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WBBiB

Wydział Biochemii, Biofizyki i Biotechnologii

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Department of Computational Biophysics and Bioinformatics

zboib.wbbib.uj.edu.pl

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

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

Mgr Adrian Kania
room: B025 (3.01.33), phone: +48 12 664 63 80, e-mail: adrian15x.kania@uj.edu.pl

Mgr Jakub Hryc
room: B010 (3.01.9), phone: +48 12 664 64 31, e-mail: jakub.hryc@uj.edu.pl

Mgr Jan Majta
room: B010 (3.01.4), phone: +48 12 664 61 49, e-mail: jan.majta@uj.edu.pl 

Lic Rafał Miłodrowski
room: A018 (4.01.19, e-mail: rafal.milodrowski@uj.edu.pl

Jan Majta, room: B010 (3.01.4), phone: +48 12 664 61 49
Wojciech Gałan, 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:  B010 (3.01.4), phone: +48 12 664 61 49
Michał Gucwa, room: B019 (3.01.9), phone: +48 12 664 64 31
Wojciech Dec, room: B019 (3.01.9), phone: +48 12 664 64 31

Clasical molecular dynamics simulation
  • Organization of the membrane/water interfacial region as well as dynamical structure of bilayers composed of various lipids
  • Correlations between physico-chemical properties of the bilayer and (a) structural characteristics of the bilayer lipids, (b) bilayer lipid composition
  • Mechanisms of action of selected membrane-active compounds of a therapeutic potential
  • Development and validation of the OPLS/AA and CHARMM force field parameters
  • Influence of natural membrane components (peptides, carotenoids, etc.) on the structural organization of the lipid bilayer
  • Properties of pure cholesterol domains in bilayers oversaturated with cholesterol
  • Translocation of small and medium size molecules across bilayers
  • Mechanical properties of bilayers composed of various lipids
  • Investigation of the non-lamellar lipid phases
  • Initial stages of atherosclerotic plaque formation – self-association of cholesterol molecules in water and the effect of Chol oxidation products on this proces
  • Research on the conformational mobility and dynamics of proteins, particularly in the context of allosteric regulation of protein activity.
Bioinformatics
  • Prediction of 3D structures and biological functions of proteins
  • Application of artificial intelligence to analyze biological data
  • Qualitative control of transcripts in the process of RNA interference and functional division of miRNAs
Software development
  • Development of software tools for analysis of the molecular dynamics simulation  trajectories and force field parameterization
  • Bioinformatics applilcations of biological data procecessing employing neural networks and genetic algorithms
  • Validation of protein structure determined by experimental methods (X-ray crystallography, cryo-electron microscopy) and theoretical methods (AlphaFold).

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 methods for prediction of the 3D structure and biological functions of proteins
  • application of machine learning methods to biological data analysis

Equipment:

  • specialized servers and workstations
  • software used for molecular modelling: Gromacs, Amber, BOSS, CHARMM, Gaussian, CP2K

  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, 2016/22/M/NZ1/00187, project budget: 351 884 PLN
  2. Krzysztof Murzyn: Structural and dynamic properties of a model outer membrane of Gram-negative bacteria. (2011-2014), OPUS 1, NCN 2011/01/B/NZ1/00081, project budget: 349 800 PLN

