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<li><a href="#intro">Introduction</a></li>
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RiboSURF
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<li><a href="#structure">Structural characterization</a></li>
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<li><a href="#molecular">Molecular modeling</a></li>
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<li><a href="#design">Structure-based design</a></li>
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<li><a href="#improve">Improve a brick</a><img src="https://static.igem.org/mediawiki/2014/c/cd/Mr_gold_nav.png" alt="gold" style="float: right;top: -2px;position: relative;"/></li>
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The aim of our project was to make it possible to combine the advantages of the nonribosomal peptide synthesis with the ribosomal pathway,
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i.e. the enormous repertoire of amino acids combined with the ability of the ribosome to synthesize huge proteins.
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<html><h2><a name="intro" class="nolink"></html>'''Introduction'''<html></a></h2></html>
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The ribosome is the primary site of protein synthesis in a cell with its advantages being the high reliability of protein synthesis combined
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with the possibility of assembling huge proteins from amino acids using mRNA as blueprint. As an adaptor that guides the correct incorporation
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of amino acids as specified in the mRNA template ribosomes use aminoacyl-tRNAs. These are generated by activation of the needed amino acid using ATP.
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The created adenylate intermediate is then transferred to the 3’ terminus of the corresponding tRNA. This loading reaction of tRNA is catalysed by an
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enzyme family of aminoacyl-tRNA synthetases (aaRSs) (Rodnina, 2013). These form multi-synthetase complexes (MSCs) in eukaryotes and archaea that
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contain not only the aaRSs themselves but also accessory protein factors for the local scaffolding of tRNAs to the aaRS (Quevillon et al., 1997).
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One of these accessory proteins, Arc1p (Figure 2), has been shown to improve the functionality of the MSC in <i>Saccharomyces cerevisiae</i> by facilitating
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tRNA binding (Simos et al., 1998).
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By contrast to the ribosome, the nonribosomal peptide synthesis occuring in the secondary metabolism of many microbes on the other hand uses modular
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multi enzyme complexes called nonribosomal peptide synthetases (NRPSs). Due to the fusion of different domains nature build highly developed catalysts
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for the production of a huge amount of biologically active compounds in evolutionary time (Strieker et al., 2010). The reactions that these modules catalyse
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can be compared to equivalent steps in the ribosomal pathway. Especially interesting in this context is the first step catalysed by an adenylation (A) domain
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which is the activation of the corresponding amino acid using ATP to yield an adenylate intermediate and thus closely resembles the corresponding step of the
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ribosomal pathway (Sieber and Marahiel, 2005). However, in contrast to the limited repertoire of amino acids the ribosome uses there are A-domains known that
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can select from hundreds of proteinogenic and non-proteinogenic building blocks. Nevertheless the peptides that are assembled seem to be limited in their size
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to about 50 amino acids (Caboche et al., 2008). Intrigued by the multitude of possibilities these A-domains offer we wanted to make their utilization within the
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ribosomal pathway possible to overcome the size limit of NRPSs.
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To reach that aim, we planned to create a fusion protein that has the capability to activate amino acids derived from NRPSs’ A-domains and tRNA binding capabilities
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derived from aaRSs.
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<html><div class="figure" style="width:75%;">
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<img src="https://static.igem.org/mediawiki/2014/2/23/MR_catalyst_overview.png" alt="figure 1">
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<span class="caption">Figure 1: Model of the RiboSURF
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</span>
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</div></html>
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<html><h2><a name="structure" class="nolink"></html>'''Structural characterization of the
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<html><a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a></html> tRNA binding domain'''<html></a></h2></html>
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Our choice for these two domains were on the one hand PheA <html><a href="parts.igem.org/Part:BBa_K1329005" target="_blank">(BBa_K1329005)</a></html> from gramicidinS synthetase
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which was already well characterized and has been shown to activate L- and D-phenylalanine also in a non-native context (Stevens et al., 2006) which is a necessary
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criterion for the construction of our enzyme. On the other hand the search for a domain that conferred tRNA binding capabilities faced the challenge that the tRNA
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binding domain is often established by the correct spatial arrangement of parts of the peptide chain. Finally; in the case of the C-terminal part of Arc1p (Arc1p-C)
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<html><a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">(BBa_K1329004)</a></html> from ''S. cerevisiae'', we found a domain that shows these binding capabilities in
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one peptide strand and thus was accessible for further engineering by the introduction to our fusion protein. However, structural information on this domain and a
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structural understanding of how this domain interacts with tRNA was crucially missing. Therefore, we crystallized
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<html><a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a></html> (Figure 2A) and determined its crystal structure
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to 1.8 Å resolution (Figure 2B). Data were collected at ID23-1 at the European Synchrotron Radiatian Facility, Grenoble, France.
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<html><div class="figure" style="width:75%;">
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<img src="https://static.igem.org/mediawiki/2014/6/66/Mr_nrps_1.png" alt="figure 2">
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<span class="caption">Figure 2: Structure determination of <a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a>. A. Crystals of
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<a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a> were obtained after 2 to 4 days in a wide range of crystallization conditions.
