Team:Imperial College London/Stomach

From 2009.igem.org

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If you want to see the effect of the protease pepsin, please enter the amino acid sequence of a polpeptide into the table below.
 
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For example, why not try the sequence for phenylalanine hydroxylase (PAH); one of the enzymes that we are delivering to the GI tract.
 
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Met S T A V L E N P G L G R K L S D F G Q E T S Y I E D N C N Q N G A I S L I F S L K E E V G A L A K V L R L F E E N D V N L T H I E S R P S R L K K D E Y E F F T H L D K R S L P A L T N I I K I L R H D I G A T V H E L S R D K K K D T V P W F P R T I Q E L D R F A N Q I L S Y G A E L D A D H P G F K D P V Y R A R R K Q F A D I A Y N Y R H G Q P I P R V E Y Met E E E K K T W G T V F K T L K S L Y K T H A C Y E Y N H I F P L L E K Y C G F H E D N I P Q L E D V S Q F L Q T C T G F R L R P V A G L L S S R D F L G G L A F R V F H C T Q Y I R H G S K P Met Y T P E P D I C H E L L G H V P L F S D R S F A Q F S Q E I G L A S L G A P D E Y I E K L A T I Y W F T V E F G L C K Q G D S I K A Y G A G L L S S F G E L Q Y C L S E K P K L L P L E L E K T A I Q N Y T V T E F Q P L Y Y V A E S F N D A K E K V R N F A A T I P R P F S V R Y D P Y T Q R I E V L D N T Q Q L K I L A D S I N S E I G I L C S A L Q K I K Stop
 
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  <form method=POST action="http://www.expasy.ch/cgi-bin/peptidecutter/peptidecutter.pl">
 
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  <textarea name="protein" rows=12 cols=50></textarea><P>
 
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  <input type="submit" value="Perform"> the cleavage of the protein.
 
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  <input type="reset" value="Reset"> the fields.<P>
 
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  <input type=hidden checked name=cleavage_map value=cleavage_map>
 
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    Table of sites, sorted alphabetically by enzyme and chemical name<br>
 
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    Table of sites, sorted sequentially by amino acid number<p><br><hr>
 
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  <b><font size=+2>P</font>lease indicate which enzymes to include in the display</b><br><br>
 
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  <input type=radio name=cleave_number checked value=all>All enzymes and chemicals
 
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  <br><input type=radio name=cleave_number value=exactly>Enzymes and chemicals cleaving exactly
 
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  <input type=text name=cleave_exactly size=4 maxlength=4> times
 
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  <br><input type=radio name=cleave_number value=range>Enzymes and chemicals cleaving at least
 
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==Duodenum==
 
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Endopeptidases (trypsin, chymotryopsin, elastase)
 
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Exopeptidases (carboxypeptidases A & B)
 
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Enteropeptidase
 
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===Trypsin===
 
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* Trypsin is found in the duodenum and serves to hydrolyse peptides into amino acids.
 
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* Trypsin has an optimal operating pH of ~8 and an optimum temperature of 37°C.
 
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* Trypsin breaks down the milk protein casein. For this reason, milk protein would be a good protein to use for secondary encapsulation.
 
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===Chymotryopsin===
 
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===Elastase===
 
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===Enterokinase===
 
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===Carboxypeptidases A & B===
 
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{{Imperial/09/Division}}
 
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Small Intestine = Aminopeptidase N
 
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Dipeptidyl aminopeptidase IV
 
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Aminopeptidase P
 
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Carboxypeptidase P
 
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Angotensin-converting enzyme
 
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Glutamyl aminopeptidase
 
{{Imperial/09/Division}}
{{Imperial/09/Division}}
=Peptide cutter=
=Peptide cutter=
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   <input type=radio name=enzyme_number value= less_enzymes>  only the following selection of<b>  
   <input type=radio name=enzyme_number value= less_enzymes>  only the following selection of<b>  
     <A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html">enzymes and chemicals</A></b>
     <A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html">enzymes and chemicals</A></b>
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  <tr><td><input type=checkbox name=enzyme  value=ArgC> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#ArgC">Arg-C proteinase</a></td>
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  <td><input type=checkbox name=enzyme  value=AspN> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#AspN">Asp-N endopeptidase</a></td>
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  <td><input type=checkbox name=enzyme  value=AspGluN> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#AspGluN">Asp-N endopeptidase + N-terminal Glu</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=BNPS> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#BNPS">BNPS-Skatole</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp1> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp1">Caspase1</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp2> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp2">Caspase2</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=Casp3> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp3">Caspase3</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp4> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp4">Caspase4</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp5> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp5">Caspase5</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=Casp6> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp6">Caspase6</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp7> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp7">Caspase7</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp8> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp8">Caspase8</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=Casp9> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp9">Caspase9</a></td>
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  <td><input type=checkbox name=enzyme  value=Casp10> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp10">Caspase10</a></td>
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  <td><input type=checkbox name=enzyme value=Enter> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Enter">Enterokinase</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=Xa> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Xa">Factor Xa</a></td>
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  <td><input type=checkbox name=enzyme  value=HCOOH> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#HCOOH">Formic acid</a></td>
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  <td><input type=checkbox name=enzyme  value=Glu> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Glu">Glutamyl endopeptidase</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=GranB> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#GranB">GranzymeB</a></td>
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  <td><input type=checkbox name=enzyme  value=Hydro> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Hydro">Hydroxylamine</a></td>
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  <td><input type=checkbox name=enzyme  value=Iodo> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Iodo">Iodosobenzoic acid</a></td>
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  <td><input type=checkbox name=enzyme  value=LysN> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#LysN">LysN</a></td>
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  <td><input type=checkbox name=enzyme  value=NTCB> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#NTCB">NTCB (2-nitro-5-thiocyanobenzoic acid)</a></td></tr>
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  <tr><td><input type=checkbox name=enzyme  value=Pn1.3>  <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH1.3)</a></td>
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  <td><input type=checkbox name=enzyme  value=Pn2> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH>2)</a></td>
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  <td><input type=checkbox name=enzyme  value=Pro> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Pro">Proline-endopeptidase</a></td>
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  <tr><td><input type=checkbox name=enzyme  value=ProtK> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#ProtK">Proteinase K</a></td>
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  <td><input type=checkbox name=enzyme  value=Staph> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Staph">Staphylococcal peptidase I</a></td>
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  <td><input type=checkbox name=enzyme  value=TEV> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#TEV">Tobacco etch virus protease</a></td>
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  <td><input type=checkbox name=enzyme  value=Therm> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Therm">Thermolysin</a></td>
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  <td><input type=checkbox name=enzyme  value=Throm> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Throm">Thrombin</a></td>
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  <td><input type=checkbox name=enzyme  value=Tryps> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Tryps">Trypsin</a></td>
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   <input type=radio tabIndex=4 name=enzyme_number value= special_enzymes> for the following enzymes an additional, more <b><A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_special_enzymes.html">sophisticated model</A> </b>can be applied that attributes a probability of cleavage to each site :
   <input type=radio tabIndex=4 name=enzyme_number value= special_enzymes> for the following enzymes an additional, more <b><A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_special_enzymes.html">sophisticated model</A> </b>can be applied that attributes a probability of cleavage to each site :
   </b><p><dl><dd><select name="special_enzyme"  size=2>
   </b><p><dl><dd><select name="special_enzyme"  size=2>

Revision as of 10:41, 2 October 2009

Contents

Human Digestive Proteases:

The stomach serves to break large proteins into peptides. These peptides are then broken down into amino acids once they enter the duodenum.


  • 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.



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 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

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