Difference between revisions of "Team:Bielefeld-CeBiTec/Project/toolbox/photolysis"

                   The non-canonical amino acid (ncAA) 2-nitrophenylalanine (2-NPA) has the special property to induce a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/photolysis">cleavage</a> of the peptide backbone when irradiated with light of a wavelength of > 300&nbsp;nm. To demonstrate the usage of 2-NPA, we designed a fusion protein (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2201321">BBa_K2201321</a>) of the green fluorescent protein (GFP) and streptavidin connected by a glycine-glycine-serine-linker containing 2-NPA (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2201200">BBa_K2201200</a>). The streptavidin compound will form a stable and highly specific non-covalent bond to biotin, so that the fusion protein can easily be immobilized on any biotinylated surface. The GFP is used as a fluorescence tag so that the fusion protein can easily be identified through its fluorescent properties. The immobilized fusion protein can then be irradiated with light by our <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Hardware">LED panel</a> to induce the cleavage of the peptide backbone and elute the target protein

                     This system is an alternative procedure of site-specific protein cleavage compared to a cleavage by proteases or chemicals. A big advantage of this light-induced cleavage is, that it can be used almost universally on any purpose. It prevents disadvantages like an undesired cleavage of the target protein by undetected cleavage sides or a denaturation of the protein through the reagents when cleaved chemically. The system has a wide range of possible applications, such as inactivating proteins by cleaving them, activating them by cleaving an inactive pre-protein releasing an active form, or a combination with other methods as demonstrated in our light-induced elution.

                     The ncAA 2-NPA is able to photochemically cleave the polypeptide backbone by an cinnoline forming reaction based on the photochemistry of (2-nitrophenyl)ethane derivatives which are used as photochemical caging groups. Peters <i>et al.</i> (2009) report that upon photolysis, the nitrobenzyl group rearranges to the α-hydroxy-substituted nitrosophenyl group. The nitroso group then undergoes an additional reaction with the N-terminal amide group to generate the cyclic azo product. Subsequent hydrolysis of the activated carbonyl group affords the terminal cinnoline and carboxylate products (Peters <i>et al.</i>, 2009).

                     <br>After using the purification column it should be easily regenerated by simply washing it with SDS-solution. The SDS will denaturate the streptavidin with the linker and the other proteins bound to the column so that they will lose their binding affinity to the biotin and be washed off the glass slides. The biotin itself should not be influenced by the SDS-solution so that the glass slides will still be usable for many purification steps.

                     <br>To implement all this, we started the development of a purification column, containing the needed biotinylated surfaces and an <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Hardware">LED panel</a> that is able to radiate the needed UV-light with a wave length of 367&nbsp;nm.

                     GFP is a fluorescent protein isolated from the jellyfish <i>Aequorea victoria</i>. It is one of the most widely studied and used proteins in biochemistry and cell biology. It has been established as a marker for gene expression and protein targeting in living cells and organisms. It is 238 amino acids long with a molecular weight of 26.5&nbsp;kDa. Inside the protein a self-assembled fluorophore is located which leads to its fluorescence properties. The wild type Aequorea protein has a major excitation peak at 395&nbsp;nm and a minor peak at 475&nbsp;nm. In aqueous solution (pH= 7.0), excitation at 395&nbsp;nm leads to an emission peak at 508&nbsp;nm, whereas excitation at 475&nbsp;nm causes a maximum emission at 503&nbsp;nm (visible green light) (Tsien, 1998). In our project, it is used as a fusion protein to provide the ability to detect it by exciting with a wave length of 485&nbsp;nm for we use eGFP.

<p class="figure subtitle"><b>Figure 4:</b> Three perspectives of the photoproduct of the tetrameric wild type Aequorea victoria green fluorescent protein from rcsb.org.

                     Besides GFP, which emits a visible green light, there are other versions of fluorescent proteins like the red fluorescent protein (RFP), able to emit all kinds of colors. They are mostly used to label more than one protein of interest and compare their localization and amount <i>in vivo</i>.

                     Streptavidin is a tetrameric protein with a molecular weight of 15 kDa for each subunit. It was isolated from the actinobacterium Streptomyces avidinii and is homologous to avidin. Both proteins can bind up to four molecules of biotin and their derivatives with high affinity resulting in the high dissociation constant Kd = 10-15 M. This leads to its widespread use in diagnostic assays and protein tags that require formation of an irreversible and specific linkage between biological macromolecules (Lichty <i>et al.</i>, 2005).  

<p class="figure subtitle"><b>Figure 6:</b> Three perspectives of the structure of a wild type streptavidin tetramer in complex with biotin from rcsb.org.  

                   In our project, streptavidin is used as a tag to provide the ability to immobilize the target protein on a biotinylated surface.

<p class="figure subtitle"><b>Figure 7:</b> Fusion protein of EGFP and Cytochrome b562 by rcsb.org.  

                     In the design process of recombinant fusion proteins, linkers are very important, as they can increase the stability, bioactivity, and expression yield of the fusion protein (Chen <i>et al.</i>., 2013). Additionally, a direct fusion of functional domains without a linker can lead to misfolding and other undesirable properties. Linker sequences can be received from natural multi-domain proteins or be rationally designed depending on the desired characteristics. They are mainly classified in three different groups: flexible linkers, rigid linkers, and cleavable linkers (see figure 8). Furthermore they can be classified as small (approximately five amino acids), medium (approximately ten) or large linkers (approximately 20 to 28 amino acids) (Weber  <i>et al.</i>, 1989).

<p class="figure subtitle"><b>Figure 8:</b> Three groups of protein linkers. Left: flexible, middle: rigid, right: cleavable.  

                     In our project, we used a rationally designed medium-sized gly-gly-ser-linker with a length of eleven amino acids. These small amino acids will allow a good expose of the 2-NPA to the UV-light while the glycines mediate the flexibility and the serines improve the solubility of the fusion protein and prevent a hydrophobic collapse.