Laboratories

Research

Main Scientific Achievements

• In collaboration with the Laboratory of Mass Spectrometry, we proposed the mechanism of Aβ1-40 peptide aggregation. The most important finding was that the experimentally determined fractal dimension of aggregates was 2, indicating the formation of flat sheet-like structures.
• We explained molecular bases of the substrate preference of bacterial AlkB dioxygenase, which were further validated for human homologs (ALKBH3 and fat mass and obesity‐associated protein [FTO]).
• Our long-term thermodynamics studies demonstrated that the contribution of halogen bonding to the free energy of ligand binding is predominated by a balance of electrostatic and hydrophobic interactions.

Research Description

The main objective of our work is the development of research tools that enable building the relationship between molecular structure and biological function. Our research is based primarily on medium- and high-resolution models that are built on the basis of structural data that are available for similar systems (e.g., modeling by homology using Protein Data Bank structures as templates), in the context of biophysical observations (thermodynamic parameters, spectroscopic data, and HD exchange monitored by mass spectrometry [MS]), biochemical observations (kinetic data and substrate selectivity), biological observations (cell viability and drug metabolic pathways), and medical observations (molecular backgrounds of genetic diseases). Our goal is to identify specific interactions or combinations thereof that explain the observed effect. We sometimes act like passive researchers who only interpret observations (mainly in the case of medical data). For most problems, however, we are building hypotheses that provide feedback for further experimental research.

• New algorithms of data analysis

We are constantly developing methodologies for the global analysis of data that are obtained under different conditions or even from different kinds of experimental approaches. We use state-of-art numerical models that allow the reliable estimation of parameters that are unavailable with standard software. We performed the first global analysis of MST (Microscale Thermophoresis) data for two independent binding sites,¹ and interpreted the ITC data (Isothermal Titration Calorimetry) for the presence of three nonequivalent binding sites (doi: 10.1371/journal.pone.0154822). Some of our models were published in the highest ranked journals (doi: 10.1021/ja907567r, doi: 10.1038/s41467-019-11900-8).

• Molecular modeling

Valuable molecular models that explain particular biophysical (e.g., the organization of peptide Aβ1-40 early stage aggregates, biochemical (e.g., substrate specificity of Arabidopsis DXO1 protein; doi: 10.1093/nar/gkz100), biological (doi: 10.1098/rsob.150238, doi: 10.3390/ijms21155268), or medical (doi: 10.15252/emmm.201809561, doi: 1002/ajmg.a.36646) observations have been proposed.

• Halogen bonding and its thermodynamic contribution to the free energy of protein-ligand interactions

We are analyzing thermodynamic effects of individual halogen atoms on the interaction between halogenated ligands and their molecular target, the catalytic subunit of protein kinase CK2.^1-4 We designed and synthesized dozens of molecular probes that contain various combinations of halogen atoms (F, Cl, Br, I) and studied their interactions with the molecular target using various thermodynamics techniques.^{5, 6} We synthesized a CK2 bisubstrate inhibitor with moderate activity. We also studied the geometry and topology of halogen bonds in protein-ligand complexes ⁷ and competition between halogen and hydrogen bonds.⁸

• Hydrophobic interactions

A new hydrophobicity scale that is based on changes in solvent density that is caused by the solute has been proposed, enabling experimental determination of the apparent volume of a single molecule. We proved that the partial molar volume can be treated as a thermodynamic parameter that describes hydrophobicity. Each hydrophobic molecule affects the organization of the proximal solvent, and higher hydrophobicity of the solute is associated with a lower density of water in the solvation shell. We use this parameter to assess the hydrophobic contribution to the free energy of ligand binding.

• Role of the Ada operon in the repair of exocyclic DNA lesions

We study mutagenic properties of several exocyclic DNA lesions, acrolein and chloroacetaldehyde adducts to cytosine and adenine, 1,N⁶-α-hydroxypropanoadenine,⁹ 3,N⁴-α-hydroxypropanocytosine, 3,N⁴-α-hydroxyethano-cytosine, 3,N⁴-ethenocytosine (εC),¹⁰ and 1,N⁶-ethenoadenine (εA) and their repair by AlkB dioxygenase and AlkA glycosylase. AlkB acts according to a previously unknown DNA repair mechanism. It removes modifications from alkylated DNA bases via oxidative dealkylation, without disturbing DNA We experimentally proved that AlkB preferentially recognizes and repairs cationic substrates. We now focuse on the biological function of AidB dehydrogenase, characterizing DNA-AlkB-AidB, RNA-AlkB-AidB, and RNA-AlkB complexes, and studies the repair of exocyclic RNA adducts. This multidisciplinary approach should provide deeper insights into fundamental aspects of cellular homeostasis maintenance (NCN grant no. 2018/29/B/NZ3/02285).

