Difference between revisions of "Team:NRP-UEA-Norwich/Modeling/3D"

 
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                                       <li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle"  data-toggle="dropdown">Project</a>
 
                                       <li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle"  data-toggle="dropdown">Project</a>
 
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Description">Overview</a></li>
 
                                         <li ><a href="/Team:NRP-UEA-Norwich/Project">Background</a></li>
 
                                         <li ><a href="/Team:NRP-UEA-Norwich/Project">Background</a></li>
 
                                         <li ><a href="/Team:NRP-UEA-Norwich/Approach">Approach</a></li>
 
                                         <li ><a href="/Team:NRP-UEA-Norwich/Approach">Approach</a></li>
 
                                         <li ><a href="/Team:NRP-UEA-Norwich/Results">Results</a></li>
 
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Notebook">Timeline</a></li>                                   
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                                     <li class="dropdown " id="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown">Modelling</a>
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                                     <li class="dropdown " id="dropdown"><a href="/Team:NRP-UEA-Norwich/ModelingAndSoftware" class="dropdown-toggle">Modelling</a>
 
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                                         <li ><a href="/Team:NRP-UEA-Norwich/Modeling/Glyco2D">Glyco2D</a></li>
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                                         <li ><a href="/Team:NRP-UEA-Norwich/Software">Glyco2D</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Modeling/Simulation">Acylation Simulation</a></li>
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                                         <li ><a href="/Team:NRP-UEA-Norwich/Modeling/3D">3D Models</a></li>
 
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                                         <li ><a href="/Team:NRP-UEA-Norwich/Modeling/HowTo">How to Build 3D Models</a></li>
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                                         <li ><a href="/Team:NRP-UEA-Norwich/Modeling">Kinetic Model</a></li>                                
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Modeling/Kinetic">Kinetic Model</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Modeling/3DPrinting">How to 3D Print Molecules</a></li>                                   
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                                     <li  ><a href="/Team:NRP-UEA-Norwich/Attributions">Attributions</a></li>
 
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                                     <li  ><a href="/Team:NRP-UEA-Norwich/Collaborations">Collaborations</a></li>
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                                    <li  ><a href="/Team:NRP-UEA-Norwich/Achievements">Achievements</a></li>                                     
 
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     <h1 class="title1">3D Modelling Overview</h2>
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     <h1 class="title1">3D Modelling Overview</h1>
 
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     <p class="space20">We built these models to see how changing the parameters such as branching degree and the number of tiers affect the overall structure of the molecule in a more chemically accurate way.</p>
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     <p class="space20">We built 3D models to see how changing parameters such as branching degree and the number of tiers affect the overall structure of the molecule in a chemically accurate way.</p>
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<p class="space20">If the interactive 3D model does not load then you may not have webGL enabled. To check if your browsers supports WebGL please click <a href="https://get.webgl.org/">here</a>.</p>
 
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     <h3 class="title">Glycogen</h2>
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     <h3 class="title1">Glycogen</h3>
 
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     <p class="space20"> Glycogen is a polysaccharide composed of glucose units linked by alpha 1-4 glycosidic bonds. Each linear chain contains approximately 13 glucose residues and, except of course for the outermost tier of the molecule, a number of alpha 1-6 glycosidic bonds, which allow branching, that are 3–4 residues apart.</p>
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     <p class="space20"> Glycogen is the glucose storage molecule in animals, bacteria and fungi. It is a polysaccharide composed of monosaccharide glucose units linked by alpha-1,4 glycosidic bonds. Each linear chain contains approximately 13 glucose residues and a number of alpha-1,6 glycosidic bonds, which allow branching, that are 3–4 residues apart. Glycogen is the analogue of starch in plants but is more extensively branched and compact.</p>
  
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        <p class="space20">This simple model - created for our wiki by the SWEET software - shows a small section of a glycogen molecule consisting of 91 glucose units which are contained within 7 branches and 3 tiers. The 1-4 linked sections can be seen to coil into a helical shape, and the 1-6 linkages form helical branches away from the centre of the molecule.</p>
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        <p class="space20">This simple model - created for our wiki by the SWEET software<sub><a data-id="ref" class="scroll-link" style = "color: #002bb8;">1</a></sub> - shows a small section of a glycogen molecule consisting of 91 glucose units which are contained within 7 branches and 3 tiers. The 1,4 linked sections can be seen to coil into a helical shape, and the 1,6 linkages form helical branches away from the centre of the molecule.</p>
  
 
<p class="space20">You can interact with the model using your mouse.</p>
 
<p class="space20">You can interact with the model using your mouse.</p>
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     <h3 class="title">Amylose</h2>
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     <h3 class="title1">3D Printing</h3>
 
