Difference between revisions of "Part:BBa K4244046"

Latest revision as of 12:39, 12 October 2022

flipUM (MMP-9 inducible)

This flipUM is designed in such a way that it will only regain its colour when it is cleaved by MMP-9. Two inserts have been made, the E5 and K5 domain. These two domains dimerize and disrupt GFP structure. MMP-9 recognizes the cleavage site and cuts off the K5 domain, restoring Ultramarine function.

The flip design is based off the following paper: Zhang, Q., Schepis, A., Huang, H., Yang, J., Ma, W., Torra, J., Zhang, S. Q., Yang, L., Wu, H., Nonell, S., Dong, Z., Kornberg, T. B., Coughlin, S. R., & Shu, X. (2019). Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals. Journal of the American Chemical Society, 141(11), 4526–4530. https://doi.org/10.1021/JACS.8B13042/SUPPL_FILE/JA8B13042_SI_002.PDF

The structure of flipUM was predicted using alphafold as shown below.

The left shows uncleaved flipUM, the middle the cleaved, active flipUM, and the right regular UM

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal EcoRI site found at 423
Illegal EcoRI site found at 514
12
INCOMPATIBLE WITH RFC[12]
Illegal EcoRI site found at 423
Illegal EcoRI site found at 514
21
INCOMPATIBLE WITH RFC[21]
Illegal EcoRI site found at 423
Illegal EcoRI site found at 514
Illegal BglII site found at 625
Illegal XhoI site found at 682
23
INCOMPATIBLE WITH RFC[23]
Illegal EcoRI site found at 423
Illegal EcoRI site found at 514
25
INCOMPATIBLE WITH RFC[25]
Illegal EcoRI site found at 423
Illegal EcoRI site found at 514
Illegal AgeI site found at 543
Illegal AgeI site found at 789
1000
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4244046 short</partinfo>
-"This flipUM is designed in such a way that it will only regain its colour when it is cleaved by MMP-9. Two inserts have been made, the E5 and K5 domain. These two domains dimerize and disrupt GFP structure. MMP-9 recognizes the cleavage site and cuts off the K5 domain, restoring Ultramarine function.
+This flipUM is designed in such a way that it will only regain its colour when it is cleaved by MMP-9. Two inserts have been made, the E5 and K5 domain. These two domains dimerize and disrupt GFP structure. MMP-9 recognizes the cleavage site and cuts off the K5 domain, restoring Ultramarine function.
 The flip design is based off the following paper:
-Zhang, Q., Schepis, A., Huang, H., Yang, J., Ma, W., Torra, J., Zhang, S. Q., Yang, L., Wu, H., Nonell, S., Dong, Z., Kornberg, T. B., Coughlin, S. R., & Shu, X. (2019). Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals. Journal of the American Chemical Society, 141(11), 4526–4530. https://doi.org/10.1021/JACS.8B13042/SUPPL_FILE/JA8B13042_SI_002.PDF"
+Zhang, Q., Schepis, A., Huang, H., Yang, J., Ma, W., Torra, J., Zhang, S. Q., Yang, L., Wu, H., Nonell, S., Dong, Z., Kornberg, T. B., Coughlin, S. R., & Shu, X. (2019). Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals. Journal of the American Chemical Society, 141(11), 4526–4530. https://doi.org/10.1021/JACS.8B13042/SUPPL_FILE/JA8B13042_SI_002.PDF
 The structure of flipUM was predicted using alphafold as shown below.
@@ Line 13: / Line 13: @@
 The left shows uncleaved flipUM, the middle the cleaved, active flipUM, and the right regular UM
 <!-- Add more about the biology of this part here