Difference between revisions of "Team:IIT Delhi/modelling"
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background-size:100% 100%; | background-size:100% 100%; | ||
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.icons{ | .icons{ | ||
position:absolute; | position:absolute; | ||
margin-top:1.5%; | margin-top:1.5%; | ||
| − | width: | + | width:6%; |
| − | padding-left: | + | padding-left:0; |
-webkit-transition: all 1s ease; | -webkit-transition: all 1s ease; | ||
-moz-transition: all 1s ease; | -moz-transition: all 1s ease; | ||
-o-transition: all 1s ease; | -o-transition: all 1s ease; | ||
transition all 1s ease; | transition all 1s ease; | ||
| + | } | ||
| + | #icon7{ | ||
| + | margin-top:2%; | ||
| + | margin-left:-0.5%; | ||
| + | width:7%; | ||
| + | } | ||
| + | #icon6{ | ||
| + | margin-top:1.5% !important; | ||
| + | width:5.5% !important; | ||
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#IITDigem_logo{ | #IITDigem_logo{ | ||
position:absolute; | position:absolute; | ||
| − | margin-top: | + | margin-top:2%; |
| − | margin-left: | + | margin-left:11%; |
| − | width: | + | width:10%; |
} | } | ||
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#tourimg{ | #tourimg{ | ||
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margin-bottom: 10px; | margin-bottom: 10px; | ||
margin-top: 30px; | margin-top: 30px; | ||
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position:fixed; | position:fixed; | ||
margin-top:0%; | margin-top:0%; | ||
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| − | height: | + | height:150px; |
| − | width: | + | width:150px; |
| + | opacity:1; | ||
z-index:999; | z-index:999; | ||
} | } | ||
ul.ldd_menu a{ | ul.ldd_menu a{ | ||
| − | + | text-decoration:none; | |
} | } | ||
ul.ldd_menu > li{ | ul.ldd_menu > li{ | ||
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| − | + | position:fixed; | |
| − | + | margin-left:-2%; | |
| − | + | width:150px; | |
| + | z-index: 9999; | ||
| + | height:150px; | ||
| + | border-radius:0 0 190px 0; | ||
| + | transition-delay: 300ms; | ||
| + | |||
| + | } | ||
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| + | ul.ldd_menu > li:hover{ | ||
| + | width:100%; | ||
| + | transition-delay: 0ms; | ||
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| + | } | ||
| + | .ldd_submenu ul{ | ||
| + | margin-left:4%; | ||
| + | } | ||
| + | .ldd_submenu ul li{ | ||
| + | padding-bottom:3%; | ||
} | } | ||
ul.ldd_menu > li > span{ | ul.ldd_menu > li > span{ | ||
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z-index:-1000; | z-index:-1000; | ||
position:absolute; | position:absolute; | ||
| − | margin-left: | + | margin-left:0%; |
| − | width: | + | width:0%; |
| − | font-size: | + | height:100%; |
| + | font-size:100%; | ||
color:green; | color:green; | ||
opacity:0; | opacity:0; | ||
| − | + | background-color:white; | |
| − | + | height:100%; | |
| − | + | line-height:100%; | |
| − | + | cursor:default; | |
| − | + | padding:0px 20px; | |
| − | + | border-radius:0 0 190px 0; | |
| − | border-radius: | + | text-shadow:0px 0px 1px #CCC; |
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| − | + | } | |
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display: inline-block; | display: inline-block; | ||
border-left:1px dotted #FFF; | border-left:1px dotted #FFF; | ||
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padding-right: 5px; | padding-right: 5px; | ||
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<a href="https://2015.igem.org/Team:IIT_Delhi"><img id="IITDigem_logo" src="https://static.igem.org/mediawiki/2015/f/ff/IITDigem_logo.png"></a> | <a href="https://2015.igem.org/Team:IIT_Delhi"><img id="IITDigem_logo" src="https://static.igem.org/mediawiki/2015/f/ff/IITDigem_logo.png"></a> | ||
