Scientific research

Prof. dr hab. Adam Liwo

The main topic of research is the coarse-grained approach to the description of biomacromolecules and molecular aggregates, formally equivalent, often used in renormalization physics. This approach ignores the degrees of freedom of the system, which are less relevant to its description. (e.g., the polypeptide chain is represented as a trace of alpha carbon atoms). A key element of the approach is to find an efficient energy function, generally identified with the potential of the mean force of the system, where averaging is done with respect to the degrees of freedom omitted in the coarse-grained model. The aim of the approach is both more efficient modeling of systems, since the number of degrees of freedom in the coarse-grained model is at least an order of magnitude lower than in full-atom approaches, and an analytical or semi-analytical description of their dynamics and structure. The modelling aspect is particularly important for predicting protein and nucleic acid structures and modelling biological processes. Using the developed UNRES force field, simulations of the dynamics of these processes require 3-4 orders of magnitude shorter computational time than full-atomic molecular dynamics.

Specific topics:

• Creating a Uniform Coarse Grain Model to simulate proteins, nucleic acids and polysaccharides based on interaction physics.
• Predicting protein structures based on interaction physics.
• Simulation studies of protein folding mechanisms.
• Simulation studies of the mechanisms of action of molecular chaperones.
• Midfield multipole-multipole interactions and the Schroedinger Discrete Nonlinear Equation in describing the structure formation of biological macromolecules.
• Study of the conformation of bioactive peptides by theoretical methods using experimental data.
• Numerical algorithms in chemistry.

Dr Magdalena Ślusarz

The main research topic are G protein-coupled receptors (GPCRs). These are integral membrane proteins constructed of a long polypeptide chain forming a characteristic domain of seven α-helical segments embedded in the cell membrane. GPCRs participate in signal transduction into the cell by interaction with the extracellular ligands. Binding of the ligand triggers the conformational changes of the receptor protein and the signal is then passed on by the G protein to a specific effector (ion channel or enzyme). Understanding the mechanism of ligand binding to the receptor enables the design of more potent and selective drugs.

Specific topics:

• Modelling of the structure of G-protein coupled receptors (GPCR).
• Study of the receptor-ligand interactions by molecular modelling methods: docking and molecular dynamics in the membrane model.
• Computer simulations of GPCR oligomerization.
• Homology modeling of proteins.