Difference between revisions of "Team:Aalto-Helsinki/Parts"

 
(15 intermediate revisions by 5 users not shown)
Line 5: Line 5:
 
<!-- Content of the page is here -->
 
<!-- Content of the page is here -->
  
−
<div id="color-block-com"><span>
+
<div id="color-block-com">
−
  <div class="text1">COMMUNITY</div>
+
    <span>
−
    <div class="text2">
+
        <div class="text1">COMMUNITY</div>
−
<a href="https://2017.igem.org/Team:Aalto-Helsinki/Community">Overview</a><br>
+
        <div class="text2">
−
        <a style="text-decoration: underline" href="https://2017.igem.org/Team:Aalto-Helsinki/Parts">Parts</a><br>
+
            <a href="https://2017.igem.org/Team:Aalto-Helsinki/Community">Overview</a>
−
        <a href="https://2017.igem.org/Team:Aalto-Helsinki/Interlab">Interlab</a><br>
+
            <br>
−
        <a href="https://2017.igem.org/Team:Aalto-Helsinki/Collaborations">Collaborations</a>
+
            <a style="text-decoration: underline" href="https://2017.igem.org/Team:Aalto-Helsinki/Parts">Parts</a>
−
  </div>
+
            <br>
−
  </span>
+
            <a href="https://2017.igem.org/Team:Aalto-Helsinki/Composite_Part">Composite Part</a>
 +
            <br>
 +
            <a href="https://2017.igem.org/Team:Aalto-Helsinki/Improve">Improved Part</a>
 +
            <br>
 +
            <a href="https://2017.igem.org/Team:Aalto-Helsinki/InterLab">InterLab</a>
 +
            <br>
 +
            <a href="https://2017.igem.org/Team:Aalto-Helsinki/Collaborations">Collaborations</a>
 +
        </div>
 +
    </span>
 
</div>
 
</div>
  
 
<div class="container">
 
<div class="container">
−
<div class="introtext">
+
    <div class="introtext">
 +
 
 +
        <h3 style="color: #006699;">Basic Parts</h3>
 +
 
 +
                <p id="paragraph">
 +
                    This section lists all the basic parts that we have made and used during our project.
 +
                </p>
 +
 
 +
 
  
−
<h3 style="color: #006699;">Parts</h3>
 
−
<p id="paragraph">
 
−
We all are in this together! With a combined effort, we can make a positive impact on our planet and on the people and other species that we share it with. The “Community” section of our wiki is about cooperative practices, such as creating and characterizing BioBrick Parts for the Registry, contributing to standardization of methods by taking part in the Interlab Study and collaboration with other iGEM teams. What is unique to iGEM, collaborations can also focus on human practices and other collaborative efforts that benefit the community, as is the case with many of our collaborations.
 
 
</p>
 
</p>
 +
 
</div>
 
</div>
 
</div>
 
</div>
  
−
<div id="quote-block-com">
+
<img src="https://static.igem.org/mediawiki/2017/f/f4/T--Aalto-Helsinki--horizontal.png">
−
<div class="quote-mark"><q></q></div>
+
 
−
<div class="quote-text">This is a shorter quote. Let us see how it looks.</div>
+
<div class="container">
−
<div class="quote-person">Short people have short quotes</div>
+
<div class="basictext">
 +
 