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<!--------------------------TOP NAV HTML STARTS------------------------------------------> | <!--------------------------TOP NAV HTML STARTS------------------------------------------> | ||
<nav> | <nav> | ||
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<!--------------------------ABSTRACT------------------------------------------> | <!--------------------------ABSTRACT------------------------------------------> | ||
<div class="iconsDiv" style="margin-left:22%;"> | <div class="iconsDiv" style="margin-left:22%;"> | ||
| − | <a href="https://2015.igem.org/Team:IIT_Delhi/abstract"><img class="icons" id="icon5" src="https://static.igem.org/mediawiki/2015/ | + | <a href="https://2015.igem.org/Team:IIT_Delhi/abstract"><img class="icons" id="icon5" src="https://static.igem.org/mediawiki/2015/b/b2/IITDabstract_copy.png"></a> |
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<!--------------------------PROJECT------------------------------------------> | <!--------------------------PROJECT------------------------------------------> | ||
<div class="iconsDiv" style="margin-left:29%;"> | <div class="iconsDiv" style="margin-left:29%;"> | ||
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<div class="iconsDiv" style="margin-left:50%;"> | <div class="iconsDiv" style="margin-left:50%;"> | ||
| − | <a href="https://2015.igem.org/Team:IIT_Delhi/modelling"><img class="icons" id="icon2" src="https://static.igem.org/mediawiki/2015/ | + | <a href="https://2015.igem.org/Team:IIT_Delhi/modelling"><img class="icons" id="icon2" src="https://static.igem.org/mediawiki/2015/a/a4/IITDmodelling1_copy.png"></a> |
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| − | <a href="https://2015.igem.org/Team:IIT_Delhi/team"><img class="icons" id="icon3" src="https://static.igem.org/mediawiki/2015/ | + | <a href="https://2015.igem.org/Team:IIT_Delhi/team"><img class="icons" id="icon3" src="https://static.igem.org/mediawiki/2015/e/e9/IITDteam1_copy.png"></a> |
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<div class="iconsDiv" style="margin-left:64%;"> | <div class="iconsDiv" style="margin-left:64%;"> | ||
| − | <a href="https://2015.igem.org/Team:IIT_Delhi/human_practices"><img class="icons" id="icon6 | + | <a href="https://2015.igem.org/Team:IIT_Delhi/human_practices"><img class="icons" id="icon6" src="https://static.igem.org/mediawiki/2015/6/61/IITDethics1.png"></a> |
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<div class="iconsDiv" style="margin-left:71%;"> | <div class="iconsDiv" style="margin-left:71%;"> | ||
| − | <a href="https://2015.igem.org/Team:IIT_Delhi/ethics"><img class="icons" id="icon7" src="https://static.igem.org/mediawiki/2015/5/ | + | <a href="https://2015.igem.org/Team:IIT_Delhi/ethics"><img class="icons" id="icon7" src="https://static.igem.org/mediawiki/2015/5/5c/IITDhp_copy.png"></a> |
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</div> | </div> | ||
| − | <a href="http://www.igem.org/Main_Page"><img id="igemlogo" style="width: | + | <a href="http://www.igem.org/Main_Page"><img id="igemlogo" style="width:14%;margin-left:82%;position:absolute;margin-top:0%;" src="https://static.igem.org/mediawiki/2015/1/19/Toronto_2015_images_igem.png" /></a> |
</nav> | </nav> | ||
<!--------------------------TOP NAV HTML BULGING ICONS ENDS------------------------------------------> | <!--------------------------TOP NAV HTML BULGING ICONS ENDS------------------------------------------> | ||
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<!---------------TOUR CANCELLED-------------------------> | <!---------------TOUR CANCELLED-------------------------> | ||
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<!---------------TOUR CANCELLED-------------------------> | <!---------------TOUR CANCELLED-------------------------> | ||
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<!------------Span sitemap image----------> | <!------------Span sitemap image----------> | ||
