On getting creative as a biochemist user-developer of AFM
Dr Liisa Lutter is a postdoctoral researcher in the laboratory of Prof. David Eisenberg at the University of California, Los Angeles (UCLA). Her work focuses on understanding protein folding and aggregation in neurodegenerative diseases such as Alzheimer’s.
Prior to working at UCLA Liisa had been deeply engaged in the development of AFM for biochemical purposes. Her ideas emerged through work on developing an algorithm for helical 3D reconstruction from AFM topographic data and applying these methods to look at polymorphic samples of amyloid fibrils, which are linked to neurodegenerative diseases.
“After that I had an idea to integrate these 3D reconstructions with other structural biological techniques to make it more universal – able to integrate with any Protein Data Bank (PDB) structure or electron microscopy database map.”
Liisa Lutter
During COVID Liisa became interested in exploring the possibility of doing single particle 3D reconstruction for AFM and this summer presented a proof of principle of her ideas to the Royal Microscopy Society (RMS) conference.
“It’s like a 3D puzzle which was intellectually very satisfying. There are lots of different ways of solving the problem, I chose one particular algorithm and presented that at RMS, though there are many other ways to explore this,” says Liisa.
“The application I presented - which enables the sample checking of our spike protein as quality control - is not what I was excited by, so much as the possibilities it opens up to combine the morphological analysis and the 3D reconstruction with some of the biophysical capabilities of AFM.”
Liisa’s ideas were well received at the RMS conference. Surrounded by people steeped in AFM and SPM Liisa was delighted that the real potential of her work was recognised. The paper connected to the work is due to be published as a preprint shortly.
How did you get involved in working with AFM?
Prior to her PhD Liisa had worked with a number of structural biology techniques such as crystallography and cryo-electron microscopy, as well as having had some exposure to AFM.
Undertaking her PhD at the University of Kent with Dr. Wei-Feng Xue set her on a new trajectory of involvement with AFM. Although Liisa was meant to work on a different biochemical project only using AFM for sample imaging, she found herself getting into the computational development aspect of the AFM.
“Dr Xue was such a wonderful mentor. He supported me in starting programming which I had always had an interest in but had never had the opportunity to learn whilst addressing a real biological problem,” says Liisa.
“Wei-Feng was developing computational tools for the AFM, as many labs do. He gave me a simple problem: to image fibrils of misfolded proteins in the amyloid state. The fibrils are hallmarks of neurodegeneration, and have different morphologies. My task was to use AFM to enable us to analyse their morphologies, and develop our understanding as to how the same protein can take on a variety of different structures, and be present in different diseases.”
The key aspect of Liisa’s PhD work became the development of the 3D reconstruction algorithms.
Taken from www.liisalutter.com
How did you get into biochemistry?
Growing up with a biochemist in her family, someone who worked as a PI within industry, was what first drew Liisa’s interest to the field.
“There are many different pathways to becoming a scientist, but knowing someone who worked in this area was key for me,” says Liisa.
“I really doubt that I would otherwise have been aware of it as a career path. It’s quite sad because the majority of people wouldn’t know any scientists. It is a sad to think that so many children are not exposed to the possibility of a scientific career in this way.”
Seeing her family member respond to challenging real-world issues, spending their time problem solving and working through them to make a difference in the world, resonated with the skills and interests Liisa was developing as a young adult. Embarking on her bachelor’s degree in biochemistry Liisa was already determined to make this her life-long career and to remain within academia as part of that ambition.
What has been your experience of working within science, both as a woman and an early career researcher?
The two areas that Liisa credits as key supports to her success within her field to date are the great mentors she has had along the way and a strong personal sense of resilience.
“I think resilience is extremely important and I do think that mentors, both male and female, have been key. Female mentors to look up to and male mentors that have supported the development of me as a student.”
Whilst Liisa hasn’t experienced discrimination directly herself in her career she believes it’s important to be aware of and to talk about gender within academia.
