Team:Peking/Modeling/Luminesensor/Optimization

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  <h3 id="title1">Parameter Analysis & Optimization</h3>
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After modeling the origin system, we attempted to optimize it in a rational way. We have tuned the parameters both up and down, one by one, and finally discovered four parameters which predominantly influence this system.
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After modeling the prototype <i>Luminesensor</i>, we attempted to optimize it in a rational way. We have tuned the parameters both up and down, one by one, and finally discovered four parameters which predominantly influence the performance of the <i>Luminesensor</i>.
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Figure 4. Results of Parameter Analysis. "Up" means tuning the parameter up to 10 times. This figure implied that tuning up these parameters can optimize the Luminesensor.
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Figure 1. Results of Parameter Analysis. "Up" means tuning the parameter up to 10 times. This figure implied that tuning up these parameters can optimize the Luminesensor.
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Within the two parameters to enhance contrast, K<sub>2</sub> (vivid association equilibrium constant) is related to the association mechanism of Vivid protein and K<sub>5</sub> (dimered LexA binding equilibrium constant) is related to the cooperative binding mechanism. As for speed optimizing, k<sub>1</sub> (vivid decay rate constant) is related to the activation mechanism of Vivid protein and k<sub>3</sub> (monomer LexA releasing rate constant from specific binding site) is related to the binding mechanism,  thus also to the LexA and sequencing. If we change the binding affinity of the sequence, then it is difficult to make constant K<sub>3</sub> (monomer LexA binding equilibrium constant with specific binding site), whose variance is predicted to ruin the contrast of this system from simulation. Therefore, we chose to apply a mutation on the Vivid protein in order to attain a faster <i>Luminesensor</i>, which has high levels of k<sub>1</sub> (vivid decay rate constant).
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Within the two parameters to enhance contrast, K<sub>2</sub> (vivid association equilibrium constant) is related to the association of Vivid protein and K<sub>5</sub> (dimerized LexA binding equilibrium constant) is related to the cooperative binding to DNA.
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   <img src="/wiki/images/1/16/Peking2012_Modeling_Optimization_74.png" alt="Figure 5. Mutation 1" title="Figure 5. Mutation 1" style="width:500px;" />
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   <img src="/wiki/images/1/16/Peking2012_Modeling_Optimization_74.png" alt="Figure 6. Mutation 1" title="Figure 6. Mutation 1" style="width:500px;" />
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Figure 5. Molecular modeling of mutation I74V, for gaining a faster <i>Luminesensor</i>. We could see that I74V is in the vicinity of Cys108, in order to enhance k1 (vivid decay rate constant).
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Figure 2. A molecular structure of VVD protein marking the position of residue 74. As shown in the figure, residue 74 (originaly isoleucine) resides in the vicinity of FAD (flavin adenine dinucleotide) molecule (the chromophore of VVD protein) and residue cystine 108. When VVD is excited by light, a covalent bound will form between residue cystine 108 and C4 of FAD, leading to VVD's conformational change to its light-state. The mutation I74V will interact with Cystine 108 and FAD molecule to destablize the adduct form, accelarating VVD's decay back to its dark-state.
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   <img src="/wiki/images/f/f4/Peking2012_Modeling_Optimization_135.png" alt="Figure 6. Mutation 2" title="Figure 6. Mutation 2" style="width:500px;" />
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   <img src="/wiki/images/f/f4/Peking2012_Modeling_Optimization_135.png" alt="Figure 7. Mutation 2" title="Figure 7. Mutation 2" style="width:500px;" />
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Figure 6. Molecular modeling of mutation M135I, for gaining a larger contrast (on/off ratio). We could see that M135I is in vivid dimerization domain, in order to increase K2 (vivid association equilibrium constant).
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Figure 3. A molecular structure of VVD protein marking the position of residue 135. As shown in the figure, residu 135(originally methionine) also resides near the FAD molecule. M135I is proposed to change the electronic environment of FAD molecule and somehow enhance VVD dimerization (possibly by stablizing light-state). The exact molecule mechanism is unclear.