 +
                <h4>1]
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342000">BBa_K2342000</a>
 +
                </h4>
 +
                <p id="paragraph">
 +
                    DCD-1L, Dermcidin derived peptide
 +
                    <br>
 +
                    <br>
 +
                    <img src="https://static.igem.org/mediawiki/2017/7/7d/T--Aalto-Helsinki--part-dcd1l.png">
 +
                    <br>
 +
                    <br>The part codes for the expression of dermcidin derived DCD-1L peptide. Dermcidin is a recently discovered
 +
                    antimicrobial peptide (AMP) found in primates with no homology to other know AMPs. It is expressed in
 +
                    a constitutive manner in eccrine sweat glands and secreted to epidermal surface as a part of the first line
 +
                    of defense. Mature dermcidin precursor is 110 amino acids long, including a signal peptide. Once antimicrobial
 +
                    peptide precursor is secreted with sweat to epidermal surface, 19 amino acid long signal peptide is cleaved,
 +
                    and it goes under further proteolytic processing leading to several dermcidin derived peptides such as
 +
                    DCD-1 and DCD-1L. DCD-1L is one of the most abundant forms of dermcidin derived peptides. DCD-1L is a 48 amino
 +
                    acid long anionic peptide active against wide spectrum of bacteria including
 +
                    <i>Staphylococcus aureus</i>,
 +
                    <i>Escherichia coli</i>, and
 +
                    <i>Propionibacterium acnes</i>.
 +
                </p>
 +
                <p id="paragraph">
 +
                    For more details on the production and usage of this part please check the composite part page:
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342006">BBa_K2342006</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342007">BBa_K2342007</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342008">BBa_K2342008</a>.
 +
                </p>
 +
 
 +
 
 +
                <h4>2]
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342001">BBa_K2342001</a>
 +
                </h4>
 +
                <p id="paragraph">
 +
                    SUMO fusion tag, Smt3
 +
                    <br>
 +
                    <br>
 +
                    <img src="https://static.igem.org/mediawiki/2017/7/7b/T--Aalto-Helsinki--part-smt3.png">
 +
                    <br>
 +
                    <br>Employing of Smt3 tag is beneficial in several aspects in expression of recombinant proteins. Ulp1 is
 +
                    a robust enzyme that specifically facilitates cleavage of Smt3, leaving protein of interest unbound to the
 +
                    tag. SUMO tag is known for its effect on solubility and preventing inclusion bodies of fusion peptide,
 +
                    significantly easing purification step.
 +
                </p>
 +
                <p id="paragraph">
 +
                    For more details on the production and usage of this part please check the composite part page:
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342006">BBa_K2342006</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342007">BBa_K2342007</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342008">BBa_K2342008</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342009">BBa_K2342009</a>.
 +
                </p>
 +
 
 +
                <h4>3]
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342002">BBa_K2342002</a>
 +
                </h4>
 +
 
 +
                <p id="paragraph">
 +
                    CBM, Cellulose Binding Domain
 +
                    <br>
 +
                    <br>
 +
                    <img src="https://static.igem.org/mediawiki/2017/d/d0/T--Aalto-Helsinki--part-CBM.png">
 +
                    <br>
 +
                    <br>This part encodes for Cellulose binding domain (CBM3) from
 +
                    <i>Clostridium thermocellum</i>. This part could be used with any other construct to bind to cellulose.
 +
                </p>
 +
 
 +
                <p id="paragraph">
 +
                    For more details on the production and usage of this part please check the composite part page:
 +
     
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342007">BBa_K2342007</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342008">BBa_K2342008</a>.
 +
                </p>
 +
 
 +
 
 +
                <h4>4]
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342003">BBa_K2342003</a>
 +
                </h4>
 +
 
 +
                <p id="paragraph">
 +
                    6x Histidine tag
 +
                    <br>
 +
                    <br>
 +
                    <img src="https://static.igem.org/mediawiki/2017/2/20/T--Aalto-Helsinki--part-his.png">
 +
                    <br>
 +
                    <br>6x Histidine tag is commonly used for purification of fusion proteins with Immobilized Metal Ion Affinity
 +
                    Chromatography (IMAC) columns designed for histidine tagged proteins.
 +
                </p>
 +
                <p id="paragraph">
 +
                    For more details on the production and usage of this part please check the composite part page:
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342006">BBa_K2342006</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342007">BBa_K2342007</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342008">BBa_K2342008</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342009">BBa_K2342009</a>.
 +
                </p>
 +
 
 +
 
 +
                <h4>5]
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342004">BBa_K2342004</a>
 +
                </h4>
 +
 
 +
                <p id="paragraph">
 +
                    10 amino acid linker, 5X GS
 +
                    <br>
 +
                    <br>
 +
                    <img src="https://static.igem.org/mediawiki/2017/5/58/T--Aalto-Helsinki--part-10linker.png">
 +
                    <br>
 +
                    <br>10 amino acid long linker contains glycine and serine repeats.
 +
                </p>
 +
 