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B. Crystal structure of Arc1p shown as ribbon (left) – and electrostatic surface representation (right). Dashed lines indicate the putative tRNA binding site. This fact
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is underlined by the presence of a glycerol from the cryosolution because glycerol likely mimics ribose sugar of a RNA.
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</span></div></html>
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<html><h2><a name="molecular" class="nolink"></html>'''Molecular modelling the Arc1p interaction with tRNA'''<html></a></h2></html>
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To understand the binding mode of tRNA to <html><a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a></html> we used the DUCK-BP server employing the FTdock
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algorithm (Gabb et al., 1997) to calculate possible binding modes (Figure 2).
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Taking functional aspects into account only the highest scoring docking model seems to represent the real binding mode since all the others lead to a blockade of the tRNA
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acceptor stem. Furthermore, solution 1 perfectly matches with the presence of a glycerol potentially mimicking a RNA backbone ribose position (see also Figure 2B). 
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<html><div class="figure" style="width:70%;">
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<img src="https://static.igem.org/mediawiki/2014/7/79/Mr_nrps_2.png" alt="figure 3">
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<span class="caption">Figure 3: Calculated docking modes of tRNA to <a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a>.
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Only the first one seems sensible from a functional point of view because all other solutions
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hide the 3’ end of the tRNA to which canonical aaRSs transfer amino acids.
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</span></div></html>
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<html><h2><a name="design" class="nolink"></html>'''Structure-based design of Arc1p-PheA catalysts'''<html></a></h2></html>
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In order to create that correct distance between those two domains we wanted to use computational methods to simulate the protein with different linker lengths between
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the two domains. As a linker we used repeated GSSG units. With the crystal structure of <html><a href="parts.igem.org/Part:BBa_K1329005" target="_blank">PheA</a></html>
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known we still needed to solve the crystal structure of
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<html><a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a></html> and find the
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binding mode of the tRNA to <html><a href="http://parts.igem.org/Part:BBa_K1329004" target="_blank">Arc1p-C</a></html> in order to build a precise molecular model of rationally design
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suitable linker lengths that balance between on the one hand enough
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flexibility for favourable positioning of tRNA and activated amino acid and a sufficient increase in local reactant concentration for efficient catalysis to occur on the
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other hand. The results of the simulation of 0, 1, 2, 4 and 8 GSSG units suggested that the best distance that should lead to the highest catalyst activity is reached with
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two GSSG units (Figure 4). For the testing of our prediction, we synthesized the fusion protein with these five different linker lengths.
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<html><div class="figure" style="width:75%;">
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<img src="https://static.igem.org/mediawiki/2014/7/74/Mr_nrps_3.png" alt="figure 4">
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<span class="caption">Figure 4: Design and functional analysis of different RiboSURF constructs. A. Computational molecular model of Arc1p-C-PheA fusion proteins with
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different linker lengths, and B. their activities in aminoacylating tRNA. C. Coomassie-stained SDS-PAGE of purified RiboSURF catalysts proteins employed in this project.
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Proteinmarker: Broad Range (New England Biolabs). D. Workflow for the detection of aminoacylation levels.
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</span></div></html>
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The 8x linker was constructed from a synthesized template and integrated into pET28a by Gibson assembly. The other lengths were created by round-the-horn site directed
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mutagenesis using phosphorylated primers and a ligation after the PCR. All the proteins (Figure 4C) were produced as His6 tagged fusion proteins. For testing the catalytic
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activity of each mutant we used an LC-MS based assay. Since the phosphate backbone leads to a multiple negative charge the direct analysis by mass spectrometry probably
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would lead to a too poor sensitivity to discriminate loaded and unloaded tRNAs (Figure 4D). Thus we decided to make an indirect measurement based on an established method.
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After the reaction mixture was incubated we separated the tRNA from all the other components by size-exclusion chromatography. The obtained mixture of loaded and unloaded
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tRNAs was split and one half kept on ice while the other was treated with a base to cleave the oxoester bond. Afterwards the amount of released amino acid in the base
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treated sample was detected by LC-MS using the untreated sample as a negative control.
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Measurements showed that all fusion constructs were able to load L- as well as D-phenylalanine onto tRNA<sup>Phe</sup>. As the computational molecular model already
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suggested the varying linker length showed a clear influence on the yield levels with the 2x-GSSG linker showing the highest catalytic activity yielding 11% loaded
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tRNA after 30 min while the 8x-construct reached only a maximum of 3% loaded tRNA as well as the linker-less version. The remaining constructs showed intermediate
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results in good correspondence with the computational model (Figure 4B).
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<html><div class="figure" style="width:75%;">
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<img src="https://static.igem.org/mediawiki/2014/7/77/Mr_nrps_4.png" alt="figure 5">
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<span class="caption">Figure 5: Negative and positive controls and measured timecourse of the aminoacylation.
