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Home page > Seminars > Séminaires théorie > Theory Club Monday January 27 2020 at 12:00 in room 412B. Edoardo Sarti: "Relating membrane protein structure, sequence and symmetry with the EncoMPASS database".

Theory Club Monday January 27 2020 at 12:00 in room 412B. Edoardo Sarti: "Relating membrane protein structure, sequence and symmetry with the EncoMPASS database"

Unless otherwise stated, seminars and defences take place at 11:30 in room 454A of Condorcet building.


Relating membrane protein structure, sequence and symmetry with the EncoMPASS database

Edoardo Sarti

Abstract: Membrane proteins represent 30% of the genome of every organism, spanning a wide range of functions and regulating all exchanges between the cell and the environment. Despite their abundance, their structural characterisation is hindered by at least two issues: firstly, experimentally determining their three-dimensional structure is very challenging (only 2% of the PDB is composed of membrane proteins). Secondly, while their broad functional diversity is reflected in the wide divergence of their amino acid sequences, the fold space available to these proteins is restricted by their anisotropic environment. Therefore, identifying differences and commonalities in their architectures might require the development of novel strategies. Another striking feature of membrane protein architectures is that they are abundant in symmetries and pseudosymmetries, which often reflect evolution and function and can be used to predict active sites, conformational changes and mechanisms. Despite their importance, the few online resources that address structural symmetries provide limited information. To address these issues, we created the Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (EncoMPASS). Instead of building a hierarchical classification, we constructed EncoMPASS around the structural and sequence similarities of all protein chains with similar transmembrane topologies. This results in networks of sequence and structural homologues for each protein chain. Uniquely, EncoMPASS also provides detailed information about both quaternary and internal structural symmetries, curating results of several symmetry detection approaches and allowing the user to select the analysis that best fits their objectives. Thanks to its comprehensive view of the structure- and sequence-wise relationships between membrane proteins, EncoMPASS is also allowing us to make wide-range analyses that aim at a deeper understanding of membrane protein transport mechanisms and evolution. EncoMPASS is online at  https://encompass.ninds.nih.gov

Monday January 27 at 12:00 in room 412B


Contact : Équipe séminaires / Seminar team - Published on / Publié le 20 January 2020


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