Difference between revisions of "Part:BBa E1010"

Revision as of 13:18, 19 October 2016

**highly** engineered mutant of red fluorescent protein from Discosoma striata (coral)

monomeric RFP: Red Fluorescent Protein. Excitation peak: 584 nm Emission peak: 607 nm

Usage and Biology

Robert E. Campbell started with Discosoma RFP (DsRed) and evolved a faster folding, monomeric variant. See paper listed in source. Codon optimized for expression in bacteria (?? DE)

iGEM11_Uppsala-Sweden: Expression of chromoproteins. The images above show E coli constitutively expressing amilCP BBa_K592009 (blue), amilGFP BBa_K592010 (yellow) and RFP BBa_E1010 (red).

Peking iGEM 2016 has fused this part with triple spytag. The fused protein is participate in Peking’s polymer network. By adding this protein, the whole polymer network become visible in most conditions. If you want to learn more about Peking’s polymer network and the role of mRFP in this network, please click here https://parts.igem.org/Part:BBa_K1989004".

Sequence and Features

Barcodes are discontinued, but one was appended to the sequence of this part. Composite parts using this part will include the barcode. More ...

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 555
Illegal AgeI site found at 667
1000
COMPATIBLE WITH RFC[1000]

Parts table

Protein data table for BioBrick BBa_E1010 automatically created by the BioBrick-AutoAnnotator version 1.0

Nucleotide sequence in RFC 10: (underlined part encodes the protein)
ATGGCTTCC ... ACCGGTGCTTAATAACGCTGATAGTGCTAGTGTAGATCGC
ORF from nucleotide position 1 to 675 (excluding stop-codon)

Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

1
101
201

MASSEDVIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFQYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFE
DGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASTERMYPEDGALKGEIKMRLKLKDGGHYDAEVKTTYMAKKPVQLPGAYKTDIKLD
ITSHNEDYTIVEQYERAEGRHSTGA*

Sequence features: (with their position in the amino acid sequence, see the list of supported features)

None of the supported features appeared in the sequence

Amino acid composition:

Ala (A)	12 (5.3%)
Arg (R)	9 (4.0%)
Asn (N)	4 (1.8%)
Asp (D)	14 (6.2%)

Cys (C)	0 (0.0%)
Gln (Q)	8 (3.6%)
Glu (E)	22 (9.8%)
Gly (G)	23 (10.2%)

His (H)	5 (2.2%)
Ile (I)	9 (4.0%)
Leu (L)	12 (5.3%)
Lys (K)	22 (9.8%)

Met (M)	9 (4.0%)
Phe (F)	10 (4.4%)
Pro (P)	12 (5.3%)
Ser (S)	12 (5.3%)

Thr (T)	14 (6.2%)
Trp (W)	3 (1.3%)
Tyr (Y)	11 (4.9%)
Val (V)	14 (6.2%)

Amino acid counting

	Total number:	225
	Positively charged (Arg+Lys):	31 (13.8%)
	Negatively charged (Asp+Glu):	36 (16.0%)
	Aromatic (Phe+His+Try+Tyr):	29 (12.9%)

Biochemical parameters

	Atomic composition:	C₁₁₃₅H₁₇₄₉N₂₉₉O₃₄₇S₉
	Molecular mass [Da]:	25423.7
	Theoretical pI:	5.65
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	32890 / 32890 (all Cys red/ox)

Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges

Codon usage

	Organism:	E. coli	B. subtilis	S. cerevisiae	A. thaliana	P. patens	Mammals
	Codon quality (CAI):	excellent (0.84)	good (0.72)	good (0.68)	good (0.74)	good (0.78)	good (0.71)

Alignments (obtained from PredictProtein.org)

	SwissProt:	Q9U6Y8 (86% identity on 221 AAs), P83690 (63% identity on 215 AAs)
	TrEML:	Q5S3G8 (95% identity on 225 AAs), D0VWW2 (94% identity on 220 AAs)
	PDB:	2h5q (94% identity on 216 AAs), 2qlg (94% identity on 215 AAs)

Predictions (obtained from PredictProtein.org)

Subcellular Localization (reliability in brackets)

	Archaea:	secreted (100%)
	Bacteria:	cytosol (52%)
	Eukarya:	cytosol (20%)

Gene Ontology (reliability in brackets)

	Molecular Function Ontology:	-
	Biological Process Ontology:	GO:0018298 (40%), GO:0008218 (27%)

Predicted features:

	Disulfid bridges:	-
	Transmembrane helices:	-

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Revision as of 13:17, 19 October 2016 (view source) Zhaosjls (Talk \| contribs) ← Older edit		Revision as of 13:18, 19 October 2016 (view source) Zhaosjls (Talk \| contribs) Newer edit →
Line 17:		Line 17:
	'''iGEM11_Uppsala-Sweden:''' Expression of chromoproteins. The images above show ''E coli'' constitutively expressing amilCP <partinfo>BBa_K592009</partinfo> (blue), amilGFP <partinfo>BBa_K592010</partinfo> (yellow) and RFP <partinfo>BBa_E1010</partinfo> (red).		'''iGEM11_Uppsala-Sweden:''' Expression of chromoproteins. The images above show ''E coli'' constitutively expressing amilCP <partinfo>BBa_K592009</partinfo> (blue), amilGFP <partinfo>BBa_K592010</partinfo> (yellow) and RFP <partinfo>BBa_E1010</partinfo> (red).

−	Peking iGEM 2016 has fused this part with triple spytag. The fused protein is participate in Peking’s polymer network. By adding this protein, the whole polymer network become visible in most conditions. If you want to learn more about Peking’s polymer network and the role of mRFP in this network, please click here https://parts.igem.org/Part:BBa_K1989004".	+	Peking iGEM 2016 has fused this part with triple spytag. The fused protein is participate in Peking’s polymer network. By adding this protein, the whole polymer network become visible in most conditions. If you want to learn more about Peking’s polymer network and the role of mRFP in this network, please click here https://parts.igem.org/Part:BBa_K1989004".