• Bibliography

1. Winiewska et al. 2017. PLoS One 12.
2. Wasiket et al. 2012. Journal of Physical Chemistry B 116, 7259-7268.
3. Winiewska et al. 2015. Biochemical and Biophysical Research Communications 456, 282-287.
4. Winiewska et al. 2015. Biochimica et Biophysica Acta-Proteins and Proteomics 1854, 1708-1717.
5. Kasperowicz et al. 2020. Iubmb Life 72, 1211-1219.
6. Marzec et al. 2020. Iubmb Life 72, 1203-1210.
7. Poznanski et al. 2016. Acta Biochim. 63, 203-214.
8. Poznanski et al. 2014. PLoS One 9.
9. Dylewska et al. 2017. Biochem. J. 474, 1837-1852.
10. Maciejewska et al. 2010 Mutat. Res. 684, 24-34.

Methodology

• In silico studies on proteins, their complexes, and modifications are based on structural models that are obtained via homology with the Yasara-Structure package. If desired, the standard force field can be extended based on ab initio The effects of residue replacements or modifications on protein stability or affinity for molecular targets are evaluated with the local UI for FoldX and AutoDock programs.
• Thermodynamics studies on protein. Ligand interactions are performed with the aid of numerous biophysical methods. They include nanoDSF (equivalent to the thermal shift assay), microscale thermophoresis, and isothermal titration calorimetry. These data can be supplemented by affinity chromatography coupled with mass spectrometry and various nuclear magnetic resonance (NMR) techniques (¹³C, ¹⁵N, and ¹⁹F nuclear relaxation, relaxation-filtered NMR, diffusion ordered spectroscopy, and chemical shift perturbation).
• Structural data can also be obtained by heteronuclear NMR or crystallography. We also support our studies with massive CSD and Protein Data Bank structural data screening.
• Density data that are determined with Anton PAAR DMA 5000M enables the determination of partial molar volumes and thermal volumetric expansion at submilimolar concentrations. We use these data to study the contribution of hydrophobic solvation in biomolecular systems.
• We collect biochemical data on “enzymes in action” with EU-OPENSCREEN facilities, but the assays for protein kinase and dioxygenase assays have already been implemented in our l
• Our chemical laboratory is sufficiently equipped to perform various types of chemical syntheses, including halogenation reactions and reactions in anhydrous conditions over a wide temperature range (-70°C to over 200°C). This allows the multi-step synthesis of designed heterogeneously halogenated heterocyclic compounds or their libraries. We are able to perform multi-component reactions and synthesize substrates for these reactions (e.g., isocyanates). We are able to synthesize bisubstrate ligands of target proteins using a multicomponent reaction.

Selected Publications

• Winiewska-Szajewska M*, Czapinska H, Kaus-Drobek M, Fricke A, Mieczkowska K, Dadlez M, Bochtler M, Poznański J* (2022). Competition between electrostatic interactions and halogen bonding in the protein–ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2α complexes. Scientific Reports 12: 18964; doi: 10.1038/s41598-022-23611-0
• Stefaniuk A, Gawinkowski S, Golec B, Gorski A, Szutkowski K, Waluk J, Poznański J* (2022) Isotope effects observed in diluted D2O/H2O mixtures identify HOD-induced low-density structures in D2O but not H2O. Scientific Reports 12: 18732; doi: 10.1038/s41598-022-23551-9
• Czapinska H, Winiewska-Szajewska M, Szymaniec-Rutkowska A, Piasecka A, Bochtler M,* Poznański J* (2021) Halogen Atoms in The Protein-Ligand System. Structural and Thermodynamic Studies of The Binding of Bromobenzotriazoles by the Catalytic Subunit of Human Protein Kinase CK2. Journal of Physical Chemistry B. 125: 2491-2503; doi: 10.1021/acs.jpcb.0c10264
• Szymaniec-Rutkowska A, Bugajska E, Kasperowicz S, Mieczkowska K, Maciejewska AM, Poznański J* (2019) Does the partial molar volume of a solute reflect the free energy of hydrophobic solvation? Journal of Molecular Liquids 293: 111527; doi: 10.1016/j.molliq.2019.111527
• Winiewska M*, Bugajska E, Poznański J* (2017) ITC-derived binding affinity may be biased due to titrant (nano)aggregation. Binding of halogenated benzotriazoles to the catalytic domain of human protein kinase CK2. PLoS ONE 12: e0173260; doi: 10.1371/journal.pone.0173260

Collaborations

• Marcin Nowotny, Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, www.iimcb.gov.pl/en/research/laboratories/6-laboratory-of-protein-structure-nowotny-laboratory
• Jerzy Bal, Department of Medical Genetics, Institute of Mother and Child, zgm.imid.med.pl/
• Michał Dadlez, Institute of Biochemistry and Biophysics PAS
• Wojciech Bal, Institute of Biochemistry and Biophysics PAS
• Ewa Świeżewska,  Institute of Biochemistry and Biophysics PAS