Skip to main content

Web Content Display Web Content Display

Web Content Display Web Content Display

Department of Computational Biophysics and Bioinformatics

Webpage

http://bioinfo.mol.uj.edu.pl/

Head

Prof. dr hab. Marta Pasenkiewicz-Gierula
room: A021 (4.01.20), phone: +48 12 664 65 18, e-mail: marta.pasenkiewicz-gierula@uj.edu.pl

Staff

Dr hab. Krzysztof Murzyn
room: B028 (3.01.36), phone: +48 12 664 63 79, e-mail: krzysztof.murzyn@uj.edu.pl

Dr Michał Markiewicz
room: A022 (4.01.21), phone: +48 12 664 65 30, e-mail: m.markiewicz@uj.edu.pl

Dr Krzysztof Sarapata
room: B025 (3.01.33), phone: +48 12 664 63 80, e-mail: krzysztof.sarapata@uj.edu.pl

Dr Anna Wójcik
room: B010 (3.01.4), phone: +48 12 664 61 49

Mgr Krzysztof Makuch
room: B010 (3.01.4), phone: +48 12 664 61 49, e-mail: krzysztof.makuch@uj.edu.pl

Mgr Janusz Mordarski
room: B025 (3.01.33), phone: +48 12 664 63 80, e-mail: janusz.mordarski@uj.edu.pl

PhD students

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

Research topics

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 natural 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.

Quantum-mechanical computations

  • Theoretical studies on enzymatic reaction mechanisms

Bioinformatics

  • 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

Software development

  • 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 specialist equipment

Main techniques:

  • 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

Equipment:

  • 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

Current projects

  1. 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).
  2. 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).

Selected publications

  1. L. Bratek, M. Markiewicz, K. Baczynski, J. Jalocha-Bratek, M. Pasenkiewicz-Gierula. Inverse hexagonal phase of poly-unsaturated monogalactolipids: a computer model and analysis. J. Mol. Liquids, 2019; 290, 111189.
  2. 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. 
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. Rog, T., Pasenkiewicz-Gierula, M., Vattulainen, I., Karttunen, M. Ordering effects of cholesterol and its analogues. Biochim. Biophys. Acta – Biomembr. 2009;1788:97-121.
  9. Murzyn, K., Rog, T., Pasenkiewicz-Gierula, M. Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane. Biophys. J. 2005;88:1091-1103.
  10. 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 thesis 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.