thesis

Summary

In-plane Membrane Anchoring Peptides : structural characterization by NMR and molecular dynamics & development of a bioinformatics prediction method

Membrane proteins represent about 25% of open reading frames in fully sequenced genomes. They can be divided into two categories : the polytopic proteins, with one or more transmembrane segments, and the monotopic proteins, which interact with a single leaflet of the phosphoilipid bilayer. In the latter case, the membrane anchor can include one or more amphipathic helices inserted at the membrane interface, parallel to the bilayer plane. This type of anchor is named in-plane membrane anchor (IPM anchor). IPM anchors are not well-understood and no bioinformatics prediction method is available to date. In this context, this thesis had two aims : (1) the study of membrane anchor of the NS5A protein from the hepatitis C virus, GB viruses and pestiviruses and (2) the development of a bioinformatics prediction method of IPM anchors.

Aim 1 led to the structural characterization of the NS5A membrane domain from the bovine viral diarrhea virus, a pestivirus, by NMR in membrane mimetic media (detergent, water-solvent mixture). Its study by molecular dynamics at the water-dodecane interface or in a phospholipid bilayer allowed us to understand how the membrane domain fit the hydrophobic-hydrophilic interface.

Aim 2 led to the creation of AmphipaSeeK, a bioinformatics method predicting IPM anchors in protein sequences. The method is based on a set of 21 monotopic membrane proteins including an experimentally characterized IPM anchor. It uses a support-vector machine in its classification process and has been shown to be highly specific. AmphipaSeeK has been implemented on NPS@, the sequence analysis Web server of the laboratory.

The overall work has allowed us to better charaterize the structural features of the IPM anchoring to the membrane bilayer.

get the manuscript (in french)

Table of content