Difference between revisions of "Part:BBa K1321340"
Line 4: Line 4:
 
Double cellulose binding domain (dCBD) using two cellulose binding domains from ''Trichoderma reesei'' cellobiohydrolases,  with an N-terminal linker and internal linker sequence between the two domains which is derived from the endogenous cellobiohydrolase linker sequence.
 
Double cellulose binding domain (dCBD) using two cellulose binding domains from ''Trichoderma reesei'' cellobiohydrolases,  with an N-terminal linker and internal linker sequence between the two domains which is derived from the endogenous cellobiohydrolase linker sequence.
  
 +
Please see below for AutoAnnotator information about the final protein product.
 
===Usage and Biology===
 
===Usage and Biology===
  
Line 11: Line 12:
 
The two CBDs are from the fungus ''T. reesei'' (Hypocrea jecorina) Exocellobiohydrolase (Exoglucanase) I (cbh1), uniprot ID [http://www.uniprot.org/uniprot/P62694 P62694]; and Exocellobiohydrolase (Exoglucanase) II, uniprot ID [http://www.uniprot.org/uniprot/P07987 P07987] (cbh2); with a linker peptide between the two CBDs and at the N-terminus of the protein.  Both linkers are the same amino acid sequence and are based on the endogenous linker sequences that exists in cbh1 and cbh2 genes. The linker sequence is PGANPPGTTTTSRPATTTGSSPGP which is the same as used by Linder ''et al'' [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)]. The first three amino acids are from the cbh2 endogenous linker, and the rest is from the cbh1 endogenous linker. CBDcbh1 is placed C-terminal to CBDcbh2 because naturally CBDcbh1 is a C-terminal domain and CBDcbh2 is an N-terminal domain. Both CBDs are from the [http://www.cazy.org/CBM1.html CBM family 1]. The precise location of the CBD within the cbh genes was slightly different according to the uniprot annotations and the sequence used by Linder ''et al'' [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)]; we chose to use the sequence from the paper since the protein was expressed and characterised successfully.
 
The two CBDs are from the fungus ''T. reesei'' (Hypocrea jecorina) Exocellobiohydrolase (Exoglucanase) I (cbh1), uniprot ID [http://www.uniprot.org/uniprot/P62694 P62694]; and Exocellobiohydrolase (Exoglucanase) II, uniprot ID [http://www.uniprot.org/uniprot/P07987 P07987] (cbh2); with a linker peptide between the two CBDs and at the N-terminus of the protein.  Both linkers are the same amino acid sequence and are based on the endogenous linker sequences that exists in cbh1 and cbh2 genes. The linker sequence is PGANPPGTTTTSRPATTTGSSPGP which is the same as used by Linder ''et al'' [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)]. The first three amino acids are from the cbh2 endogenous linker, and the rest is from the cbh1 endogenous linker. CBDcbh1 is placed C-terminal to CBDcbh2 because naturally CBDcbh1 is a C-terminal domain and CBDcbh2 is an N-terminal domain. Both CBDs are from the [http://www.cazy.org/CBM1.html CBM family 1]. The precise location of the CBD within the cbh genes was slightly different according to the uniprot annotations and the sequence used by Linder ''et al'' [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)]; we chose to use the sequence from the paper since the protein was expressed and characterised successfully.
  
−
As part of our project we carried out an assay to determine the relative binding ability of CBD-sfGFP fusions to bacterial cellulose. 
+
The binding ability of this CBD to bacterial cellulose was characterised when fused to [https://parts.igem.org/Part:BBa_K1321337 sfGFP], relative to other CBDs fused to [https://parts.igem.org/Part:BBa_K1321337 sfGFP]. The binding ability was represented by the percentage fluorescence remaining from the sfGFP-CBD fusions bound to bacterial cellulose discs, when subjected to various washes (protocol [http://2014.igem.org/Team:Imperial/Protocols here]). It was determined that the dCBD-sfGFP fusion had the greatest binding ability in comparison to four other CBDs fused to sfGFP after three washes with both dH2O and 70% EtOH (see first two graphs). When washed with PBS and 5% BSA it had on average the third greatest ability to bind bacterial cellulose (third and fourth graphs below).
−
 
+
−
In our first assay performed to determine the relative strengths of various CBDs’ binding to bacterial cellulose – represented by the percentage fluorescence left from CBDs fused to ([https://parts.igem.org/Part:BBa_K1321337 sfGFP (RFC25)]) bound to bacterial cellulose discs, when subjected to various washes - it was determined that the fusion with dCBD had the greatest binding ability in comparison to four other CBDs fused to sfGFP after three washes with both dH2O and 70% EtOH.
+
−
 
+
−
In the same assay, results suggested that dCBD had on average the third greatest ability to bind bacterial cellulose, after three washes with both PBS and 5% BSA.
+
  
 
[[File:IC14_-_dH2Obplot1.png|700px|left|]]
 
[[File:IC14_-_dH2Obplot1.png|700px|left|]]
Line 25: Line 22:
 
[[File:IC14-BSAbplot1.png|700px|left|]]
 
[[File:IC14-BSAbplot1.png|700px|left|]]
  
−
It was thus decided that dCBD was one of the top three strongest CBDs and was carried forward for use in a metal-binding assay, fusing it to synthetic phytochelatin (insert part number) to show the successful functionalisaton of bacterial cellulose as a metal-removing filter.
 