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By searching the data of mutant in vivid protein among recent papers, we focus on these mutants: M135I in vivid dimerization domain to enhance K2 (vivid association equilibrium constant)<sup><a href="#ref?" title="">[?]</a></sup> and I74V of amino acids surrounding Cys108 to enhance k1 (vivid decay rate constant)<sup><a href="#ref3" title="Mechanism-based tuning of a LOV domain photoreceptor, Brian D. Zoltowski, etc. NATURE CHEMICAL BIOLOGY">[3]</a></sup>. The experimental results validate our modeling prediction (See <a href="/Team:Peking/Project/Luminesensor/Characterization" title="">Characterization</a>).
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By searching the data of mutant vivid protein in literature, we finally focused on these mutants: M135I in vivid dimerization domain to enhance K2 (vivid association equilibrium constant) and I74V of amino acids surrounding Cys108 to enhance k1 (vivid decay rate constant)<sup><a href="#ref1" title="Zoltowski, B.D., Vaccaro, B., and Crane, B.R. (2009). Mechanism-based tuning of a LOV domain photoreceptor. Nat. Chem. Biol. 5: 827: 834 ">[1]</a></sup>. The experimental results verified  our prediction (See <a href="/Team:Peking/Project/Luminesensor/Characterization" title="">Project Luminesensor Characterization</a>).
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   <img src="/wiki/images/2/2b/Peking2012_luminesensor_wiki.png" alt="Figure 7" />
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   <img src="/wiki/images/2/2b/Peking2012_luminesensor_wiki.png" alt="Figure 8" />
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<p class="description">Figure 7. Experiment result: Effects of introduced mutations on the contrast (on/off ratio) of <i>Luminesensor</i>. We can see that the mutation on M135 obviously improves the contrast (on/off ratio) of <i>Luminesensor</i>, which validate our modeling prediction.
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<p class="description">Figure 4. Experiment result: Effects of introduced mutations on the contrast (on/off ratio) of <i>Luminesensor</i>. We can see that the mutation on M135 obviously improves the contrast (on/off ratio) of <i>Luminesensor</i>, which validate our modeling prediction.
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We also chose LexA408, the mutant of LexA, in order to increase K5 (dimered LexA binding equilibrium constant)<sup><a href="#ref5" title="A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli, M. Dmitrova. etc. Springer-Verlag Mol Gen Genet">[5]</a></sup>, even though our main reason for choosing LexA408 over the wild-type LexA is due to the bio-orthogonality.
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We also chose LexA408, the mutant of LexA, in order to increase K5 (dimered LexA binding equilibrium constant)<sup><a href="#ref2" title="Dmitrova, M.,et al.(1998) A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli. Mol. Gen. Genet., 257: 205: 212 ">[2]</a></sup>, even though our main reason for choosing LexA408 over the wild-type LexA is due to the bio-orthogonality.
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   <img src="..." alt="Figure 8. Mutation 3" title="Figure 8. Mutation 3" style="width:500px;" />
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   <img src="/wiki/images/a/ad/Peking2012_Design_LexA408mutations.png" alt="Figure 9. Mutation 3" title="Figure 9. Mutation 3" style="width:500px;" />
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Figure 8. Molecular modeling of LexA408.
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Figure 5. A molecular structure of N-terminal domain of LexA protein. The arrow points to the position of residue 40, 41 and 42. In LexA408 protein, three point mutations P40A, N41S and A42S  are introduced into the N-terminal domain. These three mutations near the DNA binding surface of the protein will change its binding specificity. LexA408 will recognize a symmetrically altered sequence different from the one recognized by wild type LexA.
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<h3 id="title2">Reference</h3>
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1. Zoltowski, B.D., Vaccaro, B., and Crane, B.R. (2009). Mechanism-based tuning of a LOV domain photoreceptor. <i>Nat. Chem. Biol.</i> 5: 827: 834
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2. Dmitrova, M., Younes-Cauet, G., Oertel-Buchheit, P., Porte, D., Schnarr, M., Granger-Schnarr, M.(1998) A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in <i>Escherichia coli.</i> <i>Mol. Gen. Genet.</i>, 257: 205: 212
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Latest revision as of 02:49, 27 September 2012

