Team:Imperial College London/Stomach

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=<b>Human Digestive Proteases:</b>=
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=<b>The Stomach & Proteolysis:</b>=
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[[Image:Digestivesystem.jpg|100px|left]]
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The stomach is the first point at which polypeptides are broken down. It is here that large polypeptides are broken down into peptides. This process broadly involves two steps. First polypeptides are denatured by stomach acid, which causes them to open up. Subsequently, these denatured polypeptides are attacked by the protease pepsin. Pepsin is a powerful protease that cleaves at the N-terminus after aromatic amino acids such as phenylalanine, tryptophan, and tyrosine. The optimum pH of pepsin is from 1.5 to 2, at a pH of above 5 denaturation occurs. This means that pepsin is only functional in the acidic environment of the stomach. Small peptides leaving the stomach are later broken down into amino acids once they enter the duodenum.
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* Pepsin = stomach
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* Trypsin = duodenum
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* Chymotrypsin
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* Carboxypeptidase
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{{Imperial/09/Division}}
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==Stomach==
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===The Stomach Simulator===
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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.
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One of the enzymes that we are showcasing is phenylalanine hydroxylase (PAH) (as a treatment for PKU). If this enzyme was simply swallowed in an unencapsulated form it would be cleaved in 146 places by pepsin in the stomach.  
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===Pepsin===
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Click on the <i>perform</i> button to see a simulated digestion of PAH by pepsin. Alternativly, paste in your own sequence into the box below to see if it would be a good candidate for encapsulation.  
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* Released by chief cells in the stomach.
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* Expressed as a zymogen pepsinogen.
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* Pepsinogen is converted to pepsin by HCl which is released by parietal cells of the stomach.
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* Cleaves at the N-terminus after aromatic amino acids such as phenylalanine, tryptophan, and tyrosine.
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* Optimum pH of 1.5 to 2. Pepsin denatures when the pH is more than 5.0.
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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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   <form method=POST action="http://www.expasy.ch/cgi-bin/peptidecutter/peptidecutter.pl" target="_blank">
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   <textarea name="protein" rows=5 cols=50>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</textarea>
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   <form method=POST action="http://www.expasy.ch/cgi-bin/peptidecutter/peptidecutter.pl">
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  <BR>
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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="submit" value="Perform">  
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   <input type="reset" value="Reset"> the fields.<P>
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   <input type=hidden name=enzyme_number value= less_enzymes checked>
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  <input type=hidden name=enzyme  value=Pn1.3 checked>
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  <input type=hidden checked name=cleavage_map value=cleavage_map>
    
    
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<select name="block_size"  size=1 style="display:none">
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  <input type=hidden name=enzyme_number value= less_enzymes checked> 
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   <option selected value= "60" selected>
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</select>
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  <input type=hidden name=alphtable checked value=alphtable>
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   <input type=hidden name=cleave_number checked value=all>  
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  </form>
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<input type=checkbox name=alphtable checked value=alphtable>
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<br><A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_references.html">references</A> /<A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_instructions.html">documentation</A>  
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    Table of sites, sorted alphabetically by enzyme and chemical name<br>
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</div>
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   <input type=checkbox name=seq_table value=seq_table>
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<div id = 'sib_last_update'></div>
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    Table of sites, sorted sequentially by amino acid number<p><br><hr>
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<div id = 'sib_footer'> </div>
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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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</div>
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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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  <input type=text name=cleave_range_min size=4 maxlength=4> times, and at most
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  <input type=text name=cleave_range_max size=4 maxlength=4> times
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{{Imperial/09/Division}}
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<html><center><a href="https://2009.igem.org/Team:Imperial_College_London/M2"><img width=150px src="https://static.igem.org/mediawiki/2009/1/10/II09_TourArrow.png"></a>
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</html>
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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
 
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{{Imperial/09/Division}}
 
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=Peptide cutter=
 
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<html>
 
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<body>
 
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<!-- ********************************************************************************************** -->
 
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<!-- START OF HEADER information on top of the page -->
 
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<div id='sib_container'>
 
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  <div id = 'sib_body'>   
 
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  <b>PeptideCutter</b> [<A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_references.html">references</A> /
 
-
  <A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_instructions.html">documentation</A>]
 
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    predicts potential cleavage sites cleaved by proteases or chemicals in a given protein
 
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    sequence. 
 
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    PeptideCutter returns the query sequence with the
 
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    possible cleavage sites mapped on it and /or a table of cleavage site positions.
 
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  <P>
 
-
  <form method=POST action="http://www.expasy.ch/cgi-bin/peptidecutter/peptidecutter.pl">
 
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    Enter a UniProtKB (Swiss-Prot or TrEMBL) protein 
 
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    identifier, ID (e.g. ALBU_HUMAN), or accession number, AC (e.g. P04406),
 
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  <B>or </B> an amino acid sequence (e.g. 'SERVELAT'):<BR>
 
-
  <textarea name="protein" rows=12 cols=50></textarea><P>
 
-
   
 
-
  <input type="submit" value="Perform"> the cleavage of the protein.
 
