The MAGPIE workflow.

<p>After models are registered on the platform (A), they are available to any user (B) for the use in analysis projects (C). A project organizes single jobs (D), which enable to run computations with the selected model and different parameter sets on the server (E). Results can be directly viewed in the browser (F). Projects and models of interests can be tagged and shared with other users (G). Steps marked with letters in red color are performed by modellers (A). Other users (green) have simplified access to the organization of projects, jobs, and results (B,C, and D). Computation in Docker containers, interactive result output, and organization by tags (blue: E, F, and G) is handled in the background by MAGPIE.</p

Collaborative research with MAGPIE.

<p>Physicians and biologists (left) can use models provided by computational experts (right) to analyse their data in MAGPIE (center). The central element of the platform comprises a computing framework and a model database.</p

Project page in MAGPIE.

<p>The header (A) shows general information on the project, such as the owner, title, version, and associated tags. The status of jobs and their results can be directly viewed in the browser (B). All output files are rendered on the page and are available for download. A new job with different parameters can be also started from the project view with one click (C).</p

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

<div><p>The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes.</p></div

Comparison of Backbone Brackets and Arginine Tweezers.

<p>(<b>A</b>) Structural representation of the Backbone Brackets motif interacting with Tryptophanyl-5’AMP ligand in TrpRS (PDB:1r6u chain A). The ligand interaction is mediated by backbone hydrogen bonds (solid blue lines). Residue numbers are given in accordance to the structure of origin. (<b>B</b>) The geometry of the Backbone Brackets motif resembles brackets encircling the ligand. (<b>C</b>) WebLogo [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref075" target="_blank">75</a>] representation of the sequence of Backbone Brackets residues (274 and 1361) and three surrounding sequence positions. Residue numbers are given in accordance to the MSA. (<b>D</b>) Structural representation of the Arginine Tweezers motif in interaction with Lysyl-5’AMP ligand in LysRS (PDB:1e1t chain A). Salt bridges (yellow dashed lines) as well as <i>π</i>-cation interactions are established. Residue numbers are given in accordance to the structure of origin. (<b>E</b>) The Arginine Tweezers geometry mimics a pair of tweezers grasping the ligand. (<b>F</b>) Sequence of Arginine Tweezers residues (698 and 1786) and surrounding sequence positions. The Backbone Brackets show nearly no conservation on sequence level since backbone interactions can be established by all amino acids, while the Arginine Tweezers rely on salt bridge interactions, always mediated by two arginines. Residue numbers are given in accordance to the MSA.</p

Integrative sequence view for aaRS Class I (A) and Class II (B).

<p>Boxes delineate sequence motifs previously described in literature [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref046" target="_blank">46</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref057" target="_blank">57</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref058" target="_blank">58</a>]. The trace depicts the sequence conservation score of each position in the MSA (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.s017" target="_blank">S5</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.s018" target="_blank">S6</a> Files). These scores were computed with Jalview [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref040" target="_blank">40</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref087" target="_blank">87</a>], positions composed of sets of amino acids with similar characteristics result in high values. Furthermore, all positions relevant for ligand binding (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.g005" target="_blank">Fig 5</a>) are depicted. Backbone Brackets and Arginine Tweezers have been emphasized by their respective pictograms. Positions of low conservation or those not encompassed by sequence motifs were intangible to studies primarily based on sequence data. Especially backbone interactions might be conserved independently from sequence. (<b>C</b>) Sequence representation of the Rodin-Ohno hypothesis [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref008" target="_blank">8</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref009" target="_blank">9</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref011" target="_blank">11</a>] with equivalents of the Backbone Brackets or Arginine Tweezers residues shown as green dots. The N-terminal residue of each, the Backbone Brackets and the Arginine Tweezers motif, is present in the Protozyme region (shaded red). Additionally, the C-terminal Backbone Brackets residue is located in the Urzyme region.</p

Geometric analysis of the ligand recognition motifs responsible for the adenosine phosphate interaction for aaRS Class I and Class II representative and nonredundant structures.

<p>The alpha carbon distance is plotted against the side chain angle <i>θ</i>. Binding modes refer to states containing an adenosine phosphate ligand (M1) or not (M2). Backbone Brackets in M1 allow for minor variance with respect to their alpha carbon distance, constrained by the position of the bound ligand. In contrast, Arginine Tweezers in M1 adapt an orthogonal orientation in order to fixate the ligand.</p

Backbone Brackets and Arginine Tweezers.

<p>Based on the analysis of 972 protein 3D structures (448 protein chains for Class I and 524 chains for Class II), Backbone Brackets and Arginine Tweezers were identified as structural motifs distinctive for their respective aaRS Class.</p

“HIGH-Motif 2” codon assignment and base pairing.

<p>First and last row are consensus residues according to the structure-based MSA, “+” indicates gaps. Signature regions according to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref008" target="_blank">8</a>] are emphasized. Sequence numbers are given according to the MSA. Middle rows indicate consensus codons; unassigned positions are indicated by dots, matches by vertical lines, and mismatches by “x”. Arginine Tweezers and Backbone Brackets residues are framed by boxes.</p

The Rodin-Ohno hypothesis states that both aaRS classes descended from the opposite strands of a single gene.

<p>The signature motifs of each class were fully complementary on this gene. Both Protozymes originated from the complementary “HIGH-Motif 2” region (shaded in red). Contemporary aaRS feature insertion domains (ID) and Connecting Peptides (CP1) as well as the addition of the anticodon binding domain (ABD). Figure adapted from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref009" target="_blank">9</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006101#pcbi.1006101.ref067" target="_blank">67</a>].</p