-CoA dehydrogenase (SCAD) deficiency.&quot; <u>J Biol  
-
the SspB adaptor to the ClpXP protease causes changes in substrate delivery.&quot;  
+
Chem</u> <b>278</b>(48): 47449-58.</span></p></li>
-
<u>J Biol Chem</u> <b>282</b>(15): 11465-73.</p></li>
+
<p>
-
<li><p ALIGN="LEFT">Schafer, E., T. Kunkel, et al. (1993). &quot;In vitro formation of a
+
<li><p ALIGN="LEFT">[12]
-
photoreversible adduct of phycocyanobilin and tobacco apophytochrome B.&quot; <u>Eur J
+
Grossman, A. D. and K. L. Griffith (2008). &quot;Inducible protein degradation in  
-
Biochem</u> <b>215</b>(3): 587-94. </p></li>
+
Bacillus subtilis using heterologous peptide tags and adaptor proteins to target  
-
<li><p ALIGN="LEFT">Su, Z., H. Li, et al. (2010). &quot;A protease-based strategy for the  
+
substrates to the protease ClpXP.&quot; <u>Mol Microbiol</u> <b>70</b>(4): 1012-25.</span></p></li>
-
controlled release of therapeutic peptides.&quot; <u>Angew Chem Int Ed Engl</u> <b>49</b>(29): 4930-3.</p></li>
+
<p>
-
<li><p ALIGN="LEFT">Voigt, C. A., A. Levskaya, et al. (2005). &quot;Synthetic biology:  
+
<li><p ALIGN="LEFT">[13]
-
engineering Escherichia coli to see light.&quot; <u>Nature</u> <b>
+
Houry, W. A., U. A. Wojtyra, et al. (2003). &quot;The N-terminal zinc binding domain  
-
438</b>(7067): 441-2.</p></li>
+
of ClpX is a dimerization domain that modulates the chaperone function.&quot; <u>J  
-
<li><p ALIGN="LEFT">Voigt, C. A., A. Levskaya, et al. (2009). &quot;Spatiotemporal  
+
Biol Chem</u> <b>278</b>(49): 48981-90.</span></p></li>
-
control of cell signalling using a light-switchable protein interaction.&quot;  
+
<li><p ALIGN="LEFT">
-
<u>Nature</u> <b>461</b>(7266): 997-1001.</p></li>
+
[14] Hughes, J., F. T. Landgraf, et al. </span>
-
<li><p ALIGN="LEFT">Zuber, P. and Y. Zhang (2007). &quot;Requirement of the zinc-binding  
+
<span>(2001).  
-
domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide  
+
&quot;Recombinant holophytochrome in Escherichia coli.&quot; <u>FEBS Lett</u> <b>508</b>(3):  
-
stress on ClpXP activity.&quot; <u>J Bacteriol</u> <b>189</b>(21):7669-80.</p></li>
+
459-62.</span></p></li>
-
</font></p></li></ul>
+
<p>
 +
<li><p ALIGN="LEFT">[15]
 +
Isacoff, E. Y. and P. Gorostiza (2008). &quot;Optical switches for remote and
 +
noninvasive control of cell signaling.&quot; <u>Science</u> <b>322</b>(5900): 395-9.</span></p></li>
 +
<li><p ALIGN="LEFT">
 +
[16] Kohchi, T., K. Mukougawa, et al. </span>
 +
<span>(2006).  
 +
&quot;Metabolic engineering to produce phytochromes with phytochromobilin,  
 +
phycocyanobilin, or phycoerythrobilin chromophore in Escherichia coli.&quot; <u>FEBS
 +
Lett</u> <b>580</b>(5): 1333-8.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[17]
 +
Kohchi, T., K. Mukougawa, et al. (2006). &quot;Metabolic engineering to produce
 +
phytochromes with phytochromobilin, phycocyanobilin, or phycoerythrobilin  
 +
chromophore in Escherichia coli.&quot; <u>FEBS Lett</u> <b>580</b>(5): 1333-8.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[18]
 +
Lagarias, J. C. and G. A. Gambetta (2001). &quot;Genetic engineering of phytochrome
 +
biosynthesis in bacteria.&quot; <u>Proc Natl Acad Sci U S A</u> <b>98</b>(19):
 +
10566-71.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[19]
 +
Lagarias, J. C., N. C. Rockwell, et al. (2006). &quot;Phytochrome structure and
 +
&nbsp;signaling mechanisms.&quot; </span><u>
 +
<span>
 +
Annu Rev Plant Biol</span></u><span>
 +
<b>57</b>: 837-58.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[20]
 +
Lagarias, J.C., M.T. McDowell (2002). &quot;Analysis and reconstitution of
 +
phytochromes.&quot; <u>Heme, Chlorophyll, and Bilins: Methods and Protocols</u>,
 +
293-309</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[21]
 +
Maurizi, M. R., R. Grimaud, et al. (1998). &quot;Enzymatic and structural  
 +
similarities between the Escherichia coli ATP-dependent proteases, ClpXP and  
 +
ClpAP.&quot; <u>J Biol Chem</u> <b>273</b>(20): 12476-81.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[22]
 +
Millar, A. J., O. Sorokina, et al. (2009). &quot;A switchable light-input,
 +
light-output system modelled and constructed in yeast.&quot; <u>J Biol Eng</u> <b>3</b>:
 +
15.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[23]
 +
Moffat, K. and A. Moglich (2010). &quot;Engineered photoreceptors as novel  
 +
optogenetic tools.&quot; <u>Photochem Photobiol Sci</u> <b>9</b>(10): 1286-300.</span></p></li>
 +
<p>
 +
<span>[24] Moffat, K., A. Moglich, et
 +
al. </span>
 +
<span>(2010).
 +
&quot;Structure and function of plant photoreceptors.&quot; <u>Annu Rev Plant Biol</u> <b>
 +
61</b>: 21-47.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[25]
 +
Moroder, L. and C. Renner (2006). &quot;Azobenzene as conformational switch in model  
 +
peptides.&quot; <u>Chembiochem</u> <b>7</b>(6): 868-78.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[26]
 +
Morrison, D. A. and S. Ahlawat (2009). &quot;ClpXP degrades SsrA-tagged proteins in  
 +
Streptococcus pneumoniae.&quot; </span><u>
 +
<span>
 +
J Bacteriol</span></u><span>
 +
<b>191</b>(8): 2894-8.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[27] Muir,  
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T. W. and A. B. Tyszkiewicz (2008). &quot;Activation of protein splicing with light
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in yeast.&quot; <u>Nat Methods</u> <b>5</b>(4): 303-5.</span></p></li>