 +
                <p id="paragraph">
 +
                   
 +
                </p>
 +
 
 +
                <h4>6]
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342005">BBa_K2342005</a>
 +
                </h4>
 +
 
 +
                <p id="paragraph">
 +
                    22 amino acid linker
 +
                    <br>
 +
                    <br>
 +
                    <img src="https://static.igem.org/mediawiki/2017/a/a9/T--Aalto-Helsinki--part-22linker.png">
 +
                    <br>
 +
                    <br>22 amino acid long linker contains serine, alanine and glycine repeats.
 +
                </p>
 +
 
 +
                <p id="paragraph">
 +
                    For more details on the production and usage of this part please check the composite part page:
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342007">BBa_K2342007</a>,
 +
                    <a href="http://parts.igem.org/Part:BBa_K2342008">BBa_K2342008</a>.
 +
                </p>
 
</div>
 
</div>
 +
</div>
 +
 +
<img src="https://static.igem.org/mediawiki/2017/f/f4/T--Aalto-Helsinki--horizontal.png">
 +
 +
<div class="container">
 +
<div class="basictext">
 +
 +
<h3 style="color: #006699;">Composite Parts</h3>
 +
 +
<p id="paragraph">
 +
This page lists all the composite parts that we have made during our project. We consider the first listed part our best part!
 +
</p>
 +
 +
<h4>1] <a href="http://parts.igem.org/Part:BBa_K2342006">BBa_K2342006</a></h4>
 +
<p id="paragraph">
 +
DCD1L peptide  linked to sumo fusion peptide with His6x tag.<br>
 +
<br>
 +
<img src="https://static.igem.org/mediawiki/2017/c/cd/T--Aalto-Helsinki--part-hissmt3dcd1l.png"><br>
 +
<br>
 +
This part comprises of a dermcidin derived antimicrobial peptide DCD-1L. This part allows expression of DCD-1L antimicrobial peptide in form of a fusion protein accompanied with His6x-Smt3 tag. The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, DCD-1L, in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitates easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide, significantly easing purification step.  After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free DCD-1L antimicrobial peptide.
 +
</p>
 +
 +
</div>
 +
</div>
 +
 +
<img src="https://static.igem.org/mediawiki/2017/f/f4/T--Aalto-Helsinki--horizontal.png">
  
 
<div class="container">
 
<div class="container">
 
<div class="basictext">
 
<div class="basictext">
−
<h4>Conferences</h4>
+
 
 +
<h4>2] <a href="http://parts.igem.org/Part:BBa_K2342007">BBa_K2342007</a></h4>
 
<p id="paragraph">
 
<p id="paragraph">
−
Before going to the Giant Jamboree in Boston we attended two iGEM conferences: <b>Nordic iGEM Conference</b> (NiC) in Copenhagen (Denmark) 9.-11.6.2017 and <b>European iGEM Meetup</b> in Delft (the Netherlands) 7.-8.7.2017. Both conferences proved to be very useful in preparing for the actual Jamboree, making contacts and especially in familiarizing ourselves with countless other projects! As a bonus, we were given a few very interesting lectures on current research topics and on science journalism.
+
DCD1L peptide linked to CBM with 22 AA linker (6XHis-Smt3_DCD1L_22Linker_CBM).<br>
 +
<br>
 +
<img src="https://static.igem.org/mediawiki/2017/6/64/T--Aalto-Helsinki--part-his_smt3_d22c.png"><br>
 +
<br>
 +
This part comprises of a dermcidin derived antimicrobial peptide DCD-1L linked to a Cellulose binding domain (CBM) with a 22 amino acid linker. Cellulose binding domain (CBM3), from <i>Clostridium thermocellum</i>, is used to immobilize DCD-1L on cellulose based materials. This part allows expression of DCD-1L antimicrobial peptide in form of a fusion protein accompanied with His6x-Smt3 tag on the N-terminus and CBM on C-terminus (6XHis-Smt3_DCD1L_22Linker_CBM) in <i>E.coli</i> without killing the host bacteria.  
 
