Team:Imperial College London/Stomach

From 2009.igem.org

(Difference between revisions)
(→Pepsin)
Line 49: Line 49:
   <input type="submit" value="Perform"> the cleavage of the protein.  
   <input type="submit" value="Perform"> the cleavage of the protein.  
   <input type="reset" value="Reset"> the fields.<P>
   <input type="reset" value="Reset"> the fields.<P>
-
   
+
 
 +
<!--
 +
 
   <hr>
   <hr>
   <P>
   <P>
-
 
   <b><font size=+2>P</font>lease, select<br></b>
   <b><font size=+2>P</font>lease, select<br></b>
   <input type=radio name=enzyme_number value= less_enzymes checked>  only the following selection of<b>  
   <input type=radio name=enzyme_number value= less_enzymes checked>  only the following selection of<b>  
Line 61: Line 62:
      
      
   <table>
   <table>
-
 
+
     
   <tr><td><input type=checkbox name=enzyme  value=Pn1.3 checked>  <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH1.3)</a></td>
   <tr><td><input type=checkbox name=enzyme  value=Pn1.3 checked>  <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH1.3)</a></td>
   
   
-
 
+
 
   </tr>
   </tr>
   </table>
   </table>
Line 71: Line 72:
   </dd></dl>
   </dd></dl>
   
   
-
  </form>
+
<input type=radio tabIndex=4 name=enzyme_number value= special_enzymes> for the following enzymes an additional, more <b>
 +
   
 +
  <option selected value="Chym">Chymotrypsin
 +
  <option value="Tryps">Trypsin
 +
  </select><br>
 +
    Please enter the lowest cleavage probability that you would like to be displayed:
 +
  <input type=text name=min_prob size=4 maxlength=4>%
 +
  </dd></dl>
 +
  <P>
 +
   
 +
   
 +
  <hr>
 +
  <p> <b><font size=+2>P</font>lease indicate the way you would like the cleavage sites to be displayed</b><br><p>
 +
  <input type=checkbox checked name=cleavage_map value=cleavage_map>
 +
    Map of cleavage sites. Please select the number of amino acid within one block: 
 +
   
 +
  <select name="block_size"  size=1>
 +
   
 +
  <option value="10">10
 +
  <option value="20">20
 +
  <option value="30">30
 +
  <option value="40">40
 +
  <option value="50">50
 +
  <option selected value="60">60
 +
  </select><br>
 +
   
 +
  <input type=checkbox name=alphtable checked value=alphtable>
 +
    Table of sites, sorted alphabetically by enzyme and chemical name<br>
 +
  <input type=checkbox name=seq_table value=seq_table>
 +
    Table of sites, sorted sequentially by amino acid number<p><br><hr>
 +
  <b><font size=+2>P</font>lease indicate which enzymes to include in the display</b><br><br>
 +
   
 +
  <input type=radio name=cleave_number checked value=all>All enzymes and chemicals
 +
  <br><input type=radio name=cleave_number value=exactly>Enzymes and chemicals cleaving exactly
 +
  <input type=text name=cleave_exactly size=4 maxlength=4> times
 +
  <br><input type=radio name=cleave_number value=range>Enzymes and chemicals cleaving at least
 +
  <input type=text name=cleave_range_min size=4 maxlength=4> times, and at most
 +
  <input type=text name=cleave_range_max size=4 maxlength=4> times
 +
  <br>
 +
   
 +
  </form>
   <HR>
   <HR>
      
      
Line 89: Line 130:
</body>
</body>
</html>
</html>
 +
 +
-->
{{Imperial/09/Division}}
{{Imperial/09/Division}}

Revision as of 08:49, 2 October 2009

Contents

Human Digestive Proteases:

  • Pepsin = stomach
  • Trypsin = duodenum
  • Chymotrypsin
  • Carboxypeptidase



Stomach

The stomach is the first point at which polypeptides are broken down. The low pH of the stomach causes enzymes to denature, opening them up to attack from proteases such as pepsin.

Pepsin

  • Released by chief cells in the stomach.
  • Expressed as a zymogen pepsinogen.
  • Pepsinogen is converted to pepsin by HCl which is released by parietal cells of the stomach.
  • Cleaves at the N-terminus after aromatic amino acids such as phenylalanine, tryptophan, and tyrosine.
  • Optimum pH of 1.5 to 2. Pepsin denatures when the pH is more than 5.0.


If you want to see the effect of the protease pepsin, please enter the amino acid sequence of a polpeptide into the table below.


the cleavage of the protein. the fields.

-->


Duodenum

Endopeptidases (trypsin, chymotryopsin, elastase)

Exopeptidases (carboxypeptidases A & B)

Enteropeptidase

Trypsin

  • Trypsin is found in the duodenum and serves to hydrolyse peptides into amino acids.
  • Trypsin has an optimal operating pH of ~8 and an optimum temperature of 37°C.
  • Trypsin breaks down the milk protein casein. For this reason, milk protein would be a good protein to use for secondary encapsulation.

Chymotryopsin

Elastase

Enterokinase

Carboxypeptidases A & B




Small Intestine = Aminopeptidase N

Dipeptidyl aminopeptidase IV

Aminopeptidase P

Carboxypeptidase P

Angotensin-converting enzyme

Glutamyl aminopeptidase


Peptide cutter

PeptideCutter [references / documentation] predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and /or a table of cleavage site positions.

Enter a UniProtKB (Swiss-Prot or TrEMBL) protein identifier, ID (e.g. ALBU_HUMAN), or accession number, AC (e.g. P04406), or an amino acid sequence (e.g. 'SERVELAT'):

the cleavage of the protein. the fields.

Please, select
 all available enzymes and chemicals
only the following selection of enzymes and chemicals

Arg-C proteinase Asp-N endopeptidase Asp-N endopeptidase + N-terminal Glu
BNPS-Skatole Caspase1 Caspase2
Caspase3 Caspase4 Caspase5
Caspase6 Caspase7 Caspase8
Caspase9 Caspase10
Chymotrypsin-high specificity (C-term to [FYW], not before P) Chymotrypsin-low specificity (C-term to [FYWML], not before P)
Clostripain (Clostridiopeptidase B) CNBr Enterokinase
Factor Xa Formic acid Glutamyl endopeptidase
GranzymeB Hydroxylamine Iodosobenzoic acid
LysC LysN NTCB (2-nitro-5-thiocyanobenzoic acid)
Pepsin (pH1.3) Pepsin (pH>2) Proline-endopeptidase
Proteinase K Staphylococcal peptidase I Tobacco etch virus protease
Thermolysin Thrombin Trypsin
for the following enzymes an additional, more sophisticated model can be applied that attributes a probability of cleavage to each site :


Please enter the lowest cleavage probability that you would like to be displayed: %

Please indicate the way you would like the cleavage sites to be displayed

Map of cleavage sites. Please select the number of amino acid within one block:
Table of sites, sorted alphabetically by enzyme and chemical name
Table of sites, sorted sequentially by amino acid number


Please indicate which enzymes to include in the display

All enzymes and chemicals
Enzymes and chemicals cleaving exactly times
Enzymes and chemicals cleaving at least times, and at most times

Mr. Gene   Geneart   Clontech   Giant Microbes

Retrieved from "http://2009.igem.org/Team:Imperial_College_London/Stomach"