  1. Hryc J, Markiewicz M, Pasenkiewicz-Gierula M. „Stacks of monogalactolipid bilayers can transform into a lattice of water channels.” iScience 2023 26:107863  
  2. Gucwa M, Lenkiewicz J, Zheng H, Cymborowski M, Cooper DR, Murzyn K, Minor W. „CMM-An enhanced platform for interactive validation of metal binding sites.” Protein Science 2023 32:e4525
  3. Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. „The current role and evolution of X-ray crystallography in drug discovery and development.” Expert Opinion inDrug Discovery  2023 18:1221-1230
  4. Lenkiewicz J, Bijak V, Poonuganti S, Szczygiel M, Gucwa M, Murzyn K, Minor W. „Structural biology and public health response to biomedical threats.” Structural Dynamics US 2023 10:034701
  5. Hryc J, Szczelina R, Markiewicz M, Pasenkiewicz-Gierula M. „Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases.” Frontiers in Molecular Biosciences 2022 9:958537 
  6. Kania A, Sarapata K. „Multifarious aspects of the chaos game representation and its applications in biological sequence analysis”. Computers in Biology and Medicine 2022 15:106243
  7. Markiewicz M, Szczelina R, Milanovic B, Subczynski WK, Pasenkiewicz-Gierula M. „Chirality affects cholesterol-oxysterol association in water, a computational study.” Computational and Structural Biotechnology Journal 2021 19:4319–4335
  8. Makuch K, Hryc J, Markiewicz M, Pasenkiewicz-Gierula M. „Lutein and zeaxanthin in the lipid bilayer : similarities and differences revealed by computational studies.” Frontiers in Molecular Biosciences 2021 8: 768449
  9. Markiewicz M, Szczelina R, Pasenkiewicz-Gierula M. „Data for molecular dynamic simulations in the OPLS/AA force field: Partial charges of cholesterol, C7-hydroxycholesterol and C7-hydroperoxycholesterol, torsional parameters for the hydroperoxy group of C7-hydroperoxycholesterol.” Data in Brief 2021 39:107483
  10. Kania A, Sarapata K. „The Robustness of the chaos game representation to mutations and its application in free-alignment methods.” 2021 Genomics 113:1428-1437
  11. Kania A. „Harnessing the information theory and chaos game representation for pattern searching among essential and non-essential genes in Bacteria.” Journal of Theoretical Biology 2021 531:110917 
  12. Subczynski WK, Pasenkiewicz-Gierula M. “Hypothetical Pathway for Formation of Cholesterol Microcrystals Initiating the Atherosclerotic Process.” Cell Biochemistry and Biophysics 2020 78:241-247
  13. Szczelina R, Baczynski K, Markiewicz M, Pasenkiewicz-Gierula M. „Network of lipid interconnections at the interfaces of galactolipid and phospholipid bilayers.” Journal of Molecular Liquids 2020 298:112002
  14. Bratek M, Wójcik-Augustyn A, Kania A, Majta J, Murzyn K. „Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields.” Acta Biochemica Polonica 2020 67:309-318
  15. Makuch K, Markiewicz M, Pasenkiewicz-Gierula M. „Asymmetric Spontaneous Intercalation of Lutein into a Phospholipid Bilayer, a Computational Study.” Computational Structural Biotechnology Journal 2019 17:516-526
  16. Plesnar E, Szczelina R, Subczynski WK, Pasenkiewicz-Gierula M. „Is the cholesterol bilayer domain a barrier to oxygen transport into the eye lens?” Biochimica et Biophysica Acta – Biomembranes 2018 1860:434-441
  17. Pasenkiewicz-Gierula M, Baczynski K, Markiewicz M, Murzyn K. „Computer modelling studies of the bilayer/water interface.” Biochimica et Biophysica Acta – Biomembranes 2016 1858:2305-2321
  18. Murzyn K, Pasenkiewicz-Gierula M. „Structural Properties of the Water/Membrane Interface of a Bilayer Built of the E. coli Lipid A.” Journal of Physical Chemistry B 2015 119:5846-5856
  19. Szczelina R, Murzyn K. „DMG-alpha-A Computational Geometry Library for Multimolecular Systems.” Journal of Chemical Information and Modeling 2014 54:3112-3123
  20. Murzyn K, Bratek M, Pasenkiewicz-Gierula M. „Refined OPLS All-Atom Force Field Parameters for n-Pentadecane, Methyl Acetate, and Dimethyl Phosphate.” Journal of Physical Chemistry B 2013 117:16388-16396

All master theses carried out at our Department are performed using computational methods.
Proposed topics:

  • construction and analyses of computer models of specific membranes (bacterial, nervous, etc.)
  • bioinformatics analyzes of various biological data
  • 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 
  • development and validation of OPLS All Atom force field parameters
  • molecular modelling software development
  • realisation of own rational ideas

Skills and willingness to use computers for scientific purposes; expected programming skills and knowledge of GNU/Linux OS; interest in basic events on the atomic/molecular level.