Researcher profile: Nikolina Sekulic
Dr Nikolina Sekulic joined NCMM in 2016. Her main research aim is to better understand the molecular mechanisms that assure genomic stability during cell division. In this profile article, Dr Sekulic discusses her group's current research strategies, her career background, and the day-to-day motivations driving her to make new discoveries.
What is your field of research and what are the main aims of your lab?
We are interested to know how chromatin is organized within cells. In particular, we are interested in chromatin organization at centromeres; the region of the chromosome necessary for accurate chromosome segregation during cell division.
What project(s) are you working on at the moment, and what do you hope to discover?
Currently, we are trying to understand how chromatin at centromeres is different to that in the rest of the chromosome.
The centromere is a part of chromosomes that plays a major role in cell division, serving as an anchor point for microtubules that pull on condensed, duplicated chromosomes to distribute them equally into two emerging ‘daughter’ cells. Each chromosome needs to have one and only one functional centromere in order to be successfully inherited by both daughter cells during cell division – failure to do so can lead to faulty cell division and potentially diseases such as cancer.
Chromosomes are made of chromatin – complex DNA-protein structures with nucleosomes as a building unit. Nucleosomes are globular complexes made of DNA wrapped around a core of proteins called histones. Our work focuses on a special type of histone that exists only within centromeres, called CENP-A. This histone is necessary and sufficient for correct formation and maintenance of a functional centromere. We would like to understand how CENP-A-containing nucleosomes shape the chromatin structure at centromeres and attract other centromeric proteins. We have used cryo-electron microscopy (cryo-EM) to define the high-resolution molecular structure of CENP-A nucleosomes, providing insights into the important molecular events that drive cell mitosis.
We are now expanding our studies to get a more complete picture of the molecular organisation at centromeres. To this end, we have started a collaboration with the Halic lab at St. Jude’s hospital in the USA, and also with our Nordic EMBL Partnership sister institute MIMS in Umeå, Sweden.
Your group recently acquired an instrument that enables ‘hydrogen-deuterium exchange coupled to mass spectrometry’ (HDX-MS). Can you tell us a bit more about this and how it will help you to reach your research goals?
Yes, we now have a state-of-art HDX-MS platform installed in our lab! This is the first and only instrument with HDX capabilities in Norway and it is now open for national collaborations.
Hydrogen-deuterium exchange is a powerful technique that gives information about protein dynamics. The technique is based on the property of hydrogen from protein peptide bonds to exchange with hydrogen (or deuterium) from a solvent at a timescale of seconds to hours (sometimes even days). This exchange is faster in the solvent-exposed parts of the protein and slower in the parts where the protein backbone is engaged in hydrogen bonding (i.e. formation of protein secondary structures) or with a ligand (binding of other proteins, drugs, lipids etc).
In our system, the extent of ‘deuteration’ and thus solvent exposure, is measured with an advanced mass spectrometer, that also has electron-transfer dissociation (ETD) and ion mobility capabilities for increased resolution. HDX provides structural and dynamic information and is therefore a very useful method in structural biology studies. Data can be generated using only a modest amount of protein, and the approach can capture almost any type of protein conformational change in solution. It has multiple applications in research and in the pharmaceutical industry, including investigating protein dynamics in different solvents, monitoring protein folding, identifying conformational changes upon ligand binding or upon post-translational modifications.
Perhaps the most attractive application of HDX is to investigate the effect of drug-protein interactions. Here, differences in HDX could identify drug-binding sites or the effect of the drug on the overall stability/dynamics of the protein and thus aid in drug-design.
In our lab, we are currently using HDX to investigate the effect of (auto)phosphorylation on an essential mitotic protein kinase complex, that is also a drug target. We have found that phosphorylation significantly rigidifies the enzyme complex and we hypothesize that rigidification is necessary for kinase activity. We next want to investigate how phosphorylation on a site that is distant from the active site can affect enzymatic activity. This would provide opportunities for the design of so-called “allosteric drugs” that have a potential for higher specificity.
