8Alternative splicing (AS), by producing several transcript isoforms from the same gene, has the po-9 tential to greatly expand the proteome in eukaryotes. Its deregulation has been associated to the 10 development of various diseases, including cancer. Although the AS mechanisms are well described 11 at the genomic level, little is known about the contribution of AS to protein evolution and the im-12 pact of AS at the level of the protein structure. Here, we address both issues by reconstructing the isoforms. PhyloSofS has broad applicability and can be used, for example, to study transcripts diver-26 sity between di erent individuals (e.g. patients a ected by a particular disease). It is freely available 27 at www.lcqb.upmc.fr/PhyloSofS. 28. CC-BY-NC 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/119891 doi: bioRxiv preprint first posted online Mar. 23, 2017; Evolution and structural impact of alternative splicing for JNKs. 3 Author Summary 29Alternative splicing (AS) is a eukaryotic regulatory process by which multiple proteins are produced 30 from the same gene. Although the mechanisms of AS have been extensively described at the level of 31 the gene, little is known about its contribution to protein evolution and its impact on the shape and 32 motions of the produced isoforms. Here, we address both issues computationally, focusing our study structures. We show that an ancient ASE having significant functional outcome induces very subtle 37 changes on the structural dynamics of the protein and we identify the residues likely responsible 38 for the functional change. We highlight a new isoform, not previously documented, and explore its 39 motions in solution. We propose that it may play a role in the cell and serve as a therapeutic target. 40Finally, we link the evolutionary conservation of transcripts to sequence and structural properties.

Scientists have to perform multiple experiments producing qualitative and quantitative data to determine if a compound is able to bind to a given target. Due to the large diversity of the potential ligand chemical space, the possibility of experimentally exploring a lot of compounds on a target rapidly becomes out of reach. Scientists therefore need to use virtual screening methods to determine the putative binding mode of ligands on a protein and then post-process the raw docking experiments with a dedicated scoring function in relation with experimental data. Two of the major difficulties for comparing docking predictions with experiments mostly come from the lack of transferability of experimental data and the lack of standardisation in molecule names. Although large portals like PubChem or ChEMBL are available for general purpose, there is no service allowing a formal expert annotation of both experimental data and docking studies. To address these issues, researchers build their own collection of data in flat files, often in spreadsheets, with limited possibilities of extensive annotations or standardisation of ligand descriptions allowing cross-database retrieval. We have conceived the dockNmine platform to provide a service allowing an expert and authenticated annotation of ligands and targets. First, this portal allows a scientist to incorporate controlled information in the database using reference identifiers for the protein (Uniprot ID) and the ligand (SMILES description), the data and the publication associated to it. Second, it allows the incorporation of docking experiments using forms that automatically parse useful parameters and results. Last, the web interface provides a lot of pre-computed outputs to assess the degree of correlations between docking experiments and experimental data.

Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms. We reconstruct phylogenetic forests relating 60 protein coding transcripts from the c-Jun N-terminal kinase (JNK) family observed in 7 species. We identify two alternative splicing events of ancient origin and show that they induce subtle changes on the protein's structural dynamics. We highlight a previously uncharacterized transcript whose predicted structure seems stable in solution. We further demonstrate that orphan transcripts, for which no phylogeny could be reconstructed, display peculiar sequence and structural properties. Our approach is implemented in PhyloSofS 1 Evolution and structural impact of alternative splicing for JNKs.