Parameter Analysis & Optimization

After modeling the prototype Luminesensor, we attempted to optimize it in a rational way. We have tuned the parameters both up and down, one by one, and finally discovered four parameters which predominantly influence the performance of the Luminesensor.

Function Parameter Description Remark
Reduce responsing time k1Vivid lighting decay rate constantMainly on process from Light to Dark
k3rate constant of monomer LexA releasing from specific binding site
Enhance contrast K2Vivid association equilibrium constantMore dimerization provides more binding opportunity
K5dimered LexA binding equilibrium constantMore binding affinity
Parameter Tuning

Figure 1. Results of Parameter Analysis. "Up" means tuning the parameter up to 10 times. This figure implied that tuning up these parameters can optimize the Luminesensor.

Within the two parameters to enhance contrast, K2 (vivid association equilibrium constant) is related to the association of Vivid protein and K5 (dimerized LexA binding equilibrium constant) is related to the cooperative binding to DNA.

Figure 6. Mutation 1

Figure 2. A molecular structure of VVD protein marking the position of residue 74. As shown in the figure, residue 74 (originaly isoleucine) resides in the vicinity of FAD (flavin adenine dinucleotide) molecule (the chromophore of VVD protein) and residue cystine 108. When VVD is excited by light, a covalent bound will form between residue cystine 108 and C4 of FAD, leading to VVD's conformational change to its light-state. The mutation I74V will interact with Cystine 108 and FAD molecule to destablize the adduct form, accelarating VVD's decay back to its dark-state.

Figure 7. Mutation 2

Figure 3. A molecular structure of VVD protein marking the position of residue 135. As shown in the figure, residu 135(originally methionine) also resides near the FAD molecule. M135I is proposed to change the electronic environment of FAD molecule and somehow enhance VVD dimerization (possibly by stablizing light-state). The exact molecule mechanism is unclear.

By searching the data of mutant vivid protein in literature, we finally focused on these mutants: M135I in vivid dimerization domain to enhance K2 (vivid association equilibrium constant) and I74V of amino acids surrounding Cys108 to enhance k1 (vivid decay rate constant)[1]. The experimental results verified our prediction (See Project Luminesensor Characterization).

Figure 8

Figure 4. Experiment result: Effects of introduced mutations on the contrast (on/off ratio) of Luminesensor. We can see that the mutation on M135 obviously improves the contrast (on/off ratio) of Luminesensor, which validate our modeling prediction.

We also chose LexA408, the mutant of LexA, in order to increase K5 (dimered LexA binding equilibrium constant)[2], even though our main reason for choosing LexA408 over the wild-type LexA is due to the bio-orthogonality.

Figure 9. Mutation 3

Figure 5. A molecular structure of N-terminal domain of LexA protein. The arrow points to the position of residue 40, 41 and 42. In LexA408 protein, three point mutations P40A, N41S and A42S are introduced into the N-terminal domain. These three mutations near the DNA binding surface of the protein will change its binding specificity. LexA408 will recognize a symmetrically altered sequence different from the one recognized by wild type LexA.

Reference

  • 1. Zoltowski, B.D., Vaccaro, B., and Crane, B.R. (2009). Mechanism-based tuning of a LOV domain photoreceptor. Nat. Chem. Biol. 5: 827: 834
  • 2. Dmitrova, M., Younes-Cauet, G., Oertel-Buchheit, P., Porte, D., Schnarr, M., Granger-Schnarr, M.(1998) A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli. Mol. Gen. Genet., 257: 205: 212
  • Totop Totop

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