Difference between revisions of "Team:UCLA/Notebook/Honeybee Silk/21 May 2015"

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{{Template:UCLA}}
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{{Template_All_Teams}}
  
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This was my approach to designing the protease sites -Phillip
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<!-- Declare that you are going to use html code instead of wiki code -->
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<html>
  
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Using the DSSP algorithm from PDB, the parts of the protein with no alpha helices, beta sheets, or turns and five or greater amino acids are the following. 
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<!-- Start of CSS-->
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30-35, 64-72, 123-129, 131-139, 216-220, 228-233, 298-302, 331-336, 417-422
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<style type="text/css">
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Revised sites in terms of location. Bold indicates insertion
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Top candidates are based on two criteria:
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/* PAGE LAYOUT */
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1. Exposure at the surface for protease accessibility
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2. Speculated to have minimal conformational changes by insertion
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In general, original proline residues on the side were kept, in case they were involved in transitioning between secondary structural elements.  Also, insertions were flanked  with glycines in order to allow extra flexibility. 
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131-139*: (KTDDNPDGA) to KTDDNPD'''GLVPRGS'''GA.  Satisfies 1 and 2.
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/* Change Background color*/
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body {
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background-color: #fff;
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}
  
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228-233: (DRTLPI) to DRTL'''GLVPRGSG'''IPI.  Satisfies 1.
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/* Creates a container that will wrap all of the content inside your wiki pages. */
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#mainContainer { 
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width: 978px;
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overflow:hidden;
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float:left;
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margin-left:20px;
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margin-bottom: 10px;
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background-color: #fff;
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border-bottom: 14px solid #565656;
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border-right: 2px solid #565656;
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border-left: 2px solid #565656;
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border-top: 2px solid #565656;
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font-family: "Trebuchet MS", Helvetica, sans-serif;
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}
  
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331-336*: (TRPILS) to TRP'''GLVPRGSG'''ILS.  Satisfies 1 and 2, depending on oligomerization geometry.
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/* Creates the container for the menu */
 +
#menuContainer {
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float:left;
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width: 134px;
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padding: 20px 0px;
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border-top: 14px solid #565656;
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background-color: #E8E8E9;
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}
  
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298-302*: (IPSGP) to IPS'''GLVPRGSG'''P.  Satisfies 1 and 2, depending on oligomerization geometry.
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/* Creates the container for the content */
 +
#contentContainer {
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padding-top:20px;
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padding-right:10px;
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margin-bottom: 20px;
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width: 814px;
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padding-left: 20px;
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float: left;
 +
background-color: #fff;
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border-top: 14px solid #565656;
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font-family: "Trebuchet MS", Helvetica, sans-serif;
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}
  
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216-220: (IDVPA) to IDV'''GLVPRGSG'''PA.
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/*Set up height place holder for the banner*/
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#bannerContainer {
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height:200px;
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margin:auto;
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text-align:center;
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                                background-image: url("https://static.igem.org/mediawiki/2015/4/48/Team_UCLA_banner.jpg");
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                                background-size: cover;
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color: #24B694;
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}
  
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64-72:  (SSQPTTGYD) to SSQPTT'''GLVPRGSG'''YD
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/*VISUAL STYLE (TABLES, FONTS, LINKS, IMAGES, UL) */
  
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417-422: (RMGAVT) to RMG'''LVPRGSG'''AVT.  Satisfies 1, depending on geometry.
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/*Change the styling of text for everything inside main container*/
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#mainContainer p {
 +
font-size: 13px;
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color: #000000;
 +
}
 +
 +
/*This changes the color and font family */
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#contentContainer h1, h2, h3, h4, h5, h6 {
 +
color: #565656;
 +
border-bottom: none;
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font-weight: bold;
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font-family: "Trebuchet MS", Helvetica, sans-serif;
 +
margin-top:10px;
 +
}
  
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For the available pymol file, downloaded the file named "2015-05-19 3vdx chains and sites"
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/*Style of the links - links are different inside the menu */
 +
#contentContainer a {
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font-weight: bold;
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color: #23b593;
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}
  
