Team:Imperial College London/Stomach

From 2009.igem.org

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{{Imperial/09/TemplateTop}}  
{{Imperial/09/TemplateTop}}  
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=<b>Human Digestive Proteases:</b>=
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=<b>The Stomach & Proteolysis:</b>=
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The stomach serves to break large proteins into peptides. These peptides are then broken down into amino acids once they enter the duodenum.
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[[Image:Digestivesystem.jpg|100px|left]]
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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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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.
{{Imperial/09/Division}}
{{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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{{Imperial/09/Division}}
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=Peptide cutter=
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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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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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<html>
<html>
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   <div id = 'sib_body'>     
   <div id = 'sib_body'>     
   <form method=POST action="http://www.expasy.ch/cgi-bin/peptidecutter/peptidecutter.pl" target="_blank">
   <form method=POST action="http://www.expasy.ch/cgi-bin/peptidecutter/peptidecutter.pl" target="_blank">
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   <textarea name="protein" rows=12 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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   <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>
      
      
   <input type="submit" value="Perform">  
   <input type="submit" value="Perform">  
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  <input type="reset" value="Reset">
 
   <input type=hidden name=enzyme_number value= less_enzymes checked>
   <input type=hidden name=enzyme_number value= less_enzymes checked>
   <input type=hidden name=enzyme  value=Pn1.3 checked>
   <input type=hidden name=enzyme  value=Pn1.3 checked>
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==Duodenum==
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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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Endopeptidases (trypsin, chymotryopsin, elastase)
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</html>
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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/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

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