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</span></div></html>
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Furthermore the linking of the two domains leading to the increase in reactant concentration and the correct spatial arrangement is indeed important for the catalytic
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effect to occur since a mixture of the unlinked domains showed only background levels of aminoacylation (Figure 5). Further negative controls included testing the
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reaction without enzyme or ATP. As a positive control to evaluate the method phenylalanyl-tRNA synthetase (PheRS) was used. A time-dependent measurement of the aminoacylation
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level showed that a maximum is reached after 30 min. To test if other tRNAs except for the tRNA<sup>Phe</sup> can be aminoacylated using our fusion construct we carried out
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aminoacylation assays with five additional <i>Escherichia coli</i> tRNAs (Figure 6). The measurements suggest in agreement with previous studies that all tRNAs were loaded
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similarly well.
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<html><div class="figure" style="width:50%;">
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<img src="https://static.igem.org/mediawiki/2014/3/35/Mr_nrps_5.png" alt="figure 5">
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<span class="caption">Figure 6: Aminoacylation activity of the 2xlinker construct using different tRNAs relative to the activity observed using tRNA<sup>Phe</sup> and L-Phe.
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</span></div></html>
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<html><h2><a name="improve" class="nolink"></html>'''Improve a brick'''<html></a></h2></html>
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Nonribosomal peptide synthetases (NRPSs) are a most fascinating subject because of the huge amount of biologically
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active compounds they produce that show a broad spectrum of clinical applications that even includes their use as
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last resort antibiotics, antitumor or antifungal agents and immunosuppressants. These interesting properties especially
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derive from the nonribosomal peptide synthetases unique feature to incorporate non-proteinogenic features such as
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heterocycles, fatty acids, macrocycles, D-amino acids and other non-proteinogenic amino acids. Last years’
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<html><a href="https://2013.igem.org/Team:Heidelberg" target="_blank">team of the university Heidelberg</a></html>  
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used nonribosomal peptide synthetases of <i>Brevibacillus parabrevis</i> in order to synthesize a tripeptide by
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interchanging modules of an already existing NRPS cluster. The problem of previous applications such as these is
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that the size of synthesized peptides is limited. Even naturally occurring peptides synthesized nonribosomally seem to
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have an upper limit of 50 amino acids (Caboche et al., 2008). Therefore it would be great to establish a system that
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uses these capabilities to introduce non-proteinogenic amino acids but is able to overcome the size limit of the
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synthesized peptides. That is why we improved the brick <html><a href="http://parts.igem.org/Part:BBa_K1152005">BBa_K1152005</a></html>
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which contains the expression cassette for NRPS synthesizing a Phe-Orn-Leu-tripeptide. In RiboSURF, we improved the A-domain that activates phenylalanine
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<html><a href="http://parts.igem.org/Part:BBa_K1329005">(BBa_K1329005)</a></html> in that
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nonribosomal peptide synthetase. Our improvement makes it possible
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to use the NRPS module even in its non-natural environment isolated from its NRPS context. By the fusion of the module
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from NRPS to a tRNA binding domain the catalytic activity of this NRPS module was introduced to the ribosomal pathway
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which has much more powerful capabilities regarding the protein synthesis as it can assemble huge proteins using RNA as a blueprint.
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<html><hr></html>
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Caboche, S., Pupin, M., Leclère, V., Fontaine, A., Jacques, P., and Kucherov, G. (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res 36: D326–31 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2238963&tool=pmcentrez&rendertype=abstract. Accessed October 14, 2014.
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Gabb, H.A., Jackson, R.M., and Sternberg, M.J. (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272: 106–20 http://www.ncbi.nlm.nih.gov/pubmed/9299341. Accessed October 14, 2014.
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Quevillon, S., Agou, F., Robinson, J.-C., and Mirande, M. (1997) The p43 Component of the Mammalian Multi-synthetase Complex Is Likely To Be the Precursor of the Endothelial Monocyte-activating Polypeptide II Cytokine. J Biol Chem 272: 32573–32579 http://www.jbc.org/cgi/doi/10.1074/jbc.272.51.32573. Accessed October 14, 2014.
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Rodnina, M. V (2013) The ribosome as a versatile catalyst: reactions at the peptidyl transferase center. Curr Opin Struct Biol 23: 595–602 http://www.ncbi.nlm.nih.gov/pubmed/23711800. Accessed October 14, 2014.
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Sieber, S.A., and Marahiel, M.A. (2005) Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev 105: 715–38 http://www.ncbi.nlm.nih.gov/pubmed/15700962. Accessed October 14, 2014.
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Simos, G., Sauer, A., Fasiolo, F., and Hurt, E.C. (1998) A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases. Mol Cell 1: 235–42 http://www.ncbi.nlm.nih.gov/pubmed/9659920. Accessed October 14, 2014.
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Stevens, B.W., Lilien, R.H., Georgiev, I., Donald, B.R., and Anderson, A.C. (2006) Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme’s mechanism and selectivity. Biochemistry 45: 15495–504 http://www.ncbi.nlm.nih.gov/pubmed/17176071. Accessed October 14, 2014.
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Strieker, M., Tanović, A., and Marahiel, M.A. (2010) Nonribosomal peptide synthetases: structures and dynamics. Curr Opin Struct Biol 20: 234–40 http://www.ncbi.nlm.nih.gov/pubmed/20153164. Accessed July 22, 2014.
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