Team:USTC/Modeling/b

From 2010.igem.org

(Difference between revisions)
(Results)
Line 17: Line 17:
== Results ==
== Results ==
-
http://2010.igem.org/wiki/images/e/e3/USTC2010_model_b_Result_1.png
+
I) Co-evolution of pdu-pdu proteins.
 +
Use the method from previous mature algorithm [http://www.ncbi.nlm.nih.gov/pubmed/10860738], we check the pdu shell microcompartment proteins as interactive partners ''in vivo''.
 +
http://2010.igem.org/wiki/images/e/e3/USTC2010_model_b_Result_1.png
== Conclusion ==
== Conclusion ==
   We calculate the correlation coefficient between the shell components and the inside components. We also cut the 20 amino acids of the N-terminal of the inside components to see if the N-terminal of the inside components can be more correlated with the inside components. To calculate the correlation coefficient, two methods, pearson and spearman (see supplementary)are utilized. To see the results more clearly we calculated the z-score of each value and draw the heat map. From the results, we can see that the components of the shell components and inside components are co-evolved, as we expected. From figure 2, we can see that PduC,E,P,Q,H are significant correlated with PduB and N thus interactions between them might exist. Also, the scores of PduK are not very high suggesting that it might be less probable to interact with N-terminal of inside components, which might be proportional to its low copies in the microcompartment.
   We calculate the correlation coefficient between the shell components and the inside components. We also cut the 20 amino acids of the N-terminal of the inside components to see if the N-terminal of the inside components can be more correlated with the inside components. To calculate the correlation coefficient, two methods, pearson and spearman (see supplementary)are utilized. To see the results more clearly we calculated the z-score of each value and draw the heat map. From the results, we can see that the components of the shell components and inside components are co-evolved, as we expected. From figure 2, we can see that PduC,E,P,Q,H are significant correlated with PduB and N thus interactions between them might exist. Also, the scores of PduK are not very high suggesting that it might be less probable to interact with N-terminal of inside components, which might be proportional to its low copies in the microcompartment.

Revision as of 15:27, 26 October 2010

An Integrated Platform Based on Bacterial Microcompartment for de novo Proteinaceous Artificial Organelles


Overview

In this section, we mainly focus on the co-evolution relationship between the pdu-pdu proteins and pdu proteins-signal peptides.

USTC2010_model_b_Flow_chart.png


Based on these modeling, we want to know more about the evolution status of pdu shell microcompartment. And furthermore, we want to prove that our artificial organelle is open to a variety of signal peptide, thus making its somehow more prone to contain disparate reactions.


Results

I) Co-evolution of pdu-pdu proteins.

Use the method from previous mature algorithm [1], we check the pdu shell microcompartment proteins as interactive partners in vivo.

USTC2010_model_b_Result_1.png

Conclusion

We calculate the correlation coefficient between the shell components and the inside components. We also cut the 20 amino acids of the N-terminal of the inside components to see if the N-terminal of the inside components can be more correlated with the inside components. To calculate the correlation coefficient, two methods, pearson and spearman (see supplementary)are utilized. To see the results more clearly we calculated the z-score of each value and draw the heat map. From the results, we can see that the components of the shell components and inside components are co-evolved, as we expected. From figure 2, we can see that PduC,E,P,Q,H are significant correlated with PduB and N thus interactions between them might exist. Also, the scores of PduK are not very high suggesting that it might be less probable to interact with N-terminal of inside components, which might be proportional to its low copies in the microcompartment.