Phd Students

• Mgr inż. Katarzyna Kluska
• Mgr Olga Kerber
• Mgr Karolina Szaro
• Mgr Sylwia Wu
• Mgr Anastasiia Antonenko
• Mgr Alicja Misiaszek

CONTACT

Head: room No. 3.12, phone +48 71375 2765
Dr Adam Pomorski, Dr Anna Kocyła, Dr Manuel Peris Diaz, Mgr Sylwia Wu: room No. 3.11, phone +48 71375 2608
Dr Anna Barg-Wojas, Mgr Olga Kerber, Mgr Karolina Szaro, Mgr Anastasiia Antonenko, Mgr Alicja Misiaszek: room No. 3.10, phone +48 71375 2608
Dr Marek Łuczkowski: room No. 2.28, phone +48 71375 7975

RESEARCH TOPICS AND THE MOST IMPORTANT RESULTS

Research conducted at the Department of Biological Chemistry focuses on inorganic biochemistry, biophysics, and biological chemistry. Of our particular interest are the metal-dependent regulation of proteins, their structure, and their stability. Our Department aims to answer the questions of how metalloproteins acquire their metal ions under cellular conditions and how these ions regulate their activity. We also focus on the development of molecular tools for regioselective and multifunctional protein labeling with chemical and enzymatic methods, analytical methods for monitoring the fluctuation and regulation of metal ions in the cell, and bioanalytical methods for studying the stability of metalloprotein and their complexes. We address the fundamental questions using a combination of modern research techniques, protein engineering tools, synthetic chemistry, structural mass spectrometry, biophysical analyses, molecular and structural biology as well as computational methods. 

Research topics include: 

• Molecular basis of the mammalian metallothioneins function. 
• Regulatory functions of metal proteins. 
• Interprotein structural motifs that bind metal ions. 
• Optimization of analytical methods useful in studying of metal ion binding to proteins. 
• The relationship between the structure of proteins and zinc domains and their stability and function. 
• Regioselective modification of proteins with the use of “click” chemistry and specific ligating enzymes. 
• Design, synthesis, and application of fluorescent probes metal and pH study in cell research.

The most important research achievements: 

• Determination of factors that drive thermodynamics of zinc-binding to zinc finger domains in the context of the cellular fluctuation of this ion. 
• Discovery and characterization of naturally altered classical zinc finger motifs and determination of their regulatory role in the transcription process. 
• Development of the coordination chemistry of interprotein zinc-binding sites in proteins. 
• Explaining the role of zinc hook motif in the Rad50 protein on the DNA repair process. 
• Application of interprotein metal ion binding motifs in biotechnology. 
• Development of the chemistry of bisarsenical dyes for the selective labeling of proteins and incorporation of specific functions. 
• Revealing the importance of metallothionein isoforms in the cellular homeostasis of zinc and copper. 

EXAMPLE DOCTORAL DISSERTATION TOPICS

• „Investigation of Zn²⁺-dependent CD4 coreceptor and Lck tyrosine kinase assembly”, Anna Kocyła, 2021.
• „Characterization of the stability and reactivity of human metallothioneins in the context of the cellular homeostasis of Zn (II) ions”, Agnieszka Drozd, 2017.
• „Biophysical and functional characterization of the hook domain of the zinc protein Rad50 and its homologues”, Tomasz Kochańczyk, 2017.
• „Preparation and characterization of biarsen dyes used for the selective modification of proteins”, Adam Pomorski, 2015.