What motivates you about your research?
Most of the time, simple curiosity. I like to understand things around me.
Faithful cell division is very intriguing to me. It is so essential that it is almost a definition of life itself. Duplication and self-propagation are prerequisites for the living world, as we know it, and accuracy in this process is absolutely critical. The phenomenon of encoding, storing, propagating and using genetic information is still so fascinating and underexplored.
I know that understanding such fundamental processes in biology has a tremendous potential for developing new technologies and therapies (CRISPR-Cas9 and directed evolution are just two recent examples). Of course, knowing that my curiosity could benefit humanity is also a great motivator.
What have been the biggest breakthroughs in your field of research in the past ten years, in your opinion?
For decades, we thought that the centromere is defined genetically, by the position of special repetitive, AT-rich DNA. This all changed in 1997, when Andy Choo (University of Melbourne, Australia) described the human neocentromere (a functional centromere in a new place on the chromosome, devoid of specific DNA) in one of his patients.
This started the wealth of research and identified histone CENP-A as an epi-genetic marker of centromeres. The idea that such an essential part of the chromosome is encoded epigentically (i.e. by the protein CENP-A) and not genetically (by DNA) is fascinating to me. We, as a research community, are still trying to understand the interplay between genetic and epigenetic elements in defining and maintaining the centromere.
Where do you think your field of research will be in ten years?
The development of new powerful techniques such as CRISPR-Cas9, cryoEM and super-resolution microscopy are advancing science in general at a great pace. In the field of genetics and epigenetics, I expect that we will learn more about the principles of chromatin folding in the nucleus. This will help us understand how genetic information is accessed by transcription factors or by the DNA repair machinery and how chromatin generates structures with specific functions, like the centromere.
I think it will be possible to use this knowledge in synthetic chemistry to design new artificial chromosomes with controlled functions that will lead to better therapies for many diseases and improvements in agriculture and biotechnology.
Tell us a little bit about what you were doing before you joined NCMM
I grew up in Zagreb, Croatia but then moved to Belgrade, Serbia to obtain a BSc in Biochemistry. Following that, I lived in the US for 15 years. During my PhD studies at the University of Illinois in Chicago, I learned a lot about protein chemistry and X-ray crystallography by studying kinases of small biomolecules.
Transitioning to a postdoc, I wanted to understand more complex molecular processes and to work with bigger protein complexes. DNA and genetics was always fascinating for me, so I joined the lab of Prof. Ben Black at the University of Pennsylvania. That is where I fell in love with chromatin and centromeres.
What has been the greatest moment in your career so far?
The opportunity to start my own lab. Having the freedom and means to do my own research is a great joy, and there are many bright and talented scientists that don’t get this opportunity. Of course, running a lab comes with many new challenges, and I am also thankful to NCMM for helping in this transition period by providing a supportive environment.
What would you be doing if you weren’t working in research?
I always wanted to understand things around me, so science was the most natural choice. Biochemistry was particularly attractive because it gives molecular insight into living matter. How amazing is that!
I didn’t think about a career a lot. I just wanted to learn. However, anybody doing science knows that research doesn’t always go as planned and there are many ups and down and results are often missing even after hard-work. During my PhD, I even went to career counselling, which revealed that I could be an architect, teacher, social worker, doctor, or programmer. I was disappointed and I thought the career test hadn’t worked for me.
However, with time, I realise it was more accurate than I appreciated at the time. I like to make logical connection between facts, I like to do things that benefit society and if you can add a dash of creativity to all of that I will love it. Many different careers fit that bill but I feel that my current job has just the perfect balance of things I love and I’m happy to be here, where I am now.
Tell us something about yourself that you think might surprise your colleagues
My family is multi-lingual. Every day we communicate with each other in 4 different languages (Croatian/Serbian, Spanish, English, Norwegian). I guess that makes our two kids, who are fluent in all of them, quadri-lingual!