Oferty pracy w projektach finansowanych przez NCN

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Oferta pracy

Nazwa jednostki: Faculty of Chemistry, University of GdańskGdańsk, Inne oferty z tego miasta »
Nazwa stanowiska: PhD Student

Project: “Modelowanie molekularne tworzenia struktury białkowej przez glikozaminoglikany oraz ich wpływ na biologicznie istotne oddziaływania białko-ligand”

The goal of the project is to determine the role of glycosaminoglycans (GAGs) in the mediation of biologically relevant protein-ligand interactions by means of molecular modeling approaches, some of which will be developed in this study for the GAG containing systems. The result of this research will serve to guide the design of new methods for tissue regeneration and healing.

In this project, we are going to model biomolecular interactions in the extracellular matrix (ECM) with a focus on one of its major components, glycosaminoglycans (GAGs). GAGs represent a class of long linear anionic periodic polysaccharides made up of repetitive disaccharide units. Owned to the interactions with diverse proteins GAGs were shown to be key players in a number of diseases associated with the pathologies of different tissue development as well as inflammatory/autoimmune disorders, cancer, prion and Alzheimer’s diseases. This renders GAGs to be very promising targets for the design of novel biomaterials to selectively control and promote the processes for potential medical applications in the field of bone and skin regeneration. However, often molecular mechanisms underlying GAG-mediated processes in the ECM are not fully elucidated, and application of experimental techniques is not sufficient alone for characterization of the interactions occurring at molecular levels. Therefore, theoretical approaches beneficially contribute to the understanding of the role of GAGs by bringing principally new and experimentally inaccessible details. Despite substantial success of the recent studies aimed to model GAG-mediated interactions, computational approaches still experience challenges due to GAGs high flexibility, long chains, symmetry, periodicity as well as their anionic nature rendering a requirement for rigorous solvent and electrostatic treatment. It is still not clear if protein/peptide-GAG recognition is predominantly electrostatically driven or specific. In our work, we plan to address the mentioned challenges. In these lines, we are going to reveal the function of GAGs in biologically relevant systems in terms of their impact on protein conformational properties and enhancement of protein-ligand interactions. To achieve the goal, we specify several tasks to accomplish:
– characterization of GAG interactions with particular protein targets;
– characterization of GAG interactions with biologically active small molecules;
– analysis of the impact of different ions on GAG structure and GAG-mediated interactions;
– analysis of the GAG effect on peptides structuring;
– creation of coarse-grained parameters for GAGs to model multicomponent molecular complexes and systems with high conformational flexibility;
– further development of computational methodologies specifically for the GAG containing systems.

– Master in Physics/Chemistry/Biology/Computer Sciences or related areas
– Experience with modeling techniques is an advantage
– Experience with Linux environment and scripting is an advantage
– Interest in the interdisciplinary aspect of the project
– Motivation, creativity, liability, ability to work both independently and as a part of the team
– Good command of English

Opis zadań:

Research tasks:
– Molecular docking and molecular dynamics-based analysis of protein-glycosaminoglycan, peptide-glycosaminoglycan, glycosaminoglycan-small molecules systems
– Contribution to the development of glycosaminoglycan-related computational methodology
– Participation in writing publications and presentation of the results at scientific meetings

Typ konkursu NCN: SONATA BIS – ST
Termin składania ofert: 31 lipca 2019, 23:59
Forma składania ofert: email
Warunki zatrudnienia:

Terms of employment: PhD fellowship for 4 years including 3 months trial time.
Starting date: 01.10.2019
Fellowship: 4000 PLN monthly (netto)

Dodatkowe informacje:

CV and contact data of two referees should be provided to Dr Sergey Samsonov via e-mail sergey.samsonov@ug.edu.pl with the topic “PhD student, Sonata BIS” until the 31.07.2019

The project is an extension and consequent continuation of the actual Polonez Project, the information for which can be found here: www.prot-gag.org

The project is going to be carried out within well established collaborations with experimental groups from Universities of Leipzig, Tours, Lyon, Hungarian Academy of Sciences and with theoretical groups from University of Gdańsk and Technical University of Munich.

The description of the project for general public could be found here:

Data dodania ogłoszenia: 2019-03-15 14:13:02

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