What research problems do you face?
Agnieszka Pietrzyk-Brzezińska: In the area of our interest are regulatory proteins, i.e. macromolecules present in cells and in this case, capturing a signal from the environment. Such a signal can be, for example, antibiotics or metal ions. Then, after recognizing the signal, the regulator activates the expression of the appropriate genes and proteins are produced that allow the bacterial cell to survive in stress conditions. Knowing how to inhibit this process would be extremely helpful in the fight against bacteria. In our research, we focus on the proteins of Escherichia coli, bacteria because it is a model organism. It is worth emphasizing here that homologous proteins are found in many pathogenic bacteria, i.a. Shigella, Salmonella, so the research may contribute to the development of new tools in the fight against infections caused by these dangerous bacteria.
Anna Cociurovscaia: The main goal of our research is to understand the spatial structure of the studied regulatory proteins and all changes occurring in their structure under the influence of specific factors, such as the presence of a given antibiotic in the environment. In addition, we can also obtain the spatial structure of a protein interacting with a substance that inhibits its action. Based on such a structure, a very specific drug can be designed to deactivate a protein with undesirable activity. Therefore, our research may contribute to the development of new drugs that will help in the fight against bacteria resistant to known antibiotics.
What stage are the studies at?
Agnieszka Pietrzyk-Brzezińska: The project on bacterial proteins started relatively recently. Still, we already have the first spatial structures of the proteins being studied, and two articles describing the results were published this year in the journal Proteins and Journal of Structural Biology. The idea for this research topic appeared during my postdoctoral fellowship. In addition to the main project carried out during the internship, concerning human proteins involved in the process of cancer formation, I also took part in a side project related to bacterial proteins. I was very interested in this topic, because bacterial resistance to antibiotics is currently becoming a global problem. Still, many of the mechanisms involved in the response of bacterial cells to changing environmental conditions, including the presence of antibiotics and antiseptics, have not been thoroughly studied.
In the field of your interests is the effect of copper and silver ions on the survival of bacterial cells. What bactericidal potential do these ions have?
Anna Cociurovscaia: Trace amounts of copper ions are necessary for the functioning of any living cell, while in excess they can inhibit metabolic processes. Silver ions work in a simmilar manner and they are even more active.
Agnieszka Pietrzyk-Brzezińska: Silver ions are often utilized as a component of bactericides, penetrate into bacterial cells and inhibit vital processes. They are also used in cosmetics, in disinfection of premises, as well as in sterilization processes in industry and agriculture.
Anna Cociurovscaia: Nevertheless, bacteria are able to combat the harmful effect of free metal ions within a certain concentration range. Therefore, in order to reduce the number of bactericides used and prevent the development of new bacterial resistance systems, we want to know exactly the mechanism of response to stress caused by the presence of heavy metals.
How can this translate into pharmacology and industry?
Anna Cociurovscaia: Currently, in pharmacological studies, high-throughput screening methods are used to find the most effective chemical compounds, e.g. inhibiting the activity of a given protein. X-ray crystallography has also reached such a level of development that allows it to be called a reliable high-throughput method. The Fragment Screening technique, which already has its successes at the level of clinical trials, allows to identify potential active molecules with the desired activation or deactivation effect in relation to the studied protein. We also plan to use this technique to look for molecules that inhibit the activity of the signalling protein in the process of bacterial cell response to the presence of copper and silver ions.
Agnieszka Pietrzyk-Brzezińska: In addition, proteins that detect the presence of copper or silver ions may be important not only for the pharmacological industry but may become components of systems that detect contamination of these metals in the environment. Therefore, our research is important and can be useful for many industries.
What were your previous scientific interests?
Agnieszka Pietrzyk-Brzezińska: My adventure with science began already during my master's studies at Wrocław University of Technology. The topic of my master's thesis was in the field of molecular biology and biochemistry, thanks to which I had the opportunity to conduct the first experiments involving the study of insect proteins. In turn, I pursued my doctorate in the group of Prof. Grzegorz Bujacz at Lodz University of Technology and in the Institute of Bioorganic Chemistry of the Polish Academy of Sciences. At that time, I was engaged in structural research of mulberry silkworm proteins. After defending my doctoral thesis, I started a postdoctoral fellowship at Freie Universitaet Berlin and after a year I obtained a prestigious scholarship from the Alexander von Humboldt Foundation, which enabled me to continue my internship for another two years. During the internship, my main project concerned proteins involved in the process of cancer formation. After completing my postdoctoral training, I returned to Lodz University of Technology in Prof. Grzegorz Bujacz's group and have been working as an assistant professor since 2018. My main focus is currently bacterial proteins associated with the cell response to the presence of bactericidal substances in the environment.
Anna Cociurovscaia: My first research experience is closely related to the choice of specialization and subject matter of diploma thesis in the field of structural biology. Even during the lectures on biochemistry, I was very interested in the fact that X-ray crystallography allows you to "see" molecules responsible for cellular processes invisible to the naked eye. Therefore, I decided to learn more about protein crystallography under the guidance of Prof. Grzegorz Bujacz and the supervision of Dr Agnieszka Pietrzyk-Brzezińska at the Institute of Molecular and Industrial Biotechnology. During the preparation of my engineering thesis, I became familiar with crystallisation techniques and the basics of protein crystallography. However, during my master's thesis, I gained experience in the production and purification of proteins, as well as in the process of solving the spatial structure of the protein, using experimental diffraction data. On the basis of the results obtained as part of my master's thesis, together with Dr Agnieszka Pietrzyk-Brzezińska, we deposited three such structures in the Protein Data Bank and described them in my first scientific publication. All these higher mentioned experiences contributed to the commencement of my studies at the Interdisciplinary Doctoral School TUL and the implementation of a doctoral project related to bacterial transcription factors.
Agnieszka Garcarek-Sikorska