</p>
 
</p>
 +
 
<p id="paragraph">
 
<p id="paragraph">
−
At the Nordic iGEM Conference the program included a presentation by one of the previous year’s iGEM teams (Cosmo crops) with a Q&A session, three workshops mostly focusing on ethics, feedback and communicating science to the outside world, as well as networking and a Boston-style PowerPoint presentation to the judges and the audience. Feedback from the presentation and our idea helped to shape our project to its final form, while we also gained some valuable experience on presenting. We even got a special mention from the judges for having a clear and visually appealing presentation!
+
The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, DCD-1L, in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitated easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide significantly easing purification step. After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free DCD-1L-22 aa linker-CBM protein.
 
</p>
 
</p>
 +
 
<p id="paragraph">
 
<p id="paragraph">
−
Picture from NiC.
+
Preventing pathogen colonization on surfaces is crucial in order to prevent spreading of infectious diseases. Therefore, immobilization of antimicrobial peptides can be a good alternative to other bactericidal agents because of their wide antibiotic spectrum, given that immobilization is a known way of increasing stability and resilience of peptides.  
 
</p>
 
</p>
 +
 
<p id="paragraph">
 
<p id="paragraph">
−
There was no PowerPoint presentation during European iGEM Meetup, but instead a poster session. We had prepared our own poster and had a chance to present it to the other teams and get their input to our project while practicing presenting a scientific poster. We had a chance to listen to presentations by Cees Dekker, Denis Murphy and Dirk Stemerding, who surely gave us a lot to think about, regarding the current state of the art and ethical questions. Nevertheless, the most important outcome from both of these conferences were the people we met and befriended with while discussing synthetic biology, iGEM and saving the world in general.
+
For this purpose, we designed a construct containing a cellulose binding domain (CBM3), from <i>Clostridium thermocellum</i>, to immobilize DCD-1L on cellulose based materials. Our CBM constructs contain 22 amino acid long linker, to avoid interference with hexameric complex formation that leads to cell death. Cellulose is a medically safe, eco-friendly, and abundant material, already present or easily incorporated into many applications. What is more, versatile nature of cellulose materials from plastic-like hard materials to hydrogels expands application possibilities. Application range can be further increased through altering the part by changing DCD-1L to another AMP in this expression system .  
 
</p>
 
</p>
 +
 +
<h4>3] <a href="http://parts.igem.org/Part:BBa_K2342008">BBa_K2342008</a></h4>
 +
 
<p id="paragraph">
 
<p id="paragraph">
−
Picture from EiC / poster / something.
+
DCD1L peptide  linked to a CBM with a 22 aa linker (His6x-Smt3_CBM_22Linker_DCD1L).<br>
 +
<br>
 +
<img src="https://static.igem.org/mediawiki/2017/7/78/T--Aalto-Helsinki--part-hissmt3c22d.png"><br>
 +
<br>
 +
This part comprises of a dermcidin derived antimicrobial peptide DCD-1L linked to a Cellulose binding domain (CBM) with a 22 amino acid linker. Cellulose binding domain (CBM3), from <i>Clostridium thermocellum</i>, is used to immobilize DCD-1L on cellulose based materials. This part allows expression of DCD-1L antimicrobial peptide in form of a fusion protein accompanied with His6x-Smt3 tag on the N-terminus followed by CBM (His6x-Smt3_CBM_22Linker_DCD1L) in <i>E.coli</i> without killing the host bacteria.
 +
</p>
 +
 
 +
<p id="paragraph">
 +
The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, DCD-1L, in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitated easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide significantly easing purification step.  After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free DCD-1L-22 aa linker CBM protein.
 +
</p>
 +
 
 +
<p id="paragraph">
 +
Preventing pathogen colonization on surfaces is crucial in order to prevent spreading of infectious diseases. Therefore, immobilization of antimicrobial peptides can be a good alternative to other bactericidal agents because of their wide antibiotic spectrum, given that immobilization is a known way of increasing stability and resilience of peptides.
 +
</p>
 +
 