“I think about it more now as I’m mentoring students. I try to be aware of whether my treatment of the students is impacted by unconscious bias. For example, if I have a student who is female and shy, who doesn’t speak up in discussions, I try to be aware of the criticisms that might unconsciously arise, such as them coming across as having nothing to say,” says Liisa.
“I don’t believe in my heart that’s the case, but I need to think how do I help that person in their development.”
“As women, or at least from personal experience, I think we have to be aware of having a sort of internalised misogyny and we have to be ready to defend against that and to act better. This is how we can make change and make things better for the students who are coming after us.”
Liisa reflects on the vulnerability of early career researchers, particularly around their limited experience of academia beyond the field they have worked in. Liisa feels extraordinarily fortunate to be working with biochemistry in this respect.
“I’ve found biochemistry to be extremely encouraging with people like Alice Pyne who are enormously supportive of early career people. I like her open code sharing approach too. That’s really important, especially for AFM where everybody’s developing their own tools in their own labs. I really like the word community, the idea that we can develop together and share these tools, I think that’s a great way forward.”
What are the challenges of working with AFM within the biochemistry field?
Liisa’s experience of working with AFM has been a positive one. She has found AFM to be a field in which there are more opportunities rather than challenges, and possibilities to collaborate.
“It’s because the AFM is not an ‘out of the box’ instrument, it requires a lot of development still, which makes it incredibly creative and fun – especially as a student, getting to develop your own tools. The possibilities are endless,” says Liisa.
“The challenge is trying to explain this to other people within the biochemistry community. We need to break the idea that AFM is a technique for sample checking only. It is worth doing though, as I believe AFM could really enable developments and breakthroughs within the biochemical field.”
What is life like at UCLA?
Liisa moved to UCLA in April 2022 and has been working as a postdoctoral researcher in the laboratory of Prof. David Eisenberg.
“I’m really enjoying the institute and the lab. It’s a large lab, there are a lot of research scientists with a depth of knowledge and experience.” says Liisa.
“The primary structural biology techniques used have been crystallography and now largely cryo-electron microscopy. I’m on the biochemical side of sample preparation at the moment, working on small molecule inhibitors of the disease-associated misfolding and aggregation. Once I’ve made more progress I will bring microscopy into my projects, including AFM.”
Liisa is keen to keep working on the development methods she explored in her PhD and beyond.
Where and how would you like to take your AFM research in the future?
Liisa’s work with AFM moved rapidly from being a biochemical user of AFM for imaging, to that of a biochemist AFM user-developer. Liisa has plenty of ideas of the kind of work she would like to do in the future and is excited to explore applying high-speed AFM to mechanistic studies of protein misfolding in neurodegeneration.
“From a user-developer perspective, there’s still a lot to be done. In terms of the type of biological questions I’m looking at there are a lot of use cases for AFM. Like specifically for the polymorphic and heterogeneous protein populations, where this carries biological significance, we really want to use single molecule techniques.” says Liisa.
“We want to image the heterogeneity at a single molecule level, which is something that can be done by an electron microscopy but AFM brings a unique high signal-to-noise ratio aspect to imaging single molecules. That complements nicely on ensemble averaging (imaging) techniques where we’re getting really high-resolution structures but they’re snapshots of the most prevalent species. In some cases we really want to look at the distribution on a single molecule level if we think it has biological relevance, which it does in the case of amyloid fibrils.”
“For my own work going forward I’d like to see combining the 3D structural reconstruction and morphological analysis with the biophysical capabilities that AFM offers – this isn’t something I’m working on at the moment but I’d love to see the work develop in this way – maybe using functionalised tips – and bringing that together with 3D construction and morphological analysis – it would require a huge development but would be interesting.”
It's clear that Liisa’s fascination with AFM is now deeply embedded, as is her analytical, creative and innovative ideas as to how AFM can be developed within the biochemical field.
For more information on Dr Liisa Lutter please check out her profile here.
For her latest papers please click here:
On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies