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    <h1 class="title1">Acylation simulation </h2>
 
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Bacterial glycogen and plant starch consist of chains of glucose residues connected by alpha-1,4-glycosidic linkages with alpha-1,6-glycosidic linkages forming branch points. Our  main aim was to produce acylated or butrylated starch. As plants are more difficult to work with, we initially expressed four putative acyltransferases in <i>E. coli </i>to see if we could modify bacterial glycogen. However, the activity on these enzymes is still unknown. We don't know at which position in the glucose molecule that the enzyme might add the acyl group. If the group is added to the free end available at a growing branch, it will compete with the glycogen synthase and disrupt the growth of the molecule. </p>
 
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<p>Even though glycogen acylation has not yet been described, phosphorylation of glycogen has been studied previously in both muscle and bacterial glycogen. Tagliabracci V. S. et al showed that the phosphate in glycogen is present as C2 and C3 phosphomonoesters <sub><a data-id="ref" class="scroll-link">1</a></sub> . Phosphorylation of starch has been also characterized2. According to Blennow A. et al, the phosphate groups bind at the free C6 and C3 hydroxyl groups of the glucose units. Both groups are located at the hydrophilic surface of the double helix, which might affect the stability of the molecule <sub><a data-id="ref" class="scroll-link">2</a></sub>.
 
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We therefore needed to model the putative changes in glycogen structure depending on the location of the modification. Our aim was to produce carbohydrate molecules with 5-10% of the residues modified since this level of butrylation (achieved by chemical modification) has positive benefits to the colon of rats <sub><a data-id="ref" class="scroll-link">3</a></sub>  Our model indicates that this level of modification is only viable if the enzyme can modify any base -  If it can only use the carbon-4 position it would impact on the growth of the molecule.
 
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<p class="space10">To create the glycogen structures we made the following assumptions: </p>
 
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<p class="space10">&bull;C1 doesn't get modified as it's forming a bond in all the residues expect the 1st one. C2, C3, C4 and C6 might get modified.<br/>&bull; The branching occurs in a one-by-one glucose addition, even though the branching enzyme (GlgB) would cut an oligosaccharide from the linear molecule and add it at a branching point <sub><a data-id="ref" class="scroll-link">4</a></sub></p>
 
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    <h3 class="title2">Results from the simulation</h3>
 
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    <h4 class="title2">Glyco2D does work!</h4>
 
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<img src="https://static.igem.org/mediawiki/2015/e/e4/NRP-UEA-Norwich-acylation-fig1.png" href="https://static.igem.org/mediawiki/2015/e/e4/NRP-UEA-Norwich-acylation-fig1.png" alt="..." class="img-responsive mautomargin fancybox" style="cursor: pointer;">
 
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    <h4 class="title2">Acylation on carbon 4</h4>
 
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<img src="https://static.igem.org/mediawiki/2015/8/8b/NRP-UEA-Norwich-acylation-fig2.png" href="https://static.igem.org/mediawiki/2015/8/8b/NRP-UEA-Norwich-acylation-fig2.png" alt="..." class="img-responsive mautomargin fancybox" style="cursor: pointer;">
 
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    <h4 class="title2">Acylation in any available position</h4>
 
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    <h2 class="title1"><a name="1"></a>References</h2>
 
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<p >1. Meléndez-Hevia E., Waddell T.G., and Shelton E.D., 1993, <i> Optimization of molecular design in the evolution of metabolism: The glycogen molecule </i>, Biochem Journal, 295, p. 477–83</p>
 
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<p><a name="2"></a>2. Meléndez R, Meléndez-Hevia E, Mas F, Mach J, Cascante M: <i>Physical constraints in the synthesis of glycogen that influence its structural homogeneity: A two-dimensional approach</i>. Biophys J 1998, 75:106–14.</p>
 
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            </div>
 
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            <div class="row space100">
 
−
                <div  class="col-md-12 text-center">
 
−
                    <h4 class="dark-gray">Designed and developed by the NRP-UEA-Norwich iGEM Team</h4>
 
−
                </div>
 
−
               
 
−
            </div>
 
−
        </div>
 
−
 
−
 
−
    </footer>
 
−
 
−
<script type="text/javascript">
 
−
$(document).ready(function() {
 
−
$(".fancybox").fancybox();
 
−
});
 
−
</script>
 
−
 
−
    <script type="text/javascript">
 
−
        $(document).ready(function()  {
 
−
       
 
−
          /*
 
−
          "Hovernav" navbar dropdown on hover
 
−
          Delete this segment if you don't want it, and delete the corresponding CSS in bst.css
 
