Difference between revisions of "Part:BBa K4044009"
Alexandr56 (Talk | contribs) |
|||
Line 9: | Line 9: | ||
The molecular dynamics of dimers was also calculated in the OPLS-AA/L force field. The BphP1 dimers molecular dynamics values were obtained in GROMACS program. We proved the stability of the BphP1-BcLOV4 and Gal4-Q-PAS1 structures binding upon 760 nm light stimulation. We compared these structures with the shortened variants of BphP1-BcLOV4 and Gal4-Q-PAS1 and turned out that both complexes were stable (RMSD < 0.5 nm for 100 ps). | The molecular dynamics of dimers was also calculated in the OPLS-AA/L force field. The BphP1 dimers molecular dynamics values were obtained in GROMACS program. We proved the stability of the BphP1-BcLOV4 and Gal4-Q-PAS1 structures binding upon 760 nm light stimulation. We compared these structures with the shortened variants of BphP1-BcLOV4 and Gal4-Q-PAS1 and turned out that both complexes were stable (RMSD < 0.5 nm for 100 ps). | ||
− | [[File:T--LMSU- | + | [[File:T--LMSU--Modeling-othBphP1-Gal4-gif.gif|400px|thumb|centre|Molecular dynamics simulation for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with full-length amino acid sequences]] |
[[File:T--LMSU--Modeling-RMSD-otherBphP1-Gal4.png|400px|thumb|centre|RMSD for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with full-length amino acid sequences]] | [[File:T--LMSU--Modeling-RMSD-otherBphP1-Gal4.png|400px|thumb|centre|RMSD for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with full-length amino acid sequences]] | ||
[[File:T--LMSU--Modeling-En-pot-otherBphP1-Gal4.png|400px|thumb|cntre|The system's potential energy for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with full-length amino acid sequences]] | [[File:T--LMSU--Modeling-En-pot-otherBphP1-Gal4.png|400px|thumb|cntre|The system's potential energy for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with full-length amino acid sequences]] | ||
Line 16: | Line 16: | ||
However, the complex of chimeric proteins with a full-length amino acid sequence had a lower potential energy but higher PyDockWEB total score (S) (Epot = -8.11×10<sup>6</sup> kJ mol<sup>-1</sup> and S = -35.312 kJ mol<sup>-1</sup>, respectively) than the complex of shortened proteins (Epot = -7.185×10<sup>6</sup> kJ mol<sup>-1</sup> and S = -36.828 kJ mol<sup>-1</sup>, respectively). As expected, the Gal4-Q-PAS1 orientation relative to BphP1-BcLOV4 in two variants prevented the BphP1-BcLOV4 and Gal4-Q-PAS1 dimers formation. PyDockWEB total score is calculated based on electrostatics, desolvation energy and limited van der Waals contribution. | However, the complex of chimeric proteins with a full-length amino acid sequence had a lower potential energy but higher PyDockWEB total score (S) (Epot = -8.11×10<sup>6</sup> kJ mol<sup>-1</sup> and S = -35.312 kJ mol<sup>-1</sup>, respectively) than the complex of shortened proteins (Epot = -7.185×10<sup>6</sup> kJ mol<sup>-1</sup> and S = -36.828 kJ mol<sup>-1</sup>, respectively). As expected, the Gal4-Q-PAS1 orientation relative to BphP1-BcLOV4 in two variants prevented the BphP1-BcLOV4 and Gal4-Q-PAS1 dimers formation. PyDockWEB total score is calculated based on electrostatics, desolvation energy and limited van der Waals contribution. | ||
− | [[File:T--LMSU--Modeling-ourBphP1-Gal4. | + | [[File:T--LMSU--Modeling-ourBphP1-Gal4-gif.gif|400px|thumb|center|Molecular dynamics simulation for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with shortened amino acid sequences]] |
[[File:T--LMSU--Modeling-RMSD-ourBphP1-Gal4.png|400px|thumb|center|RMSD for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with shortened amino acid sequences]] | [[File:T--LMSU--Modeling-RMSD-ourBphP1-Gal4.png|400px|thumb|center|RMSD for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with shortened amino acid sequences]] | ||
[[File:T--LMSU--Modeling-En-pot-ourBphP1-Gal4.png|400px|thumb|center|The system's potential energy for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with shortened amino acid sequences]] | [[File:T--LMSU--Modeling-En-pot-ourBphP1-Gal4.png|400px|thumb|center|The system's potential energy for BphP1-BcLOV4 and Gal4-Q-PAS1 complex with shortened amino acid sequences]] |
Revision as of 00:07, 22 October 2021
BphP1-BcLOV4_QPAS1-Gal4 optogenetic system
There are several states of the ontogenetic system. Under the influence of far red light, BphP1 part of the chimeric protein BphP1-BcLOV4 becomes active and binds to QPAS1-Gal4. This leads to the expression of target gene. Under the influence of red light, BphP1 is inactivated, QPAS1-Gal4 remains in the dimerized state. This leads to inhibition of transcription. At the same time, there may be residual activity of BphP1 and expression of target genes, which we do not need, therefore, under the influence of blue light, the entire BphP1-BcLOV4 complex binds to the lipid membrane, which completely eliminates the possibility of undesirable expression.
The molecular dynamics of dimers was also calculated in the OPLS-AA/L force field. The BphP1 dimers molecular dynamics values were obtained in GROMACS program. We proved the stability of the BphP1-BcLOV4 and Gal4-Q-PAS1 structures binding upon 760 nm light stimulation. We compared these structures with the shortened variants of BphP1-BcLOV4 and Gal4-Q-PAS1 and turned out that both complexes were stable (RMSD < 0.5 nm for 100 ps).
However, the complex of chimeric proteins with a full-length amino acid sequence had a lower potential energy but higher PyDockWEB total score (S) (Epot = -8.11×106 kJ mol-1 and S = -35.312 kJ mol-1, respectively) than the complex of shortened proteins (Epot = -7.185×106 kJ mol-1 and S = -36.828 kJ mol-1, respectively). As expected, the Gal4-Q-PAS1 orientation relative to BphP1-BcLOV4 in two variants prevented the BphP1-BcLOV4 and Gal4-Q-PAS1 dimers formation. PyDockWEB total score is calculated based on electrostatics, desolvation energy and limited van der Waals contribution.
Our findings confirm that this optogenetic system can be implemented and can work more efficiently with full-length chimeric proteins.
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal PstI site found at 815
Illegal PstI site found at 1112
Illegal PstI site found at 1559
Illegal PstI site found at 2608
Illegal PstI site found at 2852 - 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 7
Illegal NheI site found at 30
Illegal PstI site found at 815
Illegal PstI site found at 1112
Illegal PstI site found at 1559
Illegal PstI site found at 2608
Illegal PstI site found at 2852 - 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 301
Illegal BamHI site found at 1876
Illegal BamHI site found at 4029 - 23INCOMPATIBLE WITH RFC[23]Unknown
- 25INCOMPATIBLE WITH RFC[25]Unknown
- 1000COMPATIBLE WITH RFC[1000]