Informacje o stanowisku

CHARMM is a versatile program for atomic-level simulation of

many-particle systems, particularly macromolecules of

biological interest. - M. Karplus

Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk, Gdansk, Poland

Description

The position is associated with the grant project entitled Correlated mean-field interactions propagated along polypeptide chain as a key to understanding the structure formation, dynamics, and allostery of proteins and physics-based modeling thereof , financed by the National Science Centre of Poland (NCN). The project is directed by Prof. Jozef Adam Liwo, Faculty of Chemistry, University of Gdansk, Poland.

The candidates must fulfill the following requirements:

• Ph.D. degree in Chemistry, Physics, Biology, Biotechnology or related disciplines or evidence that the degree will be conferred by the start of the employment. By the rules of the grants agency (NCN), the date of conferring the Ph.D. degree must not be earlier than 7 years before the start of the employment financed from the project.
• Command of English sufficient to read scientific papers and for communication.
• Knowledge of molecular quantum mechanics, statistical mechanics, and methods of computational chemistry. Experience in force-field development is desirable.
• Experience in running and analysing the results of molecular dynamics simulation. Experience in metadynamics and extensions of molecular dynamics (replica exchange) is desirable.
• Knowledge of statistical methods of data analysis. Familiarity with Principal Component Analysis and machine learning is desirable.
• Knowledge of the basic principles of protein structure organization.
• Ability to work with UNIX-operated workstations at least at the medium-advanced level, including the ability to write UNIX scripts. Literacy in Fortran/C/C++ is desirable.
• Reliability and ability to solve scientific problems independently.

Project information:

Proteins are macromolecules with highly organized structures and highly concerted dynamics, which are manifested as allosteric communication enabling, e.g., signal transduction, and in motility inherent in molecular motors. Very accurate methods based on Artificial Intelligence, such as AlphaFold in the first place, have recently been developed for modeling protein structures but we are still far from understanding how interatomic interactions converge into certain structural patterns and concerted motions. The bottom-up coarse-grained approaches can be used to find the solution of this problem.

In our laboratory, we are developing the UNRES coarse-grained model of proteins, in which a polypeptide chain is represented by the alpha-carbon trace with united peptide groups and united side chains as interaction sites. This model is efficient in simulating protein structure and dynamics, enabling 1000-fold extension of the simulation time-scales compared to all-atom approaches. The physical basis of UNRES enables us also to interpret the components of the coarse-grained force field as pre-determined blocks of interactions that organize protein structure and dynamics. When all-atom approaches are used, such organized patterns could be discerned only by applying Principal Component Analysis and similar techniques. Recently, we discovered new coarse-grained terms that correspond to long-range collective interactions along extended and helical sections of polypeptide chains.

The aim of this project is (i) to determine how long-range correlations between amino-acid residues sitting on distant parts of the polypeptide chain, which do not interact with each other directly contribute to the formation of protein tertiary structure, (ii) to use the obtained results in enriching the coarse-grained UNRES force field in the respective effective energy terms, which will presumably enhance its power to correctly predict global complicated folds, (iii) to investigate if and how these correlations contribute to the protein dynamics, especially to allosteric interaction and to the exceptional performance of molecular rotatory motors.

Tasks assigned to the position:

• Parameterization of the already derived multi-torsional terms and their implementation in UNRES.
• Derivation of the site-based terms accounting for along-sequence correlation and analyzing Protein Data Bank (PDB) and AlphaFold database to find these correlations in protein structures and parameterization of these terms.
• Calibration of the UNRES force field with the new terms.
• Testing the performance of the enhanced UNRES to model complex protein folds, including the participation in the Community Wide Experiments on the Critical Assessment of Techniques for Protein Structure Prediction (CASP).

Conditions of employment:

• Full-time 1-year job contract, extendable to 2 years.
• Gross-gross salary: 12000 PLN. The gross-gross salary includes health insurance and pension plan.
• Approximate date of employment start: January 1, 2025, possibly earlier.

How to Apply

Email the electronic versions/scans of the documents specified below to Prof. J.A. Liwo at . The documents (in paper form) can also be submitted in person to the Office of the Dean of the Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland or sent by regular mail to Prof. J.A. Liwo at the above address.



The application documents must include the following:

• Cover letter. It can be contained in the email body.
• CV including the list of publications.
• A copy of Ph.D. diploma or documented proof that the applicant will obtain the Ph.D. degree (scan/electronic version acceptable).
• At least one recommendation letter from a previous supervisor; applicants who apply for the first postdoc position must supply the recommendation letter from the Ph.D. work supervisor. The recommendation letter has to be emailed by the recommender directly to .

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