MiSynPat.org

DESCRIPTION OF WEBPAGES

The Home Page provides a general overview of the web server, with a automatically updated graph that illustrates the increasing number of reported cases of correlations between mutations in mt-aaRSs and human disorders. It immediately offers to the users to test for a mutation within all parameters of the web server. Additionally, four insets are displayed that each points towards:

• A synoptic page pointing towards individual data for all human mt-aaRSs (named “All systems”). Nineteen interactive insets corresponding to the 19 human mt-aaRSs, with indications of the dates of the last up-dates, the current numbers of bibliographic entries per system, and true scale graphical representations of the modular organizations of the mt-aaRSs, with representations of existing disease-associated mutations. Of note, no gene for mt-GlnRS has been found, but it has been demonstrated recently that Gln-tRNAGln is produced via an alternate indirect pathway.
• A table file (named “Mutations overview”) containing sortable columns, which shows the exhaustive list of clinical cases, with indications of the two variants in allelic compositions, the related disorders (with OMIM access if applicable), the publication years and the Pubmed links to relevant publications.
• The statistics automatically calculated (named “Mutation statistics”), which compile the number of missense and non-sense mutations, the conservation of residues affected by the mutation, and the occurrence of each type of substitutions.
• The list of related literature (named “Bibliography”), chronologically ordered.

For each human mt-aaRS, the MiSynPat web server provides a dedicated page with four specific, interactive, and interconnected tabs.

The first tab Integrative Analysis includes, from top to bottom:

• the linear sequence of the mt-aaRS, with UniProt, NCBI or MSeqDR links, alongside the graphical representation of mt-aaRS structural modules with the location of existing disease-related missense and nonsense mutations, with following coloring code for the lollipops: missense dominant compount heterozigous (cyan), misssense recessive compound homomzygous (green), missense recessive compound heterozygous (orange) or nonsense recessive compound (black).

• a 3D representation (either the crystallographic structure, if available, or a homology model) of the mt-aaRS.

• a toolbox to load the 3D model of a chosen mutation (either a previously reported mutation or a hypothetical new mutation), to show links to the existing allelic composition, to the relevant literature, and to PolyPhen and SIFT predictions.

Users will be able to save 3D representations in high-quality png images and to download PDB files of wild type or on-the-fly generated mutant molecules. Wild-type structural models and mutated structural models are built automatically using proven tools, Atome2 site and Modeler, respectively. However, no manual quality control of the models is performed, it is therefore important not to over-interpret them. Definitive conclusions regarding gain or loss of contacts or hydrogen bonding can only be made through a specific structural study of a given mutant.

Clicking on one residue in any of the components from this tab will automatically highlight this residue in all of the components. For dimeric enzymes, only the gold monomer is responsive.

The second tab Alignment concerns the evolutionary conservation. A multiple sequence alignment is provided for each system from aaRS sequences retrieved from 93 organisms (prokaryotic and cytosolic or mitochondrial sequences from eukaryotes), representative of the phylogeny. The alignment is visible through a sliding window of 70 residues. The sequence of the human mt-aaRS is highlighted in red so as to be easily found in the alignment. Options allow different features to be displayed in the alignment (as well as on the structure in the first tab). For instance:

• Conservation: black, dark-grey and light-gray boxes corresponding to 100%, >80%, or physicochemically conserved residues, respectively

• PFAM: annotated structural and functional domains

• Module: structural domains and catalytic residues, as pictured in the graphical representation of the mt-aaRSs.

“Toggle ID” allows switching between species nomenclature (in which aminoacylation system, cellular location, Genus and Species are visible) and UniProt or RefSeq accession number. Clicking on one residue of the human mt-aaRS sequence from the alignment will automatically highlight this residue in all components of the first tab.

The alignment of 58 Vertebrates is also provided.

The third tab Bibliography lists the relevant literature for each system.

The fourth tab Mutations Statistics contains general information, including automatic calculation of number of reported mutations, and degree of conservation of affected residues.

The four tabs are interconnected. Any action in one of them is directly passed on and reflected in the others. The “Reload” option allows refreshing the webpages and resetting them to their initial states with default parameters. Help advice is provided everywhere it is necessary through mouse tooltips. Users are encouraged to contact us with questions.