−
          Uses jQuery Media Query - see http://www.sitepoint.com/javascript-media-queries/
 
−
          */
 
−
          var mq = window.matchMedia('(min-width: 768px)');
 
−
          if (mq.matches) {
 
−
            $('ul.navbar-nav li').addClass('hovernav');
 
−
          } else {
 
−
            $('ul.navbar-nav li').removeClass('hovernav');
 
−
          };
 
−
          /*
 
−
          The addClass/removeClass also needs to be triggered
 
−
          on page resize <=> 768px
 
−
          */
 
−
          if (matchMedia) {
 
−
            var mq = window.matchMedia('(min-width: 768px)');
 
−
            mq.addListener(WidthChange);
 
−
            WidthChange(mq);
 
−
          }
 
−
          function WidthChange(mq) {
 
−
            if (mq.matches) {
 
−
              $('ul.navbar-nav li').addClass('hovernav');
 
−
        } else {
 
−
              $('ul.navbar-nav li').removeClass('hovernav');
 
−
 
−
            }
 
−
          };
 
−
         
 
−
        });
 
−
 
−
        </script>
 
−
        <script type="text/javascript">
 
−
    $(document).ready(function() {
 
−
    // navigation click actions
 
−
    $('.scroll-link').on('click', function(event){
 
−
    event.preventDefault();
 
−
    var sectionID = $(this).attr("data-id");
 
−
    scrollToID('#' + sectionID, 750);
 
−
    });
 
−
    // scroll to top action
 
−
    $('.scroll-top').on('click', function(event) {
 
−
    event.preventDefault();
 
−
    $('html, body').animate({scrollTop:0}, 'slow');
 
−
    });
 
−
    // mobile nav toggle
 
−
    $('#nav-toggle').on('click', function (event) {
 
−
    event.preventDefault();
 
−
    $('#main-nav').toggleClass("open");
 
−
    });
 
−
    });
 
−
    // scroll function
 
−
    function scrollToID(id, speed){
 
−
    var offSet = 100;
 
−
    var targetOffset = $(id).offset().top - offset;
 
−
    var mainNav = $('#main-nav');
 
−
    $('html,body').animate({scrollTop:targetOffset}, speed);
 
−
    if (mainNav.hasClass("open")) {
 
−
    mainNav.css("height", "1px").removeClass("in").addClass("collapse");
 
−
    mainNav.removeClass("open");
 
−
    }
 
−
    }
 
−
    if (typeof console === "undefined") {
 
−
    console = {
 
−
    log: function() { }
 
−
    };
 
−
      }
 
−
  </script>
 
−
  <script type="text/javascript">
 
−
 
−
          $('a.scroll-link').each( function() {
 
−
                $(this).parent("li").removeClass('active');
 
−
          });
 
−
           
 
−
          $(this).parent("li").addClass('active');
 
−
 
−
 
−
 
−
  </script>
 
−
 
−
<script type="text/javascript">
 
−
    $(document).ready(function() {
 
−
    // navigation click actions
 
−
    $('.scroll-link').on('click', function(event){
 
−
    event.preventDefault();
 
−
    var sectionID = $(this).attr("data-id");
 
−
    scrollToID('#' + sectionID, 750);
 
−
    });
 
−
    // scroll to top action
 
−
    $('.scroll-top').on('click', function(event) {
 
−
    event.preventDefault();
 
−
    $('html, body').animate({scrollTop:0}, 'slow');
 
−
    });
 
−
    // mobile nav toggle
 
−
    $('#nav-toggle').on('click', function (event) {
 
−
    event.preventDefault();
 
−
    $('#main-nav').toggleClass("open");
 
−
    });
 
−
    });
 
−
    // scroll function
 
−
    function scrollToID(id, speed){
 
−
    var offSet = 0;
 
−
    var targetOffset = $(id).offset().top - offSet;
 
−
    var mainNav = $('#main-nav');
 
−
    $('html,body').animate({scrollTop:targetOffset}, speed);
 
−
    if (mainNav.hasClass("open")) {
 
−
    mainNav.css("height", "1px").removeClass("in").addClass("collapse");
 
−
    mainNav.removeClass("open");
 
−
    }
 
−
    }
 
−
    if (typeof console === "undefined") {
 
−
    console = {
 
−
    log: function() { }
 
−
    };
 
−
      }
 
−
  </script>
 
−
 
−
 
−
</body></html>
 

Latest revision as of 15:05, 18 September 2015