RESEARCH PROJECTS

• NCN project PRELUDIUM19 no. 2020/37/N/NZ1/03319: Conformational dynamics of Rad50 hook domain under controlled Zn(II) level, 2021-2023.
  Head of the project: mgr Olga Kerber.
• NCN project ETIUDA no. 2020/36/T/ST4/00404: Structural characterization of metallothionein zinc-loaded states and their role in regulation of p53 tumor supressor activity, 2020-2021.
  Head of the project: dr Manual Peris Diaz.
• NCN project OPUS17 no. 2019/33/N/ST4/00409: New regioselective chemical and biochemical strategies for proteins labeling, 2020-2023.
  Head of the project: prof. dr hab. Artur Krężel.
• NCN project PRELUDIUM17 no. 2019/33/N/ST4/00409: Biophysical and functional characterization of human MTF-1 fragments, 2020-2022.
  Head of the project: mgr inż. Katarzyna Kluska.
• NCN project OPUS16 no. 2018/31/B/NZ1/00567: Impact of metallothionein polymorphism and metamorphism on cellular zinc homeostasis – the role of sequential, structural and thermodynamic diversity, 2019-2022.
  Head of the project: prof. dr hab. Artur Krężel.
• NCN project PRELUDIUM16, no. 2018/31/N/ST4/01909: The role of metallothionein zinc-load states in regulation of p53 tumor supressor activity, 2019-2021.
  Head of the project: dr Manuel Peris Diaz.
• NCN project ETIUDA, no. 2018/28/T/NZ1/00526: Characterization, optimization and application of interprotein interactions dependent on Zn²⁺ ions, 2018-2019.
  Head of the project: dr Anna Kocyła.
• NCN project PRELUDIUM, no. 2016/23/N/NZ1/00040: Impact of the coiled-coil segment on the functioning and assembly of yeast Rad50 dimer, 2017-2018.
  Head of the project: dr Marcin Padjasek.
• NCN project OPUS, no. 2016/21/B/NZ1/02847: Interdomain allosteric communication in Rad50 protein and its role in genome maintence by Mre11 complex, 2017-2019.
  Head of the project: prof. dr hab. Artur Krężel.
• NCN project PRELUDIUM, no. 2016/21/N/NZ1/02775: Impact of palmitoylation on the Zn(II)-dependent interaction between CD4 coreceptor and Lck tyrosine kinase, 2017-2019.
  Head of the project: dr Artur Kocyła.
• NCN project OPUS, no. 2014/13/B/NZ1/00935: Structural and biophysical characteristics of highly conserved zinc hook domain of Rad50 protein – Studies on stability and diverse coordination dynamics in various domains of life, 2015-2017.
  Head of the project: prof. dr hab. Artur Krężel.
• NCN project SONATA BIS, no. 2012/07/E/NZ1/01894: Exploration of zinc proteome – Identification and characterization of new zinc domains and their function in stabilization of proteins and protein-protein interactions, 2013-2018.
  Head of the project: prof. dr hab. Artur Krężel.

LABORATORY EQUIPMENT

• Compact ESI-Q-ToF mass spectrometer with UHPLC (Bruker)
• Glove box (Hoger)
• Isothermal titration nanocalorimeter ITC (TA Instruments)
• Spectropolarimeter CD (Jasco J1500 Model 150)
• Peptide synthesizer (Activotec)
• Microwave peptide synthesizer (CEM Liberty One)
• Liquid chromatography systems FPLC, HPLC, LC: ÄKTA pure (GE Healthcare), NGC (Bio-Rad), UltiMate 3000 (Dionex), Flash (Gilson PLC2020)
• Fluorescence lifetime spectrometer (Horiba DeltaFlex)
• Fluorescence spectrofluorimeter (Horiba FluoroMax 4)
• UV-Vis spectrophotometers (Jasco V-630, V-650, V-750)

SELECTED PUBLICATIONS

ADDITIONAL INFORMATION

• Scholarship of the Minister of Science and Higher Education for outstanding young scientists in 2021 – Manuel David Peris Diaz.
• “The Metallomics Young Investigator’s Award” (2019) – dr Anna Kocyła.
• Scholarship under the Bekker Program by the National Agency for Academic Exchange – implementation of the project “Engineering ClpXP protein assembly for single molecule protein sequencing” at the University of Technology in Delft (the Netherlands) in 2019-2021 – dr Adam Pomorski.
• “Diamond Grant” of the Ministry of Science and Higher Education, no .: DI2011 031341 “Understanding the mechanism of interaction of the Rad50 zinc hook domains and creating molecular tools based on these domains for biotechnological applications” (2012-2016) – Tomasz Kochańczyk.