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https://drive.google.com/drive/folders/0ByuQle2_4oafS3N2b1RiajZsWTQ/0ByuQle2_4oafflNRbnktanJJRmx0Y3hLb2NCR1NWRlpoOVE4ZnRHUXM5U1FtcEtRekhWck0/0B7kb5ShZyyqVfm5HVmt4ZGlqeFJVLUdmc2ZsRUZleWo5MjQ0U1B3eFB5V3BKcHZEYzl3TDQ/0B7kb5ShZyyqVflZSdjZmZzlBV185ZDd4VXNyMkNoZzlzYXl2MHRhSURIazAwV0xWWGt1U00
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  /* Styling links on hover- links are different inside the menu */
 +
#contentContainer a:hover {
 +
color: #59bf92;
 +
}
 +
 
 +
/*Change the styling of tables */
 +
        #contentContainer table {
 +
    border: 1px solid #565656;
 +
    border-collapse: collapse;
 +
    width: 90%
 +
    margin: auto;
 +
    margin-bottom: 15px;
 +
    margin-top: 15px;
 +
    margin-right: 10px;
 +
    margin-left: 10px;
 +
    }
 +
 
 +
/*Change the styling of table cells*/
 +
    #contentContainer  td {
 +
    padding: 10px;
 +
    border: 1px solid #565656;
 +
    border-collapse: collapse;
 +
    vertical-align: text-top;
 +
    }
 +
 
 +
/*Change the styling of table headers */
 +
    #contentContainer th {
 +
    background-color: #E8E8E9;
 +
    padding: 10px;
 +
    border: 1px solid #565656;
 +
    border-collapse: collapse;
 +
    vertical-align: text-top;
 +
    }
 +
 
 +
 
 +
 
 +
/*MENU STYLING */
 +
 
 +
/*Styling for the links in the menu */
 +
#menuContainer a {
 +
color: #565656;
 +
text-decoration:none;
 +
font-weight: bold;
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}
 +
 
 +
/* Sets the style for lists inside menuContainer  */
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#menuContainer ul {
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list-style: none;
 +
margin-left:0px;
 +
}
 +
 
 +
/*Styles the list items to become menu buttons */
 +
#menuContainer ul li {
 +
text-align: center;
 +
display: block;
 +
width: 100%;
 +
height:30px;
 +
padding-top:10px;
 +
}
 +
 
 +
/*For the menu buttons, changes the color when hovering*/
 +
#menuContainer li:hover {
 +
color:  #FFF;
 +
background-color: #24B694;
 +
}
 +
 
 +
/*Submenus are not displayed as default*/
 +
#menuContainer li ul {
 +
display: none;
 +
padding-top:15px;
 +
margin-left: -19px;
 +
}
 +
 
 +
/*Submenus are displayed when hovering the menu button */
 +
#menuContainer li:hover ul {
 +
/*display: inline-block; */
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display: block;
 +
position: absolute;
 +
float:right;
 +
margin-left: 134px;
 +
margin-top:-42px;
 +
}
 +
 
 +
/*Style the submenu buttons*/
 +
#menuContainer li ul li{
 +
background-color: #59BF92;
 +
padding-left:20px;
 +
padding-right:20px;
 +
height:30px;
 +
padding-top:10px;
 +
                                padding-bottom:10px;
 +
margin-top:-2px;
 +
color: #565656;
 +
width: 150px;
 +
}
 +
 
 +
/*CLASSES */
 +
 
 +
/*Clear class for all the pages, adds spacing too*/
 +
.clear{
 +
clear:both;
 +
height: 10px;
 +
}
 +
 
 +
 
 +
/* highlight box for special messages */
 +
    .highlightBox {
 +
        width:500px;
 +
        margin:auto;
 +
        background-color: #E8E8E9;
 +
margin-bottom: 15px;
 +
margin-top: 15px;
 +
padding: 15px;
 +
padding-top: 5px;
 +
    }
 +
 
 +
 
 +
</style>
 +
<!-- End of CSS -->
 +
 
 +
 
 +
<!-- Start of the template html elements. -->
 +
<div id ="mainContainer"><!--The closing tag for mainContainer should be placed at the bottom of each content page.-->
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 +
 