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<p>
 +
<li><p ALIGN="LEFT">[28]
 +
Quail, P. H. (2002). &quot;Phytochrome photosensory signalling networks.&quot; <u>Nat Rev
 +
Mol Cell Biol</u> <b>3</b>(2): 85-93.</span></p></li>
 +
<li><p ALIGN="LEFT">
 +
[29] Quail, P. H., R. Khanna, et al. </span>
 +
<span>(2004). &quot;A
 +
novel molecular recognition motif necessary for targeting photoactivated
 +
phytochrome signaling to specific basic helix-loop-helix transcription factors.&quot;
 +
<u>Plant Cell</u> <b>16</b>(11): 3033-44.</span></p></li>
 +
<li><p ALIGN="LEFT">
 +
[30] Quail, P. H., E. Schafer, et al. </span>
 +
<span>(2006). &quot;Photoactivated
 +
phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated
 +
degradation.&quot; </span><u>
 +
<span>
 +
Mol Cell</span></u><span>
 +
<b>23</b>(3): 439-46.</span></p></li>
 +
<li><p ALIGN="LEFT">
 +
[31] Quail, P. H., S. Shimizu-Sato, et al. </span>
 +
<span>(2002). &quot;A
 +
light-switchable gene promoter system.&quot; <u>Nat Biotechnol</u> <b>20</b>(10):  
 +
1041-4.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT">[32]
 +
Rosen, M. K., D. W. Leung, et al. (2008). &quot;Genetically encoded photoswitching of  
 +
actin assembly through the Cdc42-WASP-Arp2/3 complex pathway.&quot; <u>Proc Natl Acad
 +
Sci U S A</u> <b>105</b>(35): 12797-802.</span></p></li>
 +
<p>
 +
<li><p ALIGN="LEFT"><span>[33] Schafer, E., T. Kunkel, et  
 +
al. </span>
 +
<span>(1993).  
 +
&quot;In vitro formation of a photoreversible adduct of phycocyanobilin and tobacco
 +
apophytochrome B.&quot; <u>Eur J Biochem</u> <b>215</b>(3): 587-94.</span></p></li>
 +
<p>
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<li><p ALIGN="LEFT"><span>[34] Schaffner, K., C. Hill, et  
 +
al. </span>
 +
<span>(1994).  
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&quot;Expression of phytochrome apoprotein from Avena sativa in Escherichia coli and
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formation of photoactive chromoproteins by assembly with phycocyanobilin.&quot; <u>
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Eur J Biochem</u> <b>223</b>(1): 69-77.</span></p></li>
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<p>
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Sejnowski, T. J. and M. U. Gillette (2005). &quot;Physiology. Biological clocks
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coordinately keep life on time.&quot; </span><u>
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<span>
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Science</span></u><span>
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Sharrock, R. A. (2008). &quot;The phytochrome red/far-red photoreceptor superfamily.&quot;
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<u>Genome Biol</u> <b>9</b>(8): 230.</span></p></li>
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<p>
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<li><p ALIGN="LEFT">[37] Su,  
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Z., H. Li, et al. (2010). &quot;A protease-based strategy for the controlled release  
 +
of therapeutic peptides.&quot; <u>Angew Chem Int Ed Engl</u> <b>49</b>(29): 4930-3.</span></p></li>
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<p>
 +
<li><p ALIGN="LEFT">[38]
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Voigt, C. A., A. Levskaya, et al. (2005). &quot;Synthetic biology: engineering  
 +
Escherichia coli to see light.&quot; </span><u>
 +
<span>
 +
Nature</span></u><span>
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<b>438</b>(7067): 441-2.</span></p></li>
 +
<li><p ALIGN="LEFT">
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[39] Voigt, C. A., A. Levskaya, et al. </span>
 +
<span>(2009).  
 +
&quot;Spatiotemporal control of cell signaling using a light-switchable protein  
 +
interaction.&quot; <u>Nature</u> <b>461</b>(7266): 997-1001.</span></p></li>
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<p>
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Weaver, D. R. and S. M. Reppert (1997). &quot;Forward genetic approach strikes gold:
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cloning of a mammalian clock gene.&quot; </span><u>
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<span>
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Cell</span></u><span>
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<b>89</b>(4): 487-90.</span></p></li>
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<p>
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</span>
 +
<span>Weitz, C. J., K. F.
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Storch, et al. </span>
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<span>(2002).
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&quot;Extensive and divergent circadian gene expression in liver and heart.&quot; <u>
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Nature</u> <b>417</b>(6884): 78-83.</span></p></li>
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<p>
 +
<li><p ALIGN="LEFT">[42]
 +
</span>
 +
<span>Zuber, P. and Y.  
 +
Zhang (2007). </span>
 +
<span>
 +
&quot;Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus  
 +
subtilis and effects of disulfide stress on ClpXP activity.&quot; </span><u>
 +
<span>
 +
J Bacteriol</span></u><span>
 +
<b>189</b>(21): 7669-80.</span></p></li>
 +
</ul>