 +
<p id="paragraph">
 +
For this purpose, we designed a construct containing a cellulose binding domain (CBM3) to immobilize DCD-1L on cellulose based materials. Since cellulose is a medically safe, eco-friendly, and abundant material, already present or can easily be incorporated in many applications. Furthermore, versatile nature of cellulose materials from plastic-like hard materials to hydrogels expands application possibilities. Application range can be further increased through altering the part by changing DCD-1L to another AMP in this expression system.
 +
</p>
 +
 
 +
<h4>4] <a href="http://parts.igem.org/Part:BBa_K2342009">BBa_K2342009</a></h4>
 +
 
 +
<p id="paragraph">
 +
LL-37 peptide  linked to sumo fusion peptide with His6x (His6x-Smt3-LL-37).<br>
 +
<br>
 +
<img src="https://static.igem.org/mediawiki/2017/2/27/T--Aalto-Helsinki--HisSmt3LL37.png"><br>
 +
<br>
 +
This part allows expression of LL-37 antimicrobial peptide in the form of a fusion protein accompanied with His6x-Smt3 tag. The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, LL37 in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitated easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide significantly easing purification step.  After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free LL-37 antimicrobial peptide.  
 
</p>
 
</p>
 
</div>
 
</div>
 
</div>
 
</div>
  
−
<!-- FOOTER -->
+
        <!--Space for footer-->
 +
        <br>
 +
        <br>
 +
        <br>
 +
        <br>
 +
        <br>
 +
 
 +
        <!-- FOOTER -->
 
         <footer>
 
         <footer>
 
             <div class="footer-social">
 
             <div class="footer-social">
−
                      <div class="texts">
+
                <div class="texts">
−
                        <ul class="pe-social">
+
                    <ul class="pe-social">
 
                         <a href="https://2017.igem.org/Team:Aalto-Helsinki">HOME</a>
 
                         <a href="https://2017.igem.org/Team:Aalto-Helsinki">HOME</a>
 
                         <a href="http://www.aalto.fi/en/">AALTO UNIVERSITY</a>
 
                         <a href="http://www.aalto.fi/en/">AALTO UNIVERSITY</a>
−
                         <a href="http://www.aaltohelsinki.com/2017/index.html"><img class="some" src="https://static.igem.org/mediawiki/2017/f/f1/T--Aalto-Helsinki--home_icon.png"></a>
+
                         <a href="http://www.aaltohelsinki.com/2017/index.html">
−
                         <li><a href="https://www.facebook.com/AaltoHelsinki/"><i class="pe-so-facebook pe-hover pe-2x"></i></a></li>
+
                            <img class="some" src="https://static.igem.org/mediawiki/2017/f/f1/T--Aalto-Helsinki--home_icon.png">
−
                         <li><a href="https://www.instagram.com/aaltohelsinki_igem/"><i class="pe-so-instagram pe-hover pe-2x"></i></a></li>
+
                        </a>
−
                         <li><a href="https://twitter.com/aaltohelsinki?lang=en"><i class="pe-so-twitter pe-hover pe-2x"></i></a></li>
+
                         <li>
−
                         <li><a href="https://www.linkedin.com/company-beta/16253263/"><i class="pe-so-linkedin pe-hover pe-2x"></i></a></li>
+
                            <a href="https://www.facebook.com/AaltoHelsinki/">
 +
                                <i class="pe-so-facebook pe-hover pe-2x"></i>
 +
                            </a>
 +
                        </li>
 +
                         <li>
 +
                            <a href="https://www.instagram.com/aaltohelsinki_igem/">
 +
                                <i class="pe-so-instagram pe-hover pe-2x"></i>
 +
                            </a>
 +
                        </li>
 +
                         <li>
 +
                            <a href="https://twitter.com/aaltohelsinki?lang=en">
 +
                                <i class="pe-so-twitter pe-hover pe-2x"></i>
 +
                            </a>
 +
                        </li>
 +
                         <li>
 +
                            <a href="https://www.linkedin.com/company-beta/16253263/">
 +
                                <i class="pe-so-linkedin pe-hover pe-2x"></i>
 +
                            </a>
 +
                        </li>
 