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<ul id="ldd_menu" class="ldd_menu" style="position:absolute;"> | <ul id="ldd_menu" class="ldd_menu" style="position:absolute;"> | ||
<li> | <li> | ||
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<!--- | <!--- | ||
<img id="spanimg" src="https://static.igem.org/mediawiki/2015/6/6b/IITDSitemap.png"> | <img id="spanimg" src="https://static.igem.org/mediawiki/2015/6/6b/IITDSitemap.png"> | ||
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</ul> | </ul> | ||
<ul> | <ul> | ||
| − | <li class="ldd_heading"><a style="color:white;" href="https://2015.igem.org/Team:IIT_Delhi/human_practices"> | + | <li class="ldd_heading"><a style="color:white;" href="https://2015.igem.org/Team:IIT_Delhi/human_practices">ETHICS</a></li> |
<li><a href="https://2015.igem.org/Team:IIT_Delhi/human_practices#collaborations">COLLABORATIONS</a></li> | <li><a href="https://2015.igem.org/Team:IIT_Delhi/human_practices#collaborations">COLLABORATIONS</a></li> | ||
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</ul> | </ul> | ||
<ul> | <ul> | ||
| − | <li class="ldd_heading"><a style="color:white;" href="https://2015.igem.org/Team:IIT_Delhi/ethics"> | + | <li class="ldd_heading"><a style="color:white;" href="https://2015.igem.org/Team:IIT_Delhi/ethics">HUMAN PRACTICES</a></li> |
<li><a href="https://2015.igem.org/Team:IIT_Delhi/ethics#orientation">ORIENTATION</a></li> | <li><a href="https://2015.igem.org/Team:IIT_Delhi/ethics#orientation">ORIENTATION</a></li> | ||
<li><a href="https://2015.igem.org/Team:IIT_Delhi/ethics#openhouse">OPEN HOUSE</a></li> | <li><a href="https://2015.igem.org/Team:IIT_Delhi/ethics#openhouse">OPEN HOUSE</a></li> | ||
Revision as of 22:52, 18 September 2015
IntroductionOf the proteins used in our project, three of them are Cytochrome C protein, wherein Heme has a very important role to play. However, the pathway of Heme biosynthesis is extremely complicated. In fact, no one has modeled it properly till date. As heme synthesis was our fundamental problem, we put on a lot of efforts in modelling it properly. What follows next is a brief insight to all that we have done. |
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Mathematical model
Pathway of heme production in E. coli (C-5 pathway from glutamate):
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The rest of the reactions in this pathway are assumed to proceed via Henri-Michaelis-Menten kinetics:
| Enzyme | Km (micromol/l) |
|---|---|
| Uroporphyrinogen decarboxylase ( hemE) | 6.0 |
| Coproporphyrinogen iii dehydrogenase | 210 |
| Protoporphyrinogen dehydrogenase (HemG) | 7 |
| Ferrochelatase(hemH) | 4.7 |
| Glutamate-tRNA synthase | 1.9 |
| Glutamate-1-semialdehyde 2,1-aminomutase | 46 |
| Porphobilinogen synthase | 800 |
Km and Vmax values of hydroxymethylbilane synthase:
Stimulation
After putting in the rate laws and the values of various parameters in Copasi software, following graphs were obtained for the concentrations and rate of formation of various species involved (Copasi has been used for obtaining all graphs and mathematical equations):
 Fig 1: Amount of ferroheme b formed in the cytoplasm. |
Fig 2: Amount of ferroheme transported to the periplasm |
Fig 3: rate of formation of ferroheme in the cytosol |
Fig 4: rate of transfer of ferroheme from the cytoplasm to the periplasm. |
The following are the differential equations associated with the above processes:
After production of ferroheme, the cytochrome –c protein and the ferroheme are transported to the periplasm, where they form a complex via covalent bonding. At this point the protein becomes completely active.
Interpretation
After this, the following reactions take place, depending on the protein produced:
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3. Nitrous oxide reduction (NosZ protein; Km = 0.007 mM)
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