Team:Lethbridge/Modeling
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David.franz (Talk | contribs) (Putting up Jeff's homology blurb) |
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As with any fusion protien, the addition of this polyarginine tail to the protein has the very real potential of blocking (at least partially) the active site of a protein. Thus if one can predict the structure of the protein with the addition of the tail, it is possible to avoid creating inactive/ low efficiency fusion proteins. | As with any fusion protien, the addition of this polyarginine tail to the protein has the very real potential of blocking (at least partially) the active site of a protein. Thus if one can predict the structure of the protein with the addition of the tail, it is possible to avoid creating inactive/ low efficiency fusion proteins. | ||
- | ==<font color="white">The Method== | + | ==<font color="white">The Method and Results== |
+ | [[Image:homology1.png|x250px|right|text-top]] | ||
+ | [[Image:homology2.png|x250px|right|text-top]] | ||
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+ | To model the XylE structure, the sequence for XylE from Pseudomonas putida (NCBI accession number NP_542866) was aligned with the primary sequence from the crystal structure of XylE from the same organism (pdb: 1MPY; several differences in amino acid sequence were observed) using CLUSTALW (1). Based on this sequence alignment, a homology model was generated using the alignment mode in SWISSMODEL (2-4). To model the placement of an N-terminal arginine tag, the tag was manually added to the N-terminus of the model. Energy minimization was carried out in SWISS-PDB viewer in vacuo utilizing a GROMOS96 energy minimization (2). The resulting pdb file was visualized and manipulated using PYMOL, images were taken using the same software (5). | ||
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+ | =<font color="white">References= | ||
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+ | 1. Higgins, D. G., Thompson, J. D., and Gibson, T. J. (1996) Using CLUSTAL for multiple sequence alignments, Methods Enzymol. 266, 383-402. | ||
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+ | 2. Guex, N., and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling, Electrophoresis 18, 2714-2723. | ||
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+ | 3. Kiefer, F., Arnold, K., Künzli, M., Bordoli, L., and Schwede, T. (2009) The SWISS-MODEL Repository and associated resources, Nucleic Acids Res 37, D387-D392. | ||
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+ | 4. Arnold, K., Bordoli, L., Kopp, J., and Schwede, T. (2006) The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling., Bioinformatics 22, 195-201. | ||
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+ | 5. DeLano, W. L. (2006) PyMOL, DeLano Scientific. | ||
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