-
  <input type="reset" value="Reset"> the fields.<P>
 
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  <hr>
 
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  <P>
 
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  <b><font size=+2>P</font>lease, select<br></b>
 
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  <input type=radio name=enzyme_number value= all_enzymes checked>  all available enzymes and chemicals  <br>
 
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  <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>
 
-
  <dl><dd>
 
-
  <table >
 
-
  <tr><td>
 
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  <table>
 
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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>
 
-
  <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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  </tr>
 
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  <tr>
 
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  <td><input type=checkbox name=enzyme  value=Ch_hi> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Chym">Chymotrypsin-high specificity (C-term to [FYW], not before P)</a></td>
 
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  <td><input type=checkbox name=enzyme  value=Ch_lo> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Chym">Chymotrypsin-low specificity (C-term to [FYWML], not before P)</a></td></tr>
 
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  <tr><td><input type=checkbox name=enzyme  value=Clost> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Clost">Clostripain (Clostridiopeptidase B)</a></td>
 
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  <td><input type=checkbox name=enzyme  value=CNBr> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#CNBr">CNBr</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>
 
-
  <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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  </tr>
 
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  <tr><td><input type=checkbox name=enzyme  value=LysC> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#LysC">LysC</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>
 
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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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  </tr>
 
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  <tr>
 
-
  <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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  </tr>
 
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  </table>
 
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  </td></tr>
 
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  </table>
 
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  </dd></dl>
 
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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 :
 
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  </b><p><dl><dd><select name="special_enzyme"  size=2>
 
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  <option selected value="Chym">Chymotrypsin
 
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  <option value="Tryps">Trypsin
 
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  </select><br>
 
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    Please enter the lowest cleavage probability that you would like to be displayed:
 
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  <input type=text name=min_prob size=4 maxlength=4>%
 
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  </dd></dl>
 
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  <P>
 
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  <hr>
 
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  <p> <b><font size=+2>P</font>lease indicate the way you would like the cleavage sites to be displayed</b><br><p>
 
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  <input type=checkbox checked name=cleavage_map value=cleavage_map>
 
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    Map of cleavage sites. Please select the number of amino acid within one block: 
 
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  <select name="block_size"  size=1>
 
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  <option value="10">10
 
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  <option value="20">20
 
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  <option value="30">30
 
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  <option value="40">40
 
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  <option value="50">50
 
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  <option selected value="60">60
 
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  </select><br>
 
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  <input type=checkbox name=alphtable checked value=alphtable>
 
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    Table of sites, sorted alphabetically by enzyme and chemical name<br>
 
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  <input type=checkbox name=seq_table value=seq_table>
 
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    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>
 
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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
 
-
  <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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  <input type=text name=cleave_range_min size=4 maxlength=4> times, and at most
 
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  <input type=text name=cleave_range_max size=4 maxlength=4> times
 
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  <br>
 
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  </form>
 
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  <HR>
 
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</div> <!-- sib_body -->
 
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<!-- ********************************************************************************************** -->
 
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<!-- START OF FOOTER information at the bottom of the page -->
 
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<div id = 'sib_last_update'></div>
 
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<div id = 'sib_footer'> </div>
 
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<!-- END OF FOOTER -->
 
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<!-- ********************************************************************************************** -->
 
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</div> <!-- sib_container -->
 
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</body>
 
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</html>
 
{{Imperial/09/TemplateBottom}}
{{Imperial/09/TemplateBottom}}

Latest revision as of 23:30, 19 October 2009

The Stomach & Proteolysis:

Digestivesystem.jpg

The stomach is the first point at which polypeptides are broken down. It is here that large polypeptides are broken down into peptides. This process broadly involves two steps. First polypeptides are denatured by stomach acid, which causes them to open up. Subsequently, these denatured polypeptides are attacked by the protease pepsin. Pepsin is a powerful protease that cleaves at the N-terminus after aromatic amino acids such as phenylalanine, tryptophan, and tyrosine. The optimum pH of pepsin is from 1.5 to 2, at a pH of above 5 denaturation occurs. This means that pepsin is only functional in the acidic environment of the stomach. Small peptides leaving the stomach are later broken down into amino acids once they enter the duodenum.


The Stomach Simulator

One of the enzymes that we are showcasing is phenylalanine hydroxylase (PAH) (as a treatment for PKU). If this enzyme was simply swallowed in an unencapsulated form it would be cleaved in 146 places by pepsin in the stomach.

Click on the perform button to see a simulated digestion of PAH by pepsin. Alternativly, paste in your own sequence into the box below to see if it would be a good candidate for encapsulation.


references /documentation



Mr. Gene   Geneart   Clontech   Giant Microbes

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