Research in Biochemistry

Biochemistry is the study of the chemical processes in living organisms. Modern biochemistry tries to answer questions that are related, for example, to the regulation of gene expression or the structure and function of cellular proteins. The research performed by the Biochemistry division in the University of Turku is focused on the structural and functional analysis of mammalian and bacterial proteins, enzymology, microbial molecular biology and immunochemistry.

Focus areas

Protein structure and function

For a protein to function, it has to fold correctly. For example, the side chains of amino acids corresponding to the activity of the enzyme should be located in just the right places in the folded protein. Thus, the function of many proteins can be investigated by solving its three-dimensional structure. Additionally, various binding experiments and activity assays can be used. The proteins can also be mutated and the effects of mutations examined at both molecular and cellular levels.

Interactions between cell and its environment

The cells sense various molecules of their environment through their receptors and change their activity according to these signals. Cells also produce different signal molecules and enzymes, thereby modifying their environment. For example, a cancer cell can secrete factors that accelerate the production and secretion of cancer-promoting proteins in normal cells. Immune cells have their own receptors to identify a foreign protein or microbe and cause immune response. Some bacteria and viruses may also exploit cellular receptors to alter cell behavior for their own benefit or to intrude into the cell.

Research groups

Biofilm-host Interaction in Chronic Infection

Biofilms, bacterial communities surrounded by protecting extracellular matrix, are resistant to antibiotics and the host defense systems. Most recent research results suggest that the inter-kingdom signaling between biofilm forming bacteria and the host cells might elucidate the different phases in chronic biofilm infection. The aim of our studies is to illuminate the molecular mechanisms of biofilm-host crosstalk in periodontitis, a chronic infection destroying the tooth supporting tissues.
We are part of the European Network of Aggregatibacter actinomycetemcomitans research
Read more

Contact: Dr. Riikka Ihalin

 

Antibiotic Biosynthetic Enzymes (ABE)

Our research is focused on the chemical biology of bioactive secondary metabolites produced by different members of the bacterial genus Streptomyces. We study how these soil bacteria are able to synthesize highly complex natural products that are widely used in medicine, agriculture and other fields of commerce. Central areas of our research involve molecular genetics and natural product chemistry that are combined with protein chemistry and structural biology. Project Leaders: Mikko Metsä-Ketelä / Jarmo Niemi

Group web pages

Cell Adhesion and Cancer

Cancer progression involves uncontrolled proliferation and motility of cells. Integrins, transmembrane cell surface adhesion receptors, are proteins known to regulate cell behaviour by transducing extracellular signals to cytoplasmic protein complexes. We have performed genome-wide screens to identify integrin-binding intracellular proteins and demonstrated that recruitment of specific protein complexes by the cytoplasmic domains of integrins is important in tumorigenesis. We have also expanded our research into new integrin-binding proteins and thus gained more information on the diverse biological roles of integrins in cancer.​

Contact:  Academy Professor Johanna Ivaska

Ivaska lab web page

Immunochemistry

Our environment contains a great variety of infectious microbes –viruses, bacteria, fungi, protozoa and multicellular parasites. These can cause disease, and if they multiply unchecked they will eventually kill their host. Most infections in normal individuals are short-lived and leave little permanent damage. This is due to the immune system, which combats infectious agents. Since micro-organisms come in many different forms a wide variety of immune responses are required to deal with each type of infection. On the other hand, there are many beneficial commensal micro-organisms, which compete effectively with many potential pathogens. Read more

Contact: Dr. Jari Nuutila, Dr. Janne Atosuo

Structure and Function of Collagen Receptor Integrins


Integrins are signaling transmembrane cell adhesion receptors that connect the cell to the extracellular matrix composed of collagen and other matrix molecules. Integrins play crucial roles in growth, development, migration, defense mechanisms and apoptosis of the cell. We are focused on the collagen receptor integrins. Small molecule drugs targeted to these integrins could be used to cure cancers, inflammations, and cardiovascular diseases. We are currently elucidating the activation mechanism of the collagen receptor integrins and its influence to intracellular signaling. We are also studying integrin internalization from the plasma membrane. In addition to common methods in molecular, structural and cell biology, we use combined atomic force/confocal microscopy and proteomics in our research. Read more

Contact: Prof. Jyrki Heino

Regulation of Eukaryotic Transcription (RET)

Cell employs RNA polymerase enzymes to read genomic information in response to its ever-changing needs. Our research focuses on RNA polymerase I (Pol I) that produces ribosomal RNA – the building block of cellular protein factories. Excessively active Pol I allows cancer cells to grow beyond normal controls. To understand how the function of Pol I is regulated in normal and sick cells, we investigate the molecular events that take place when Pol I begins the production of ribosomal RNA. Read more

Contact: Dr. Anssi malinen

RNA polymerase and Mechanism of Transcription

RNA polymerase is the enzyme that carries out the first step in gene expression, synthesis of RNA. We study RNA polymerase catalytic mechanism with emphasis on translocation, a step specific to processive polymerases and motor enzymes. Read more

Contact: Dr. Georgi Belogurov

Recent publications

Structural basis for Acinetobacter baumannii biofilm formation (2018)

Proceedings of the National Academy of Sciences of the United States of America
Natalia Pakharukova, Minna Tuittila, Sari Paavilainen, Henri Malmi, Olena Parilova, Susann Teneberg, Stefan D. Knight, Anton V. Zavialov
(A1 Journal article – refereed)