Department of Computational Biophysics and Bioinformatics

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Head

Professor Marta Pasenkiewicz-Gierula, PhD, DSc
room: A021 (4.01.20), phone: +48 12 664 65 18

Staff

Michał Markiewicz, PhD, room: A022 (4.01.21), phone: +48 12 664 65 30
Krzysztof Murzyn, PhD, room: B028 (3.01.36), phone: +48 12 664 63 79
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
Andrzej Dubrowski, room: B026 (3.01.34), phone: +48 12 664 63 74

PhD students

Maciej Bratek, room: B010 (3.01.4), phone: +48 12 664 61 49
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
Bożena Milanović, room: B010 (3.01.4), phone: +48 12 664 61 49
Dymitr Szemel, room: B019 (3.01.9), phone: +48 12 664 64 31

Research topics

We carry out mainly basic research and its main aims are:

  • Understanding the organisation of the membrane/water interfacial region as well as dynamical structure of bilayers composed of various lipids
  • Finding correlations between physico-chemical properties of the bilayer and (a) structural characteristics of the bilayer lipids, (b) bilayer lipid composition
  • Prediction of 3D structures and biological functions of proteins
  • 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 domains in bilayers containing cholesterol
  • Studying translocation of small and medium size molecules across bilayers
  • Assessment of mechanical properties of bilayers composed of various lipids
  • Studying intercalation into the membrane and membrane location of certain drugs, sterols and terpenoids
  • Description of the non-lamellar lipid phases
  • Studying self-association of lipid molecules in water and non-polar solvents
  • Biomedical text data mining
  • Development of software for analyses of trajectories generated with MD simulation and lipid force fields

Methods and specialistic equipment

Main techniques:

  • molecular modelling with atomic resolution to investigate biophysical properties of model membranes at the atomistic level description
  • bioinformatics to predict the structure and biological functions of proteins
  • bioinformatics for biomedical text data mining;

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

Current projects

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 Cetre (NCN).

Selected publications

  1. Baczynski, K., Markiewicz, M., Pasenkiewicz-Gierula, M. A computer model of a polyunsaturated monogalactolipid bilayer. Biochimie. 2015;118: 129-140.
  2. 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.
  3. Pasenkiewicz-Gierula, M., Markiewicz, M. Computer modelling of the lipid matrix of biomembranes in: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes – from bioinformatics to molecular quantum mechanics. Ed. A. Liwo, Springer Verlag, Berlin, Heidelberg. 2013, pp. 317-356.
  4. Plesnar, E., Subczynski, W. K., Pasenkiewicz-Gierula, M. Comparative computer simulation study of cholesterol in hydrated unary and binary lipid bilayers and in an anhydrous crystal. J Phys Chem B. 2013;117:8758−8769,
  5. Plesnar, E., Subczynski, W. K., Pasenkiewicz-Gierula, M. Saturation with cholesterol increases vertical order and smoothes the surface of the phosphatidylcholine bilayer: A molecular simulation study. Biochim Biophys Acta – Biomemb. 2012;1818:520–529.
  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., and 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 – Biomemb. 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
  • Diffusion of small molecules on the surface and across lipid bilayers
  • Intra-molecular protein dynamics
  • Molecular modelling software development
  • Biomedical text data mining
  • 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.