                         <a href="https://www.helsinki.fi/en">UNIVERSITY OF HELSINKI</a>
 
                         <a href="https://www.helsinki.fi/en">UNIVERSITY OF HELSINKI</a>
 
                         <a href="https://2017.igem.org/Team:Aalto-Helsinki/Map">SITE MAP</a>
 
                         <a href="https://2017.igem.org/Team:Aalto-Helsinki/Map">SITE MAP</a>
−
                        </ul>
+
                    </ul>
−
                    </div>
+
 
                 </div>
 
                 </div>
 +
            </div>
 
         </footer>
 
         </footer>
−
</body>
+
        </body>
 +
 
 
</html>
 
</html>

Latest revision as of 20:51, 15 December 2017

Aalto-Helsinki



Basic Parts

This section lists all the basic parts that we have made and used during our project.

1] BBa_K2342000

DCD-1L, Dermcidin derived peptide



The part codes for the expression of dermcidin derived DCD-1L peptide. Dermcidin is a recently discovered antimicrobial peptide (AMP) found in primates with no homology to other know AMPs. It is expressed in a constitutive manner in eccrine sweat glands and secreted to epidermal surface as a part of the first line of defense. Mature dermcidin precursor is 110 amino acids long, including a signal peptide. Once antimicrobial peptide precursor is secreted with sweat to epidermal surface, 19 amino acid long signal peptide is cleaved, and it goes under further proteolytic processing leading to several dermcidin derived peptides such as DCD-1 and DCD-1L. DCD-1L is one of the most abundant forms of dermcidin derived peptides. DCD-1L is a 48 amino acid long anionic peptide active against wide spectrum of bacteria including Staphylococcus aureus, Escherichia coli, and Propionibacterium acnes.

For more details on the production and usage of this part please check the composite part page: BBa_K2342006, BBa_K2342007, BBa_K2342008.

2] BBa_K2342001

SUMO fusion tag, Smt3



Employing of Smt3 tag is beneficial in several aspects in expression of recombinant proteins. Ulp1 is a robust enzyme that specifically facilitates cleavage of Smt3, leaving protein of interest unbound to the tag. SUMO tag is known for its effect on solubility and preventing inclusion bodies of fusion peptide, significantly easing purification step.

For more details on the production and usage of this part please check the composite part page: BBa_K2342006, BBa_K2342007, BBa_K2342008, BBa_K2342009.

3] BBa_K2342002

CBM, Cellulose Binding Domain



This part encodes for Cellulose binding domain (CBM3) from Clostridium thermocellum. This part could be used with any other construct to bind to cellulose.

For more details on the production and usage of this part please check the composite part page: BBa_K2342007, BBa_K2342008.

4] BBa_K2342003

6x Histidine tag



6x Histidine tag is commonly used for purification of fusion proteins with Immobilized Metal Ion Affinity Chromatography (IMAC) columns designed for histidine tagged proteins.

For more details on the production and usage of this part please check the composite part page: BBa_K2342006, BBa_K2342007, BBa_K2342008, BBa_K2342009.

5] BBa_K2342004

10 amino acid linker, 5X GS



10 amino acid long linker contains glycine and serine repeats.

6] BBa_K2342005

22 amino acid linker



22 amino acid long linker contains serine, alanine and glycine repeats.

For more details on the production and usage of this part please check the composite part page: BBa_K2342007, BBa_K2342008.

Composite Parts

This page lists all the composite parts that we have made during our project. We consider the first listed part our best part!

1] BBa_K2342006

DCD1L peptide linked to sumo fusion peptide with His6x tag.



This part comprises of a dermcidin derived antimicrobial peptide DCD-1L. This part allows expression of DCD-1L antimicrobial peptide in form of a fusion protein accompanied with His6x-Smt3 tag. The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, DCD-1L, in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitates easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide, significantly easing purification step. After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free DCD-1L antimicrobial peptide.

