<p>For in vivo characterization, we constructed candidate uTP sequences by concatenating the consensus sequences of discovered motif patterns. The uTP sequence classifiers were used to select the correct motifs for the fluorescent proteins we planned to use, mVenus and mNeonGreen. The two sequences with the highest confidence values (uTP1 and uTP2) were selected for in vivo experiments. These sequences were also submitted to the Parts Registry.</p>
<p>To further validate the constructed sequences, their predicted structure was examined. Structural prediction was performed on all 206 selected uTP-containing <em>B. bigelowii</em> proteins, to uncover the 3D conformation of uTP. The predicted structures were aligned and a consensus structure was created by averaging the aligned regions. This revealed a highly-conserved (stdev per residue position <1.8Å)structuralregionwith2alpha-helicesarrangedintoaU-bend(Fig5).ThestructureofconstructedmNeonGreenandmVenus+uTP1,uTP2sequenceswaspredictedandtheconsensusstructurealignedontothem,yieldinggoodalignment(RMSD<=4.0Å),confirmingthatourconstructswilllikelybehavesimilartonativeuTP-containingproteins.</p>
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<imgsrc="https://static.igem.wiki/teams/5054/structures2.svg"alt="Fig 1: Graphical overview of the experiment plan."style="background: white;">
<imgsrc="https://static.igem.wiki/teams/5054/structures2.png"alt="Fig 1: Graphical overview of the experiment plan."style="background: white;">
<figcaption>Figure 5: Structural predictions. (a) Consensus structure of all uTP sequences extracted from UCYN-A imported proteins. (b) Consensus structure of all uTP sequences with charged residues shown (red=negative, blue=positive). (c) Consensus structure aligned onto uTP1 + mNeonGreen construct (RMSD=4.00Å). (d) Consensus structure aligned onto uTP2 + mNeonGreen construct (RMSD=3.77Å). </figcaption>
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<p>In the case of mitochondrial and chloroplast imported proteins, there is a well-known overlap: numerous proteins have twin transit peptides or ambiguous targeting sequences targeting both organelles. To investigate whether there is a similar overlap between the potential UCYN-A import system and other known cellular transport systems, we used established protein localization prediction tools on the potential list of UCYN-A imported proteins. These predictions proved to be inconclusive. A large minority (28%) of them were classified as secreted (Fig 6). This suggests that the UCYN-A import system, similar to other protein transport mechanisms, might be related to the Sec system.