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What does the amino acid composition analysis show as the most common amino acid in this protein? (Is that unusual?)
What is the chemical formula for the query protein?
What is the predicted extinction coefficient at 280 nm, in 6M guanidium HCl, 0.02M phosphate, pH6.5 buffer, assuming all cysteines appear as half cysteines?
In what way could it be helpful to know the extinction coefficient?
According to the instability index, is this protein classified as stable or unstable?
Return again to the ExPASy tools . Notice there are two sections dealing with structure prediction, secondary structure prediction tools and tertiary structureprediction and visualization tools. The secondary structure prediction tools are designed to predict features such as the helical content, the betasheet formations, and the turns, loops, and coil regions within a protein, given the sequence.
Explore the secondary structure tools independently, and submit the diacylglycerol kinase sequenceabove to any of the available secondary structure prediction tools. Most of these tools will email the results, with at leasta 20 minute delay between submission and receipt of results. Forward a results summary to the instructor, outlining the predictions created bythe program of choice.
Tertiary structure prediction tools match the query sequence with sequences, or partial sequences, of proteins where the 3-Dstructure has been published in the Protein Data Bank (PDB). These tools will produce a model of the query protein by piecing together the structuralregions from the best matches in the PDB, and threading the query sequence through the predicted structure. For more detailed explanations of available3-D structure prediction software, view the Swiss-Model demo page and the Geno3D reference page . Although both of these tools are searching for templates from existing PDB entries, they are doing this in different ways.
What program does Swiss-Model use to match the query sequence with sequences of known structures?
What program does Geno3D use to match the query sequence with sequences of known structures?
Notice that the template selection process and the model structure refinement processes are different between these two programs as well.
Finally, in the tertiary structure section of the ExPASy tools page, Swiss PDB Viewer is a graphical tool for the visualization, comparison and analysis of3-D coordinate files. Swiss PDB Viewer can superimpose 3-D structures by finding the rotation and translation that most closely aligns the two proteinstructures. Additionally, the Swiss PDB Viewer will perform amino acid mutations, prediction of hydrogen bonds, and calculation of angles anddistances between atoms. Best of all, Swiss PDB Viewer is freeware and available for many different platforms, including Macintosh, PC, SGI IRIX,and Linux.
View this supplemental SPDBV web page . What other function does Swiss PDB Viewer have, when used in conjunction withother applications such as OpenGL or POV-Ray?
ExPASy provides a very large library of tools, for proteomics as well as other bioinformatics applications.For those students interested in future research in the field of proteomics,this web server will be an important resource.
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