Revision as of 17:26, 27 October 2010

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References
  
Let me guide you

References

  • [1] Baker, T. A., R. T. Sauer, et al. (2009). "Engineering synthetic adaptors and substrates for controlled ClpXP degradation." J Biol Chem 284(33): 21848-55.

  • [2] Baker, T. A., R. T. Sauer, et al. (2009). "Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine." Cell 139(4): 744-56.

  • [3] Baker, T. A., R. T. Sauer, et al. (2010). "Control of substrate gating and translocation into ClpP by channel residues and ClpX binding." J Mol Biol 399(5): 707-18.

  • [4] Baker, T. A., R. T. Sauer, et al. (2005). "Versatile modes of peptide recognition by the AAA+ adaptor protein SspB." Nat Struct Mol Biol 12(6): 520-5.

  • [5] Baker, T. A., R. T. Sauer, et al. (2005). "Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines." Nature 437(7062): 1115-20.

  • [6] Baker, T. A., R. T. Sauer, et al. (2006). "Engineering controllable protein degradation." Mol Cell 22(5): 701-7.

  • [7] Baker, T. A., R. T. Sauer, et al. (2007). "Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery." J Biol Chem 282(15): 11465-73.

  • [8] Deisseroth, K., F. Zhang, et al. (2006). "Channelrhodopsin-2 and optical control of excitable cells." Nat Methods 3(10): 785-92.

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