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    <p class="space20"> <b>Colon cancer is the second most common cause of cancer death </b> with 30,000 new cases diagnosed every year in England and Wales and a registered cause of death in half that number. </p>
 
  
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        <p class="space20">Recent studies have suggested that <b>high dietary intake of resistant starch</b> may reduce colon cancer and inflammatory bowel disease. Resistant starches escape digestion in the small intestine and are fermented by microbiota in the colon. A small proportion of these colonic bacteria produce <b>short chain fatty acids including butyrate</b>, which can activate apoptosis in colon cancer cells.</p>
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<p class="space20">Our knowledge of developments in 3D printing suggested that we could take advantage of this to generate physical models of the molecules we are interested in. This would be helpful in explaining the chemical structure of these molecules because the models would be truly interactive.</p>
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    <p class="space20">The process of creating a model that is valid to be 3D printed from a PDB file, which is a textual file format describing the three-dimensional structures of molecules, turned out to be very challenging. After what seemed like an impossible task and a number of failed attempts, we managed to successful create a valid 3D model that could be printed. The print itself took just over 28 hours.</p>
  
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<p class="space20">Our project is focused on increasing the amount of butyrate in the colon.</p>
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<p class="space20">You can see some the pictures from our 3D printing adventure in our 3D printing gallery!</p>
  
  
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    <p class="space20"> <b>Colon cancer is the second most common cause of cancer death </b> with 30,000 new cases diagnosed every year in England and Wales and a registered cause of death in half that number. </p>
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        <p class="space20">Recent studies have suggested that <b>high dietary intake of resistant starch</b> may reduce colon cancer and inflammatory bowel disease. Resistant starches escape digestion in the small intestine and are fermented by microbiota in the colon. A small proportion of these colonic bacteria produce <b>short chain fatty acids including butyrate</b>, which can activate apoptosis in colon cancer cells.</p>
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                <img class="img-responsive fancybox mautomargin" src="https://static.igem.org/mediawiki/2015/9/95/NRP-UEA-Norwich-modelpc.png" href = "https://static.igem.org/mediawiki/2015/9/95/NRP-UEA-Norwich-modelpc.png" style="cursor: pointer;">
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    <p class="space20">http://www.biotopics.co.uk/jsmol/glycogen.html</p>
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<p>1. SWEET - a program for constructing 3D models of saccharides from their sequences using standard nomenclature. <a href="http://glycosciences.de/modeling/sweet2/doc/index.php">http://glycosciences.de/modeling/sweet2/doc/index.php</a></p>
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<p class="space20">http://watcut.uwaterloo.ca/webnotes/Metabolism/glycogenStructure.html. </p>
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<p class="space20">"Photonic" and "spintronic" computing is the principle of transferring information by light or electron spin.</p>
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            <p class="space20">Currently, copper wires transfer information in a computer; the process is slowed down as the wires heat up. "Photonic" and "spintronic" computing is the principle of transferring information by light or electron spin.</p>
 
 
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                     <h2 class="gray">MANY THANKS TO OUR SPONSORS</h2>
 
                     <h2 class="gray">MANY THANKS TO OUR SPONSORS</h2>
 
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    <li><img src="https://static.igem.org/mediawiki/2015/e/e3/NRP-UEA-Norwich-Wellcome_Trust_logo.png" width="250" height="100" class="img-grey mautomargin"></a></li>
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    <li><img src="https://static.igem.org/mediawiki/2015/7/74/NRP-UEA-Norwich-IBBA_logo.png" width="125" height="125" class="img-grey mautomargin"></a></li>
 +
    <li><img src="https://static.igem.org/mediawiki/2015/d/d0/NRP-UEA-Norwich-SfAM-Logo.png" width="220" height="100" class="img-grey mautomargin" width="200" height="100"></a></li>
  
  
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$("#glmol01_src").html(ret);
 
$("#glmol01_src").html(ret);
 
glmol01.loadMolecule();
 
glmol01.loadMolecule();
−
});
 
−
 
−
var glmol03= new GLmol('glmol03', true);
 
−
glmol03.defineRepresentation = function() {
 
−
  var all = this.getAllAtoms();
 
−
  var hetatm = this.removeSolvents(this.getHetatms(all));
 
−
  this.colorByAtom(all, {});
 
−
  this.colorByChain(all);
 
−
  var asu = new THREE.Object3D();
 
−
 
 
−
  this.drawBondsAsStick(asu, hetatm, this.cylinderRadius, this.cylinderRadius);
 