  
 +
<!-- -->
  
−
 
−
<!-- -->
 
−
Please see below for AutoAnnotator information about the final protein product.
 
  
 
<partinfo>BBa_K1321340 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1321340 SequenceAndFeatures</partinfo>

Revision as of 04:06, 2 November 2014

Double CBD (dCBD) with N-terminal linker

Double cellulose binding domain (dCBD) using two cellulose binding domains from Trichoderma reesei cellobiohydrolases, with an N-terminal linker and internal linker sequence between the two domains which is derived from the endogenous cellobiohydrolase linker sequence.

Please see below for AutoAnnotator information about the final protein product.

Usage and Biology

This part is based on the double cellulose-binding domain construct (CBDcbh2-linker-CBDcbh1) synthesised and characterised by Linder et al [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)] who found that this double CBD had higher affinity for cellulose than either of the two CBDs on their own. The main difference is that our part contains an additional linker sequence on the N-terminus of the protein.

The two CBDs are from the fungus T. reesei (Hypocrea jecorina) Exocellobiohydrolase (Exoglucanase) I (cbh1), uniprot ID [http://www.uniprot.org/uniprot/P62694 P62694]; and Exocellobiohydrolase (Exoglucanase) II, uniprot ID [http://www.uniprot.org/uniprot/P07987 P07987] (cbh2); with a linker peptide between the two CBDs and at the N-terminus of the protein. Both linkers are the same amino acid sequence and are based on the endogenous linker sequences that exists in cbh1 and cbh2 genes. The linker sequence is PGANPPGTTTTSRPATTTGSSPGP which is the same as used by Linder et al [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)]. The first three amino acids are from the cbh2 endogenous linker, and the rest is from the cbh1 endogenous linker. CBDcbh1 is placed C-terminal to CBDcbh2 because naturally CBDcbh1 is a C-terminal domain and CBDcbh2 is an N-terminal domain. Both CBDs are from the [http://www.cazy.org/CBM1.html CBM family 1]. The precise location of the CBD within the cbh genes was slightly different according to the uniprot annotations and the sequence used by Linder et al [http://dx.doi.org/10.1074/jbc.271.35.21268 (1)]; we chose to use the sequence from the paper since the protein was expressed and characterised successfully.

The binding ability of this CBD to bacterial cellulose was characterised when fused to sfGFP, relative to other CBDs fused to sfGFP. The binding ability was represented by the percentage fluorescence remaining from the sfGFP-CBD fusions bound to bacterial cellulose discs, when subjected to various washes (protocol [http://2014.igem.org/Team:Imperial/Protocols here]). It was determined that the dCBD-sfGFP fusion had the greatest binding ability in comparison to four other CBDs fused to sfGFP after three washes with both dH2O and 70% EtOH (see first two graphs). When washed with PBS and 5% BSA it had on average the third greatest ability to bind bacterial cellulose (third and fourth graphs below).

IC14 - dH2Obplot1.png
IC14-EtOHbplot1.png
IC14-PBSbplot1.png
IC14-BSAbplot1.png




Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Protein data table for BioBrick BBa_K1321340 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25: (underlined part encodes the protein)
 ATGGCCGGC ... CTTACCGGTTAA
 ORF from nucleotide position 1 to 381 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 		MAGPGANPPGTTTTSRPATTTGSSPGPQACSSVWGQCGGQNWSGPTCCASGSTCVYSNDYYSQCLPGANPPGTTTTSRPATTTGSSPGPTQSHYGQCGGI
GYSGPTVCASGTTCQVLNPYYSQCLTG*
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)8 (6.3%)
Arg (R)2 (1.6%)
Asn (N)5 (3.9%)
Asp (D)1 (0.8%)
Cys (C)10 (7.9%)
Gln (Q)8 (6.3%)
Glu (E)0 (0.0%)
Gly (G)21 (16.5%)
His (H)1 (0.8%)
Ile (I)1 (0.8%)
Leu (L)3 (2.4%)
Lys (K)0 (0.0%)
Met (M)1 (0.8%)
Phe (F)0 (0.0%)
Pro (P)15 (11.8%)
Ser (S)17 (13.4%)
Thr (T)21 (16.5%)
Trp (W)2 (1.6%)
Tyr (Y)7 (5.5%)
Val (V)4 (3.1%)
Amino acid counting
Total number:127
Positively charged (Arg+Lys):2 (1.6%)
Negatively charged (Asp+Glu):1 (0.8%)
Aromatic (Phe+His+Try+Tyr):10 (7.9%)
Biochemical parameters
Atomic composition:C522H794N150O188S11
Molecular mass [Da]:12531.6
Theoretical pI:7.45
Extinction coefficient at 280 nm [M-1 cm-1]:21430 / 22055 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.79)good (0.71)acceptable (0.59)good (0.63)excellent (0.84)good (0.80)
Alignments (obtained from PredictProtein.org)
   There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.
Predictions (obtained from PredictProtein.org)
   There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.


References

1. Linder, M.; Salovuori, I.; Ruohonen, L.; Teeri, T.T., 1996. Characterization of a Double Cellulose-binding Domain. SYNERGISTIC HIGH AFFINITY BINDING TO CRYSTALLINE CELLULOSE. Journal of Biological Chemistry, 271(35), pp.21268–21272. Available at: http://www.jbc.org/content/271/35/21268.full