2] BBa_K2342007

DCD1L peptide linked to CBM with 22 AA linker (6XHis-Smt3_DCD1L_22Linker_CBM).



This part comprises of a dermcidin derived antimicrobial peptide DCD-1L linked to a Cellulose binding domain (CBM) with a 22 amino acid linker. Cellulose binding domain (CBM3), from Clostridium thermocellum, is used to immobilize DCD-1L on cellulose based materials. This part allows expression of DCD-1L antimicrobial peptide in form of a fusion protein accompanied with His6x-Smt3 tag on the N-terminus and CBM on C-terminus (6XHis-Smt3_DCD1L_22Linker_CBM) in E.coli without killing the host bacteria.

The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, DCD-1L, in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitated easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide significantly easing purification step. After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free DCD-1L-22 aa linker-CBM protein.

Preventing pathogen colonization on surfaces is crucial in order to prevent spreading of infectious diseases. Therefore, immobilization of antimicrobial peptides can be a good alternative to other bactericidal agents because of their wide antibiotic spectrum, given that immobilization is a known way of increasing stability and resilience of peptides.

For this purpose, we designed a construct containing a cellulose binding domain (CBM3), from Clostridium thermocellum, to immobilize DCD-1L on cellulose based materials. Our CBM constructs contain 22 amino acid long linker, to avoid interference with hexameric complex formation that leads to cell death. Cellulose is a medically safe, eco-friendly, and abundant material, already present or easily incorporated into many applications. What is more, versatile nature of cellulose materials from plastic-like hard materials to hydrogels expands application possibilities. Application range can be further increased through altering the part by changing DCD-1L to another AMP in this expression system .

3] BBa_K2342008

DCD1L peptide linked to a CBM with a 22 aa linker (His6x-Smt3_CBM_22Linker_DCD1L).



This part comprises of a dermcidin derived antimicrobial peptide DCD-1L linked to a Cellulose binding domain (CBM) with a 22 amino acid linker. Cellulose binding domain (CBM3), from Clostridium thermocellum, is used to immobilize DCD-1L on cellulose based materials. This part allows expression of DCD-1L antimicrobial peptide in form of a fusion protein accompanied with His6x-Smt3 tag on the N-terminus followed by CBM (His6x-Smt3_CBM_22Linker_DCD1L) in E.coli without killing the host bacteria.

The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, DCD-1L, in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitated easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide significantly easing purification step. After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free DCD-1L-22 aa linker CBM protein.

Preventing pathogen colonization on surfaces is crucial in order to prevent spreading of infectious diseases. Therefore, immobilization of antimicrobial peptides can be a good alternative to other bactericidal agents because of their wide antibiotic spectrum, given that immobilization is a known way of increasing stability and resilience of peptides.

For this purpose, we designed a construct containing a cellulose binding domain (CBM3) to immobilize DCD-1L on cellulose based materials. Since cellulose is a medically safe, eco-friendly, and abundant material, already present or can easily be incorporated in many applications. Furthermore, versatile nature of cellulose materials from plastic-like hard materials to hydrogels expands application possibilities. Application range can be further increased through altering the part by changing DCD-1L to another AMP in this expression system.

4] BBa_K2342009

LL-37 peptide linked to sumo fusion peptide with His6x (His6x-Smt3-LL-37).



This part allows expression of LL-37 antimicrobial peptide in the form of a fusion protein accompanied with His6x-Smt3 tag. The construct can be purified with commercially available and widely used affinity chromatography columns designed for His6x tag. Smt3 tag is used to keep antimicrobial peptide, LL37 in inactive form by blocking its adhesion to phospholipid bilayer of the production host due to relatively large size of the tag. One major advantage of the fusion system used is that it facilitated easier detection of the peptide with a conventional method, SDS-PAGE. Also, SUMO tag is beneficial due to its effect on solubility of fusion peptide significantly easing purification step. After purification, to cleave off His6x-Smt3 tag, Ulp1 enzyme that is known for its robust and specific proteolytic activity against SUMO fusion proteins, is used to obtain free LL-37 antimicrobial peptide.