−
  this.drawBondsAsStick(asu, this.getResiduesById(this.getSidechains(this.getChain(all, ['A'])), [58, 87]), this.cylinderRadius, this.cylinderRadius);
 
−
  this.drawBondsAsStick(asu, this.getResiduesById(this.getSidechains(this.getChain(all, ['B'])), [63, 92]), this.cylinderRadius, this.cylinderRadius);
 
−
  this.drawCartoon(asu, all, this.curveWidth, this.thickness);
 
−
 
−
  this.drawSymmetryMates2(this.modelGroup, asu, this.protein.biomtMatrices);
 
−
  this.modelGroup.add(asu);
 
−
};
 
−
 
−
$.get("https://2015.igem.org/Team:NRP-UEA-Norwich/Model/Branched?action=raw&ctype=text", function(ret) {
 
−
$("#glmol03_src").html(ret);
 
−
glmol03.loadMolecule();
 
−
});
 
−
 
−
var glmol02= new GLmol('glmol02', true);
 
−
glmol02.defineRepresentation = function() {
 
−
  var all = this.getAllAtoms();
 
−
  var hetatm = this.removeSolvents(this.getHetatms(all));
 
−
  this.colorByAtom(all, {});
 
−
  this.colorByChain(all);
 
−
  var asu = new THREE.Object3D();
 
−
 
 
−
  this.drawBondsAsStick(asu, hetatm, this.cylinderRadius, this.cylinderRadius);
 
−
  this.drawBondsAsStick(asu, this.getResiduesById(this.getSidechains(this.getChain(all, ['A'])), [58, 87]), this.cylinderRadius, this.cylinderRadius);
 
−
  this.drawBondsAsStick(asu, this.getResiduesById(this.getSidechains(this.getChain(all, ['B'])), [63, 92]), this.cylinderRadius, this.cylinderRadius);
 
−
  this.drawCartoon(asu, all, this.curveWidth, this.thickness);
 
−
 
−
  this.drawSymmetryMates2(this.modelGroup, asu, this.protein.biomtMatrices);
 
−
  this.modelGroup.add(asu);
 
−
};
 
−
 
−
$.get("https://2015.igem.org/Team:NRP-UEA-Norwich/Model/Amylopectin?action=raw&ctype=text", function(ret) {
 
−
$("#glmol02_src").html(ret);
 
−
glmol02.loadMolecule();
 
 
});
 
});
 
</script>
 
</script>

Latest revision as of 10:36, 21 October 2015

House of Carbs

3D Modelling Overview

We built 3D models to see how changing parameters such as branching degree and the number of tiers affect the overall structure of the molecule in a chemically accurate way.

If the interactive 3D model does not load then you may not have webGL enabled. To check if your browsers supports WebGL please click here.

Glycogen

Glycogen is the glucose storage molecule in animals, bacteria and fungi. It is a polysaccharide composed of monosaccharide glucose units linked by alpha-1,4 glycosidic bonds. Each linear chain contains approximately 13 glucose residues and a number of alpha-1,6 glycosidic bonds, which allow branching, that are 3–4 residues apart. Glycogen is the analogue of starch in plants but is more extensively branched and compact.

This simple model - created for our wiki by the SWEET software1 - shows a small section of a glycogen molecule consisting of 91 glucose units which are contained within 7 branches and 3 tiers. The 1,4 linked sections can be seen to coil into a helical shape, and the 1,6 linkages form helical branches away from the centre of the molecule.

You can interact with the model using your mouse.

3D Printing

Our knowledge of developments in 3D printing suggested that we could take advantage of this to generate physical models of the molecules we are interested in. This would be helpful in explaining the chemical structure of these molecules because the models would be truly interactive.

The process of creating a model that is valid to be 3D printed from a PDB file, which is a textual file format describing the three-dimensional structures of molecules, turned out to be very challenging. After what seemed like an impossible task and a number of failed attempts, we managed to successful create a valid 3D model that could be printed. The print itself took just over 28 hours.

You can see some the pictures from our 3D printing adventure in our 3D printing gallery!

References

1. SWEET - a program for constructing 3D models of saccharides from their sequences using standard nomenclature. http://glycosciences.de/modeling/sweet2/doc/index.php

MANY THANKS TO OUR SPONSORS

Useful Links

Contact Us

  • nrpuea.igem2015@gmail.com

  • Norwich Research Park,
  • Colney,
  • Norwich, NR4 7UH, UK.

We are the NRP-UEA-Norwich 2015 iGEM Team.

Designed and developed by the NRP-UEA-Norwich iGEM Team