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<div id="bannerContainer">
 +
</div>
 +
 
 +
<!-- Start of menu -->
 +
<div id="menuContainer">
 +
 
 +
<!-- This list is your menu, every list item is a menu button and nested listed become submenu buttons -->
 +
<ul>
 +
<a href="https://2015.igem.org/Team:UCLA"><li>HOME</li></a>
 +
 
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<a href="https://2015.igem.org/Team:UCLA/Team"><li>TEAM</li></a>
 +
 
 +
<a href="#"><li>PROJECTS
 +
            <ul>
 +
<!-- <a href="https://2015.igem.org/Team:UCLA/Description"><li>Description</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Experiments"><li>Experiments &amp; Protocols</li></a> 
 +
<a href="https://2015.igem.org/Team:UCLA/Results"><li>Results</li></a> 
 +
<a href="https://2015.igem.org/Team:UCLA/Design"><li>Design</li></a>-->
 +
<a href="https://2015.igem.org/Team:UCLA/Projects/Silks"><li>Silk Genetics</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Projects/Functionalization"><li>Functionalization</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Projects/Materials"><li>Materials Processing</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Projects/Protein_Cages"><li>Protein Cages</li></a>
 +
</ul>
 +
</li></a>
 +
 
 +
<a href="#"><li>PARTS
 +
            <ul>
 +
<a href="https://2015.igem.org/Team:UCLA/Parts"><li>Team Parts</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Basic_Part"><li>Basic Parts</li></a> 
 +
<a href="https://2015.igem.org/Team:UCLA/Composite_Part"><li>Composite Parts</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Part_Collection"><li>Part Collection</li></a> 
 +
</ul>
 +
</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook"><li>NOTEBOOKS
 +
                                                <ul>
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/Spider_Silk_Genetics"><li>Spider Silk Genetics</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/Honeybee_Silk"><li>Honeybee Silk</li></a> 
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/Recombinant_Expression"><li>Recombinant Silk Functionalization</li></a> 
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/Materials"><li>Materials  Processing</li></a> 
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/Protein_Cages"><li>Protein Cages</li></a>
 +
                                                        <a href="https://2015.igem.org/Team:UCLA/Notebook/Interlab_Study"><li>UCLA Measurement Interlab Study</li></a>
 +
</ul>
 +
                                        </li></a>
 +
 
 +
<a href="#"><li>MEETING NOTES
 +
                                                <ul>
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/General_Meetings"><li>General Meetings</li></a>
 +
                                                        <a href="https://2015.igem.org/Team:UCLA/Notebook/Coordinator_Meetings"><li>Coordinator Meetings</li></a>
 +
<a href="https://2015.igem.org/Team:UCLA/Notebook/Advisor_Meetings"><li>Advisor Meetings</li></a>   
 +
</ul>
 +
                                        </li></a>
 +
 
 +
     
 +
<a href="https://2015.igem.org/Team:UCLA/Attributions"><li>ATTRIBUTIONS</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Collaborations"><li>COLLABORATIONS</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Practices"><li>HUMAN PRACTICES</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Safety"><li>SAFETY</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Modeling"><li>MODELING</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Measurement"><li>MEASUREMENT STUDY</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Software"><li>SOFTWARE</li></a>
 +
 
 +
<a href="https://2015.igem.org/Team:UCLA/Entrepreneurship"><li>ENTREPRENEURSHIP</li></a>
 +
 
 +
</ul>
 +
</div>
 +
<!-- End of menu  -->
 +
 
 +
<!-- Start of content -->
 +
<div id="contentContainer"> <!--The closing tag for contentContainer should be placed at the bottom of each content page.-->
 +
</html>
 +
 
 +
='''Inoculation of 5/19 Transformation'''=
 +
 
 +
*I picked four colonies from the 1:1 kanamycin plate and suspended each in 100uL ddH2O
 +
*Each sample was inoculated in 3 different culture tubes with 5mL LB broth and 5uL 1000X kanamycin and was incubated at 37C.

Latest revision as of 21:15, 10 July 2015