Professor Marta Pasenkiewicz-Gierula, PhD, DSc
room: A021 (4.01.20), phone: +48 12 664 65 18, e-mail: firstname.lastname@example.org
Michał Markiewicz, PhD, DSc
room: A022 (4.01.21), phone: +48 12 664 65 30, e-mail: email@example.com
Krzysztof Murzyn, PhD
room: B028 (3.01.36), phone: +48 12 664 63 79, e-mail: firstname.lastname@example.org
Krzysztof Sarapata, PhD
room: B025 (3.01.33), phone: +48 12 664 63 80, e-mail: email@example.com
Anna Wójcik, PhD
room: B010 (3.01.4), phone: +48 12 664 61 49
Janusz Mordarski, MSc
room: B025 (3.01.33), phone: +48 12 664 63 80, e-mail: firstname.lastname@example.org
Wojciech Gałan, room: B019 (3.01.9), phone: +48 12 664 64 31
Jan Majta, room: B010 (3.01.4), phone: +48 12 664 61 49
Krzysztof Makuch, room: B010 (3.01.4), phone: +48 12 664 61 49
Jakub Hryc, room: B019 (3.01.9), phone: +48 12 664 64 31
Adrian Kania, room: B019 (3.01.9), phone: +48 12 664 64 31
Clasical molecular dynamics simulation
- Studies of the organisation of the membrane/water interfacial region as well as dynamical structure of bilayers composed of various lipids
- Looking for correlations between physico-chemical properties of the bilayer and (a) structural characteristics of the bilayer lipids, (b) bilayer lipid composition
- Studying mechanisms of action of selected membrane-active compounds of a therapeutic potential
- Studying the mutual effects of non-lipid membrane components (peptides, carotenoids, etc.) on the structural organisation of the lipid bilayer
- Revealing properties of pure cholesterol domains in bilayers oversaturated with cholesterol
- Studying translocation of small and medium size molecules across bilayers
- Assessment of mechanical properties of bilayers composed of various lipids
- Investigation of the non-lamellar lipid phases
- Studying initial stages of atherosclerotic plaque formation – self-association of cholesterol molecules in water and the effect of Chol oxidation products on this process.
- Theoretical studies on enzymatic reaction mechanisms
- Prediction of 3D structures and biological functions of proteins
- Application of artificial intelligence to analyse biological data
- miRNA functional subdivision – verification of the hypothesis
- Testing hypothesis of the qualitative control of transcripts in the process of RNA interference
- Development of software for analyses of trajectories generated with MD simulation and lipid force fields
- Development of bioinformatics software for scientific purposes (artificial neural networks, genetic algorithms)
Methods and specialistic equipment
- molecular modelling with atomic resolution (MD simulation, umbrella sampling, free energy perturbation etc.) to investigate biophysical properties of model membranes
- quantum-mechanical methods (DFT, MP2, QM/MM etc.) used in investigations on mechanisms of catalytic reactions and refinement of the OPLS-AA force field parametrization
- bioinformatics to predict the structure and biological functions of protein
- unsupervised and supervised machine learning
- A high-performance computing cluster (HPC) is based on x86_64 processor architecture. Cluster is running under CentOS operating system (equivalent to Red Hat Enterprise Linux). The queue software /PBS/ is used to manage access to computational nodes.
- Several servers and work stations, disk array, etc.
- Software used for molecular modelling: Gromacs, Amber, BOSS, CHARMM, Gaussian, CP2K
- Marta Pasenkiewicz-Gierula: Self-association of cholesterol molecules near the membrane oversaturated with cholesterol modelling initial stages of processes leading to atherosclerotic plaque formation: computer simulation and experiment.(2017-2020). HARMONIA 8, National Science Centre (NCN).
- Anna Wójcik: Refinement of the OPLS All-Atom force field for selected phospholipids based on quantum mechanics and ab-initio molecular dynamics simulations. (2016-2019). SONATA 9, National Science Centre (NCN).
- E. Plesnar, R. Szczelina,W. K. Subczynski, M. Pasenkiewicz-Gierula. Is the cholesterol bilayer domain a barrier to oxygen transport into the eye lens? Biochim. Biophys. Acta – Biomembr., 2018;1860, 434-441,
- A. Rugor, A. Wójcik-Augustyn, E. Niedzialkowska, S. Mordalski, J. Staroń, A. Bojarski, M. Szaleniec. Reaction mechanism of sterol hydroxylation by steroid C25 dehydrogenase – Homology model, reactivity and isoenzymatic diversity, J. Inorg. Biochem. 2017;173, 28–43;
- M. Pasenkiewicz-Gierula, K. Baczynski, M. Markiewicz, K. Murzyn. Computer modelling studies of the bilayer/water interface. Biochim. Biophys. Acta – Biomembr., 2016;1858, 2305-2321.
- Murzyn, K., Pasenkiewicz-Gierula, M. Structural properties of the water/membrane interface of a bilayer built of the E. coli lipid A. J. Phys. Chem. B. 2015;119:5846−5856.
- A. Wójcik A., E. Broclawik, Per E. M. Siegbahn, M. Lundberg, G. Moran, T. Borowski. The role of substrate positioning in the catalytic reaction of 4-hydroxyphenylpyruvate dioxygenase – a QM/MM study. J. Am. Chem. Soc., 2014;136,14472-14485.
- Kneller, G., Baczynski, K., Pasenkiewicz-Gierula, M. Consistent picture of lateral subdiffusion in lipid bilayers: Molecular dynamics simulation and exact results. J. Chem. Phys. 2011;135:141105.
- Rog, T., Murzyn, K., Milhaud, J., Karttunen, M., Pasenkiewicz-Gierula, M. Water isotope effect on the phosphatidylcholine bilayer properties: a molecular dynamics simulation study. J. Phys. Chem. B. 2009;113:2378-2387.
- Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M. Ordering effects of cholesterol and its analogues. Biochim. Biophys. Acta – Biomembr. 2009;1788:97-121.
- Murzyn, K., Rog, T., Pasenkiewicz-Gierula, M. Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane. Biophys. J. 2005;88:1091–1103.
- Pasenkiewicz-Gierula, M., Takaoka, Y., Miyagawa, H., Kitamura, K., Kusumi, A. Hydrogen bonding of water to phosphatidylcholine in the membrane as studied by a molecular dynamics simulation: location, geometry, and lipid-lipid bridging via hydrogen-bonded water. J. Phys. Chem. A. 1997;101:3677-3691.
Batchelor/master theses topics
All master theses carried out at the Department are performed using computational methods. Proposed topics:
- Construction and analyses of computer models of specific membranes (bacterial, nervous, etc.)
- Prediction of biological functions of a protein using fold recognition and homology modelling methods
- Effects of membrane active compounds on the structure and dynamics of lipid bilayers
- Oxysterol effects on stability of cholesterol domains in the bilayer oversaturated with cholesterol
- Application of quantum chemistry methods to study mechanisms of enzymatic reactions (oxygenase, oxidase, reductase, sulfurylase)
- Diffusion of small molecules on the surface and across lipid bilayers
- Intra-molecular protein dynamics
- Molecular modelling software development
- Realisation of own rational ideas
Requirements for candidates
Skills and willingness to used computer for scientific purposes; expected knowledge of programming languages and operating systems; interest in basic events on the atomic/molecular level.