Approach a New Expression/Purification Project

Each student will have 15 minutes to analyze the sequence of the same protein, using different databases and software (see list below). If you have finished your task, examine other tasks too. Than we'll go through the different steps together, compile all the data and try to suggest alternative means to express and purify this protein.

Open the sequences document. (Complete document)
Open The bioinformatic tools page.


Program
Section
Instructions
Backup
Interpro
(sequence search)
 Motifs and Repeats in  Proteins 1. Examine the Interpro entries AND the entries pr..., pf..., ps... etc. 
2. If you have time, examine the related Pubmed entries.
Results
CDD
 Motifs and Repeats in  Proteins 1. Examine the related entry and the related Pubmed link 
2. Determine the beginning and end of this domain in our protein.
3. If you have time, examine the option "show domain relatives".
Results
Brenda
 Preliminary Search Using Keywords  1. Use the search according to E.C. number. Enter 1.14.18.1 . Go through the whole entry. Pull out all the details that may influence the expression / purification strategy
Results
(Large File)
ELM
 Motifs and Repeats in  Proteins 1. Select from list of organisms the appropriate organism , as appears in the sequences document.
2. Examine related links in the results. See if you get bright ideas.		 Results
Prosite
(scroll down to: Tools for PROSITE)		 Motifs and Repeats in  Proteins 1. Examine the results. Compare the putative modifications with the data in the page Co- and Post-translational Modifications, and see if you can rule out putative sites. Results
Protparam
 Physicochemical properties  1. Analyze, examine the "References and documentation " to understand the results. Compare results with those of Protein Calculator Results
Protein Calculator
 Physicochemical properties 1. Select molecular weight, Isoelectric Point (pI) and other parameters, compare results with those of Protparam
EMBOSS   Pepinfo/Pepwindow/Pepstats
 Physicochemical properties 1. Run your sequence using pepinfo and pepstats
2. compare results with those of Protparam and Protein Calculator		 Pepinfo
Pepstat
Recombinant Protein Solubility Prediction
 Physicochemical properties Results
Peptide Cutter
 Proteolytic Cleavage  Select "only the following selection" and the following enzymes: factor Xa, thrombin, enterokinase, tev Results
All glycosylation options + Netphos
 Co- and Post-translational Modifications  1. Examine the results. Compare the putative modifications with the data in the page Co- and Post-translational Modifications, and see if you can rule out putative sites. YingOyang
NetOGlyc
NetNGlyc
NetPhos
Appropriate options in Psort , TargetP Server,  PLoc, Softberry.
 Sub-cellular Localization and Signal Peptides  1. Choose all the appropriate options, select plant and go.
2. in targetP select "plant" and "Perform cleavage site predictions. "		 psort,psort-plant, 
ipsort
TargetP Server
SoftBerry Protein Location Finding 
ProtComp 
 Sub-cellular Localization and Signal Peptides Choose ProtComp ProtComp
1. Cyspred
2. Cysteines Bonding State and Connectivity Predictor
 S-S bonds (in PTM section)   Cyspred results, Predictor results
Rare Codon Caltor
 Codon Usage and Translation Frames  Paste the nucleotides sequens according to the CDS info in the sequence page Results
Translate a DNA Sequence
 Codon Usage and Translation Frames  What sequence should you paste? What additional information do you need?
Nevertheless, paste the nucleotides sequence according to the CDS info in the sequence page and run the program.
RNA secondary structure prediction
 Secondary Structure of mRNA  What sequence should you paste? What additional information do you need?