Project description:

During biosynthesis, membrane and secreted proteins are modified by covalent addition of complex sugars – glycans. Glycans typically do not interact strongly with the surface of the protein they are attached to and remain very mobile, shielding the protein surface from direct contact with other proteins and ligands. As became evident for the protein mediating SARS-CoV-2 entry into host cells, glycan shields hinder immune responses and are a key contributor to the success of coronaviruses. The majority of protein-protein interactions are affected by glycan shielding, which is further fine-tuned by cell type-dependent variations of glycan composition. Despite their general importance, glycan shields have so far been characterized for only very few proteins and we know surprisingly little about their structural and functional impact. 

Within this project, you will work at the interface between computational biology, biophysics and glycomics to establish the core principles of glycan shielding in collaboration with experts in experimental and computational biology. By combining physics-based high-performance computer simulations, structure prediction tools and glycoproteomics datasets, you will:

1. Characterize the molecular mechanisms of the shielding
2. Explore the impact of glycan heterogeneity on protein shielding, with a particular focus on atypical glycans present in cancer, important factors in cancer immunotherapy.
3. Contribute to expanding our open-access glycan shielding database GlycoSHIELD

The perfect Candidate should have: 

• MSc or equivalent degree in physics, chemistry, biophysics, computer science or similar
• Interest in physics of biological systems 
• Previous experience in programming/scripting (Python, bash, etc.), biomolecular simulations engines (GROMACS, NAMD, Charmm) are not required but are a plus. 
• Excellent communication skills and strong working proficiency in English. 

Starting date: 1st of May 2023 

How to apply?

In case of further questions about the project, do not hesitate to contact Mateusz (Matt) Sikora directly.

Please send your application documents to the following e-mail addresses: biomedical.phd@uj.edu.pl and to the Project Manager dr Mateusz (Matt) Sikora masikora@biophys.mpg.de

Schedule of the competition:

• Opening of the competition: 04.11.2022
• Application submission deadline: 08.11.2022, noon CET
• Entrance exams: 24.11-25.11.2022
• Committee meeting - no later than: 25.11.2022
• Exam results: 28.11.2022
• Entries to the Doctoral School: 29.11-01.12.2022
• Entries to the Doctoral School - reserve list: 02.12.2022

The environment:

You will join the Dioscuri Centre for Modelling of Post-translational Modifications led by Mateusz (Matt) Sikora. Dr Sikora is an expert in computer simulations of biological systems with particular focus on glycosylation and other modifications of proteins. The Malopolska Centre of Biotechnology is a world-renowned research institute offering a supportive and interdisciplinary research environment at the international level. We offer very good financial conditions and a cooperative working environment with access to cutting-edge computing facilities. By joining the Centre, you will have an opportunity to be involved in joint scientific and networking activities together with the Theoretical Biophysics dept. at the Max Planck Institute of Biophysics in Frankfurt, Germany, led by prof. Gerhard Hummer, partner of the Centre. 

The Malopolska Centre of Biotechnology and the Dioscuri Centre strive to ensure a workplace with equal opportunities. We celebrate diversity and are committed to creating an inclusive environment for all members irrespective of gender, nationality or disabilities.

Detailed terms and procedures of admission.

Documents required at the recruitment application stage:

• a curriculum vitae (CV) with particular emphasis on scientific achievements;
• a motivation letter, explaining how the applicant’s background and research interests make
• them a suitable candidate for the position;
• the names of the researchers giving references to the candidate (their contact number
• and academic title);
• documents demonstrating the scientific achievements listed in the curriculum vitae, e.g. first
• page of the article;
• transcript of grades: diploma supplement or the official transcript of grades, or another
• document listing completed courses and grades. Information about the grading scale must be
• included.

In the event of the persons referred to in Article 186, section 2 of the Act,

• two opinions confirming the high quality of their research work and the high level of
• advancement of such work, issued by: a research fellow holding at least the academic degree
• of doctor habilitated or being an employee of a foreign higher education institution or a
• research institution, that has significant achievements in academic issues related to the
• curriculum.

Any document submitted in a language other than Polish or English must be accompanied by a certified translation into Polish or English.

Documents required for enrollment:

• the original application and a photograph;
• a photocopy and the original for inspection:
• a. a diploma certifying the holding of a degree of Master, Master Engineer or equivalent in a field of study from among those indicated in the detailed conditions of recruitment, or
• b. a diploma of completion of studies abroad, giving the right to enrol in a course of doctoral  studies in the issuing country or recognised as equivalent to the appropriate Polish diploma confirming the qualifications of the second degree;
• if the candidate has not yet been issued such a diploma by the deadline for admission,
• he/she shall submit a certificate of completion of such studies and a written undertaking to provide the diploma of higher education entitling to enrol in a course of doctoral studies within the prescribed deadline;
• for inspection: identity document (passport in case of foreigners);
• originals of all other documents provided at the registration stage in the form of a scan.
• In the event of exposure to harmful, noxious or hazardous factors, the applicant will, at the time of registration, be referred for a medical examination by an occupational medicine physician. The candidate shall be obliged to deliver, within the time limit set by the programme manager, a medical certificate confirming the absence of contraindications to take up education.

Higher education diplomas awarded abroad should:

• bear an apostille clause if the issuing country is covered by the Convention abolishing the requirement legalisation for foreign public documents, done at The Hague on 5 October 1961 (Journal of Laws of 2005, No. 112, item 938) or
• be subjected to legalisation, in other cases.

Any document submitted in a language other than Polish or English must be accompanied by a certified translation into Polish or English.

Insurance:

Each doctoral student, including a foreigner, admitted to the doctoral school is obligatorily subject to health insurance if he/she is not covered by such insurance on other grounds (e.g. employment relationship, contract of mandate, business activity, insured as a family member under 26 years of age, as the spouse of an insured person). The health insurance contribution is paid by Jagiellonian University and is financed from the State budget. In addition, a doctoral student receiving a doctoral scholarship is subject to compulsory retirement and disability insurance and accident insurance.

IMPORTANT:

A person admitted to the doctoral school begins education and acquires doctoral student rights upon taking the oath. The Department of Personal Affairs reports each doctoral student admitted to the School to compulsory health and social insurance at the commencement of education, i.e. from 1 October at the earliest. Until that time foreign candidates are obliged to cover the costs of insurance for the time of travel, treatment, etc. individually.