dr Paweł Zawadzki

@article{doi:10.1093/nar/gky1143,
title = {Single-molecule imaging of DNA gyrase activity in living Escherichia coli},
author = {Mathew Stracy and Adam JM Wollman and Elżbieta Kaja and Jacek Gapiński and Ji-Eun Lee and Victoria A Leek and Shannon J McKie and Lesley A Mitchenall and Anthony Maxwell and David J Sherratt and Mark C Leake and Paweł Zawadzki},
url = {http://dx.doi.org/10.1093/nar/gky1143},
doi = {10.1093/nar/gky1143},
year = {2019},
date = {2019-01-10},
journal = {Nucleic Acids Research},
volume = {47},
number = {1},
pages = {210-220},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Zawadzka2018,
title = {MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin},
author = {Katarzyna Zawadzka and Paweł Zawadzki and Rachel Baker and Karthik V Rajasekar and Florence Wagner and David J Sherratt and Lidia K Arciszewska},
url = {https://doi.org/10.7554/elife.31522},
doi = {10.7554/elife.31522},
year = {2018},
date = {2018-01-01},
journal = {eLife},
volume = {7},
publisher = {eLife Sciences Organisation, Ltd.},
abstract = {The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Stracy2016,
title = {Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli},
author = {Mathew Stracy and Marcin Jaciuk and Stephan Uphoff and Achillefs N Kapanidis and Marcin Nowotny and David J Sherratt and Paweł Zawadzki},
url = {http://www.nature.com/doifinder/10.1038/ncomms12568},
doi = {10.1038/ncomms12568},
issn = {2041-1723},
year = {2016},
date = {2016-08-01},
journal = {Nature Communications},
volume = {7},
pages = {12568},
publisher = {Nature Publishing Group},
abstract = {Nucleotide excision repair is able to identify and remove a wide range of DNA helix distorting lesions from the genome. Here the authors use single molecule imaging of UvrA and UvrB molecules and suggest a two-step ‘scan and recruit' model for UvrA function.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Pinkney2012,
title = {Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence},
author = {J N M Pinkney and Paweł Zawadzki and Jarosław Mazuryk and L K Arciszewska and D J Sherratt and A N Kapanidis},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23184986 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3529024 http://www.pnas.org/cgi/doi/10.1073/pnas.1211922109},
doi = {10.1073/pnas.1211922109},
issn = {0027-8424},
year = {2012},
date = {2012-12-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {109},
number = {51},
pages = {20871--20876},
abstract = {Site-specific recombination plays key roles in microbe biology and is exploited extensively to manipulate the genomes of higher organisms. Cre is a well studied site-specific recombinase, responsible for establishment and maintenance of the P1 bacteriophage genome in bacteria. During recombination, Cre forms a synaptic complex between two 34-bp DNA sequences called loxP after which a pair of strand exchanges forms a Holliday junction (HJ) intermediate; HJ isomerization then allows a second pair of strand exchanges and thus formation of the final recombinant product. Despite extensive work on the Cre-loxP system, many of its mechanisms have remained unclear, mainly due to the transient nature of complexes formed and the ensemble averaging inherent to most biochemical work. Here, we address these limitations by introducing tethered fluorophore motion (TFM), a method that monitors large-scale DNA motions through reports of the diffusional freedom of a single fluorophore. We combine TFM with Foerster resonance energy transfer (FRET) and simultaneously observe both large- and small-scale conformational changes within single DNA molecules. Using TFM-FRET, we observed individual recombination reactions in real time and analyzed their kinetics. Recombination was initiated predominantly by exchange of the "bottom-strands" of the DNA substrate. In productive complexes we used FRET distributions to infer rapid isomerization of the HJ intermediates and that a rate-limiting step occurs after this isomerization. We also observed two nonproductive synaptic complexes, one of which was structurally distinct from conformations in crystals. After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Zawadzki2010,
title = {A fluorescence correlation spectroscopy study of ligand interaction with cytokinin-specific binding protein from mung bean},
author = {Paweł Zawadzki and Genowefa Ślósarek and Jerzy Boryski and Przemysław Wojtaszek},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19919180 https://www.degruyter.com/view/j/bchm.2010.391.issue-1/bc.2010.005/bc.2010.005.xml},
doi = {10.1515/bc.2010.005},
issn = {1437-4315},
year = {2010},
date = {2010-01-01},
journal = {Biological Chemistry},
volume = {391},
number = {1},
pages = {43--53},
abstract = {Cytokinins are essential plant hormones that regulate numerous physiological processes. Recently, a protein was identified in mung bean (Vigna radiata) and characterized as a cytokinin-specific binding protein (VrCSBP). Fluorescence correlation spectroscopy was used to investigate the interaction between VrCSBP and its ligands. The synthetic cytokinin, N-phenyl-N'-(4-pyridyl) urea, was labeled with two fluorophores, 7-nitro-2,1,3-benzoxadiazole and rhodamine B. Protein-ligand binding was analyzed in an equilibrium saturation binding experiment and confirmed by the competition assay. Surprisingly, it was found that VrCSBP binds not only to cytokinins, but also to gibberellins. In addition, in the presence of natural cytokinins and gibberellins, two populations of VrCSBP that differ in their diffusion coefficients were detected. The diffusion coefficients of these two populations could be related to mono- and dimeric states, which suggests a new mode of operation in ligand binding by VrCSBP, in which dimerization induced by natural ligands enhances the ligand binding capacity of the protein.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}