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Protein structure analysis, prediction and flexibility in the light of a structural alphabet

Abstract : DSIMB is the second team of INSERM UMR_S 1134 (Integrated biology of Red Blood Cell) unit. The unit is a mixed unit between INSERM and University Paris Diderot of Sorbonne Paris Cite. Our team is also associated to University of Reunion Island, and one of the other team to University des Antilles. We are located at the French National Institute of Institute of Blood Transfusion (INTS) and are also part of Laboratory of Excellence GR-Ex. After a short presentation of the lab, I will present some of our tools available at ( 13 webservers, 9 databases and 7 tools are provided to the scientific community, going from the selection of transmembrane protein structural model to analyses of Post Translational Modifications in the PDB, the cutting of protein structures in small protein domains or the Knottin protein family. One of the specialties of DSIMB is the analysis of protein structure at a local level. Description of local protein structures has hence focused on the elaboration of complete sets of small prototypes or "structural alphabets" (SAs) that help to approximate every part of the protein backbone. Each residue is associated to one of these prototypes; the whole 3D protein structure can be translated into a series of prototypes (letters) in 1D, as the sequence of prototypes. Our structural alphabet is named Protein Blocks. PBs have been used to efficiently superimposed protein structures, both for pairwise and multiple superimposition, it was also used to help the design of a very efficient fold recognition approach and even to perform flexibility prediction. We worked on the integrin αIIbβ3; it is a large transmembrane protein complex found on platelet and involved in blood regulation, such as clotting. It is implicated in two pathological cases, Glanzmann thrombasthenia (GT) and alloimmune disorders (FNAIT), and mainly associated to punctual structural mutation (variants). We have analyzed through molecular dynamics (i) the human platelet alloantigen (HPA)-1 system, the first cause of alloimmune thrombocytopenia in Caucasians, results from leucine-to-proline substitution (alleles 1a and 1b) of residue 33 in β3 subunit of the integrin αIIbβ3, and (ii) all the GT variants of Calf-1 domain. The use of PBs shows it is possible to distinguish rigid region encompass in ‘flexible’ region. Moreover, Calf-1 domain shows subtle conformational changes, not close to the mutation spots but at another long-distance area. This recent last results raised questions about allosteric issues and how PBs can be useful.
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Submitted on : Thursday, November 16, 2017 - 4:53:36 PM
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  • HAL Id : inserm-01636581, version 1


Alexandre de Brevern. Protein structure analysis, prediction and flexibility in the light of a structural alphabet. 1ère réunion du GT MASIM du GDR BIM, GDR BIM (CNRS), Nov 2017, Paris, France. ⟨inserm-01636581⟩



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