Feedback of Olga Makshakova: guest researcher at Glyco@Alps

on the December 13, 2018

Olga Makshakova, researcher, Kazan Institute of Biochemistry and Biophysics FRC KazSC RAS, received a Glyco@Alps grant as a guest researcher for two months at CERMAV (Grenoble), molecular and structural glycobiology group.
Photography of Olga MakshakovaOlga Makshakova :
"My research stay in CERMAV was dedicated to the computer modelling of interactions between MGD1 and chloroplast membrane. The chloroplast monogalactosyldiacylglycerol synthase (MGD1) is a glycosyltransferase involved in the construction of a galactolipid essential for photosynthesis. Its product, monogalactosyldiacylglycerol is a representative of the most abundant lipid class on the Earth. MGD1 brings UDP-Gal and attaches the sugar moiety to a minor component of the inner envelope membrane (iEM) – diacylglycerol, with the assistance of lipid activators. Thereby, it provides the maintaining of galactolipid concentration about 80% of total lipid content in the chloroplast. However, the molecular details of substrate recognition and MGD1 activation remain to be established.

Molecular dynamics simulations were performed on the level of Coarse-Grained representation to reveal spontaneous and protein-induced association of the lipids, comprising the main constituents of the iEM where MGD1 is located in planta. The analysis of MD trajectories of the glycolipid bilayer mimicking iEM revealed the spontaneous assembly of lipid molecules in form of clusters where the substrate molecules could be accumulated. Moreover the presence of MGD1 attached to the surface of bilayer induces a reorganization of the lipids in these domains thus resulting in a higher local concentration of diacylglycerol molecules in the protein vicinity. This finding could partially explain efficient recognition of the substrate lipid molecules by the protein. Further analysis of the intramolecular motions within MGD1 demonstrates that C-domain undergoes excursions bringing it in the vicinity of the membrane. The oscillations between two orientations of the protein toward the membrane surface would explain part of the mechanism when MGD1 needs to entrap both hydrophobic acceptor substrate and hydrophilic  donor substrate.

In the course of modelling the spatial structure of MGD1 recently resolved in CERMAV was used. All calculations were performed using the facilities of High Performance Computing center of University Grenoble Alpes. A part of the results have been embedded in an article which is currently under evaluation in The Plant Journal."

 
Figure
 

Figure
. Three-dimensional depictions of the macromolecular assembly showing the interaction of MGD1 with a DAG-PG bilayer (1:3 mol/mol) in QuickSurf representation. Color coding: PG (grey), DAG (yellow), N-domain of MGD1 (magenta), C-domain of MGD1 (green), putative PG recognition site (red), putative catalytic residue (blue).  A) An overall view of the assembly comprising MGD1, B) View in the membrane plane of the bilayer without protein (left) and with bound MGD1 (right) showing the local concentration of DAG in the vicinity of the protein, which location is indicated by red circle and its orientation in relation to the membrane is given apart. C) Two representative orientations of MGD1 with respect to the membrane plane showing the position of catalytic residue away from the membrane (top) and close to the membrane surface (bottom) as a result of the dynamics of internal motions of C- and N-domains of MGD1.
 
 
Published on December 13, 2018