11:15 a.m.
*Title:
Implementation of an incremental docking method to study long-sugar chains interactions
with proteins: p17-heparin case study
*Abstract:
Glyco-bioinformatics is an emerging subfield of bioinformatics aimed at expediting
research in the field of glycomics. Unfortunately, the development of sugar-based virtual
structures is made difficult by some structural features of sugar such as their high
charge density, conformational flexibility and the torsional angles between glycosidic
bonds. As a consequence, automated prediction of the binding poses of long sugar with
proteins (that is a pivotal aspect of many biological processes) has been evaded so far,
also due to the solvation/desolvation, weak surface complementarity and large
electrostatic interactions of sugar/protein interactions.
My PhD activity is aimed at overcoming these limits. To this aim, I have implemented a new
computational method based on incremental docking that has been so far successfully
applied to two important biological interactions such as that of heparin with the HIV-1
p17 matrix protein in the field of AIDS and VEGF with its VEGF receptor-2 in the field of
tumor neovascularization. Perspective developments include the development of an algorithm
able to automatize the developed computational methods and their application to other
sugar/protein interactions of biological importance.
*Speaker:
Giulia Paiardi has completed her MSc in Bioinformatics and medical biotechnology at
University of Verona in 2016. She then moved to the University of Brescia where she worked
as data analyst on the project "Neuroendocrine and behavioural aspects of
experimental autism” at the section of Pharmacology of the Department of Molecular and
Translational Medicine (DMMT). She is now frequenting the PhD in Technology for Health at
University of Brescia, where under the supervision of Prof. Marco Rusnati, at the
Macromolecular Interaction Analysis Unit of the DMMT, she is in charge of all the
computational aspects of the projects currently ongoing in the Unit. To this aim, in 2018,
under the supervision of Dr. Pasqualina D’Ursi, she has frequented the Bioinformatics
group at the Institute for Biomedical Technologies-National Research Council (ITB-CNR) in
Milan, leaded by Prof. Luciano Milanesi, with which she is still in close collaboration
and that currently provides her the computing systems.
*Date:
Wednesday, 16th of October 2019, 12:00-13:00
*Location:
Manno, Galleria 1, 2nd floor, room G1-201
*Doodle registration:
Pizza and drinks will be offered at the end of the talk. If you plan to attend, please
register in a timely fashion (before the day of the talk) at the following link so that we
will have no shortage of food:
https://doodle.com/poll/hfn2byfr7mv2mp4u