Team:Oxford/alternatives to microcompartments

From 2014.igem.org

(Difference between revisions)
Line 433: Line 433:
<h1>The star peptide- an introduction</h1>
<h1>The star peptide- an introduction</h1>
The degradation pathway of DCM by DcmA produces a number of intermediates. A number of these, such as formaldehyde, are suspected to be toxic to our host bacteria above certain concentrations. In addition to expressing enzymes which break down these intermediates, we are considering two different approaches to further minimize the accumulation of these compounds. Alongside the original idea of using micro-compartments, we have also collaborated with UniMelb iGEM and considered attaching our different enzymes to the arms of a star peptide (link to Melbourne wiki here). In doing so, this increases the likelihood of our intermediates, produced by one enzymatic reaction, interacting with the next enzyme in the reaction pathway thereby limiting their accumulation.
The degradation pathway of DCM by DcmA produces a number of intermediates. A number of these, such as formaldehyde, are suspected to be toxic to our host bacteria above certain concentrations. In addition to expressing enzymes which break down these intermediates, we are considering two different approaches to further minimize the accumulation of these compounds. Alongside the original idea of using micro-compartments, we have also collaborated with UniMelb iGEM and considered attaching our different enzymes to the arms of a star peptide (link to Melbourne wiki here). In doing so, this increases the likelihood of our intermediates, produced by one enzymatic reaction, interacting with the next enzyme in the reaction pathway thereby limiting their accumulation.
 +
 +
</div>
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
<head>
 +
<style type="text/css">
 +
.row { vertical-align: top; height:auto !important; }
 +
.list {display:none; }
 +
.show {display: none; }
 +
.hide:target + .show {display: inline; }
 +
.hide:target {display: none; }
 +
.hide:target ~ .list {display:inline; }
 +
@media print { .hide, .show { display: none; } }
 +
</style>
 +
 +
 +
 +
<div class="row">
 +
<a href="#hide1" class="hide" id="hide1"><div class="orange_news_block2">
 +
<h1white>Our reaction</h1white>
 +
<img src="https://static.igem.org/mediawiki/2014/4/4d/Oxford_plus-sign-clip-art.png" style="float:right;position:relative; width:2%;" />
 +
</div></a>
 +
 +
<a href="#show1" class="show" id="show1"><div class="orange_news_block2">
 +
<h1white>Our Reaction</h1white>
 +
</div></a>
 +
<div class="list">
 +
<div class="white_news_block">
<br><br>
<br><br>
Our reaction pathway is as follows:
Our reaction pathway is as follows:
<br><br>
<br><br>
-
Reaction 1: DCM + DcmA toxic intermediate (formaldehyde)
+
Reaction 1: DCM + DcmA --> toxic intermediate (formaldehyde)
<br><br>
<br><br>
-
Reaction 2: toxic intermediate (formaldehyde) + FdhA neutral product (formate)
+
Reaction 2: toxic intermediate (formaldehyde) + FdhA --> neutral product (formate)
<br><br>
<br><br>
The Melbourne star peptide length can be varied in order to control the rate of reaction. Melbourne, however, were unsure of the form of the relationship between these length and rate and asked Oxford to develop a model of this. We hypothesized that, broadly speaking, the effect of increasing the length of the tether would result in a decrease in reaction rate due to two factors- the increased time taken to diffuse from one enzyme to the other and the decreased likelihood of colliding with an enzyme as the distance travelled increases.
The Melbourne star peptide length can be varied in order to control the rate of reaction. Melbourne, however, were unsure of the form of the relationship between these length and rate and asked Oxford to develop a model of this. We hypothesized that, broadly speaking, the effect of increasing the length of the tether would result in a decrease in reaction rate due to two factors- the increased time taken to diffuse from one enzyme to the other and the decreased likelihood of colliding with an enzyme as the distance travelled increases.
Line 447: Line 485:
<h1>A visualization of the star peptide- the key variable is the distance between the active sites of the two key enzymes. We were asked to propose a relationship between this distance and reaction rate.</h1>
<h1>A visualization of the star peptide- the key variable is the distance between the active sites of the two key enzymes. We were asked to propose a relationship between this distance and reaction rate.</h1>
</div>
</div>
 +
</div>
 +
</div>
 +
 +

Revision as of 15:06, 19 September 2014

#list li { list-style-image: url("https://static.igem.org/mediawiki/2014/6/6f/OxigemTick.png"); } }


Alternatives to micro-compartments


Collaboration with Melbourne iGEM team

The star peptide- an introduction

The degradation pathway of DCM by DcmA produces a number of intermediates. A number of these, such as formaldehyde, are suspected to be toxic to our host bacteria above certain concentrations. In addition to expressing enzymes which break down these intermediates, we are considering two different approaches to further minimize the accumulation of these compounds. Alongside the original idea of using micro-compartments, we have also collaborated with UniMelb iGEM and considered attaching our different enzymes to the arms of a star peptide (link to Melbourne wiki here). In doing so, this increases the likelihood of our intermediates, produced by one enzymatic reaction, interacting with the next enzyme in the reaction pathway thereby limiting their accumulation.
Our reaction
Our Reaction


Our reaction pathway is as follows:

Reaction 1: DCM + DcmA --> toxic intermediate (formaldehyde)

Reaction 2: toxic intermediate (formaldehyde) + FdhA --> neutral product (formate)

The Melbourne star peptide length can be varied in order to control the rate of reaction. Melbourne, however, were unsure of the form of the relationship between these length and rate and asked Oxford to develop a model of this. We hypothesized that, broadly speaking, the effect of increasing the length of the tether would result in a decrease in reaction rate due to two factors- the increased time taken to diffuse from one enzyme to the other and the decreased likelihood of colliding with an enzyme as the distance travelled increases.



A visualization of the star peptide- the key variable is the distance between the active sites of the two key enzymes. We were asked to propose a relationship between this distance and reaction rate.