Heme-Containing Sensor Proteins The Group of M. Martinkova

I should perhaps start by highlighting the unifying element of the whole subject, hemoproteins, the proteins containing a heme molecule as a low-molecular cofactor. The best-known hemoprotein is probably hemoglobin, whose role in blood is to transport oxygen molecules throughout the body. The research goal of our team stems from an area of interest that is traditionally studied at the Department of Biochemistry, namely, the heme enzymes. These enzymes play a pivotal role in the metabolism of drugs, as well as in processes that lead to pathological conditions such as tumours development. As a unique opportunity to take the exploration of these and other heme proteins on a new level, I have been offered a postdoc position at Professor Toru Shimizu’s laboratory. Thanks to this experience, our hemoprotein’s research focuses on a different hemoprotein class, namely on the hemoproteins able to detect molecules of various gases and other ligands. Generally, there is a variety of proteins containing heme – they are often similar in terms of their structure and, probably, also in terms of their evolution.

As I have already mentioned, hemoglobin consists of a heme molecule and a protein part (globin). There is an iron ion in the centre of the porphyrin skeleton, and this iron ion plays a key role in the heme structure. The heme surroundings formed by the protein part are highly important, too. Thanks to hemoglobin’s protein structure, the transported molecule of oxygen does not interact with an electron. As a consequence, the oxygen is not activated, i.e. is not changed in any way, and can therefore be transported as it is. According to its role in the organism, we call this best-known class of hemoproteins as “transfer and storage group”.

It is not that simple. The hemoproteins whose role is to transport gases form just one of four classes. The main focus of both this new paper and the other research projects of our team are so called sensor hemoproteins. Sensor hemoproteins make use of their ability to reversibly bind molecules detected in cellular cytoplasm. It is important to know that any concentration change of the detected substance has an impact upon the biochemical functions of the concerned sensor protein. The detected molecules may be some of the above mentioned gases. However, there are also sensor hemoproteins that detect changes in the concentration of their own cofactor, i.e. changes in the heme concentration.

Yes, they are. A good example is a protein that we have investigated in detail, the eukaryotic heme-regulated inhibitor of proteosynthesis (HRI). This sensor hemoprotein detects changes in the heme concentration. Like all sensor hemoproteins, also this protein consists of two domains. One of them, the sensor domain, is able to detect heme molecules in its surroundings. Changes in this domain structure caused by the sensoring process alter the functional domain, which makes it possible to control a number of intracellular processes of high importance. For example, it has been shown that the heme-regulated inhibitor is associated with lung tumours – this sensor protein often bears a specific mutation in lung cancer patients.

The paper deals with a sensor protein-related phenomenon that is even more specific – it is a situation when the heme is already firmly bound to a sensor domain and just reversibly interacts with a gas molecule, e.g. a molecule of oxygen (O₂), nitric oxide (NO) or carbon monoxide (CO). The binding of such molecule alters the protein structure of the sensor protein and modulates its function. In contrast, hemoglobin just binds and then releases the oxygen molecule.

We would like to know how exactly the structure of sensor domain is changed after the signal is set up (gas molecule) and how such change is transduced to the functional domain (“signal transduction“). This area is yet to be explored. Moreover, a large number of these proteins exhibit also enzyme activity, and this feature is highly important, too.

It certainly can. The heme-containing gas sensor proteins are important inter alia for bacteria. You can imagine that bacteria need to “know” whether or not they are in an environment rich in O₂. Using this information, they are able to adapt their metabolism. Sensor proteins therefore have an impact on bacterial virulence, sporulation, etc. Proper identification of these processes might trigger off discovery of new, long-expected antibiotics. Then the signal to which the sensor hemoproteins respond could be induced artificially to “confuse” the bacteria and then destroy them. On the contrary, such knowledge would make it possible to optimise the metabolism of beneficial bacteria such as lactobacilli.

Indeed, and it is also the reason why editors of the Chemical Reviews have requested us to share our experience of heme-containing sensor proteins. Our paper describes our expertise in the area of heme sensor proteins and highlights the benefits of this knowledge in exploring heme-containing gas sensor proteins. The position of our research group is apparently quite unique, because most of the other laboratories working in this area tend to explore just the microbiological aspects of these systems. In contrast, I am an enzymologist from the bottom of my heart, so I utilize my experience in exploring the enzyme activities of functional domains of these proteins.

Currently we focuses on the heme-containing gas sensor proteins form several selected bacteria and we are interested in their detail characterization. We have identified three different bacterial systems that have some common properties and also some properties that are slightly different from each other. Special selection of various systems is necessary for their subsequent comparison. For example, we would like to know how exactly bacteria identify the signal. Chemists can agree that the C-O, N-O and O-O bonds and the biatomic molecules in which they occur are very similar in terms of their charges, lengths, sizes, etc. Our results show that the proteins we explore can often identify and differentiate among these highly similar molecules. Our ambition is to describe what exactly the interactions between the proteins and these gases are like, i.e. the interaction areas, amino acids responsible for gas identification as a signal, how this signal is transduced to the functional domain, how it influences the enzyme parameters of the reaction, etc.

We have just submitted a paper regarding the histidine kinase activity in the functional domain of one of the explored sensor proteins to Biochemistry. We are also completing a paper whose ambition is to describe the protein structure dynamics of the explored protein using the H-D exchange experiments. This process, observation of hydrogens (H) in the molecule that can be exchanged by deuterium (D), is used to describe molecules that are difficult to be crystallized and therefore reach the limits of crystallography, a traditional and exact method for exploring the structure of protein molecules.

Yes, of course, I believe that our research work is fun for the students that already work in our lab and that it will also attract a new generation of explorers!