Attendees at the CNIO-CaixaResearch Frontiers Meeting Machines acting on DNA. / Laura M. Lombardía. CNIO.
Advances in microscopy reveal the 3D structure of large protein complexes –real nanomachines in our cells–, in great detail
The discoveries, presented by speakers from Europe, the USA and China, enable the design of more precise drugs, the search for new antibiotics and the development of better gene-editing methods.
“People are doing incredible things in this field”, according to Óscar Llorca, researcher at the CNIO and co-organiser together with his colleague, Rafael Fernández-Leiro and with Eva Nogales, from the University of California, Berkeley (USA).
What makes everything work in the body is the task of countless proteins: molecular nano-machines that make up a complex cog in constant motion inside each cell. These nano-machines can now be visualised in action. This helps us to understand like never before essential processes, such as the production of antibodies or the repair of DNA damage. Avenues are opened up to design more precise drugs, search for new antibiotics or create new and better methods of gene editing.
“People are doing incredible things in this field”, sums up Óscar Llorca, Head of the Structural Biology Programme at the Spanish National Cancer Research Centre (CNIO).
Together with Eva Nogales, from the University of California in Berkeley (USA), and Rafael Fernández Leiro, also from the CNIO, Llorca has co-organised the CNIO-CaixaResearch Frontiers Meeting Machines acting on DNA and RNA, which brought together around twenty experts from the United States, Europe and China to present at the CNIO the latest findings in structural biology. The congress has been supported by the ‘la Caixa’ Foundation.
Nogales: “Seeing this complexity transforms our understanding of cellular processes”
Structural biology deals with determining the three-dimensional structure or the shape of proteins. Proteins interact by fitting together, like in a complex and tiny 3-D puzzle that is also dynamic, which is why understanding their shape is one of the great challenges of biology. Until recently, progress in this area had been very slow because crystals had to be obtained from proteins, which was a slow and painstaking process. Now, progress is being made “in leaps and bounds”, according to the organisers.
“With the knowledge we now have, and thanks to the power of the techniques we use, we can study more complex systems with a level of detail that would have been impossible ten years ago”, assures Nogales.
“Now we can not only see the structure of proteins, but also how it changes; we are starting to be able to visualise the full picture. The structures tell a story: there are characters that come and go, those that move, interact and separate… Seeing this complexity is transforming our understanding of cellular processes”.
“We are going all out, exploring what we can do”
Over the past decade, a microscopy technique, cryo-electron microscopy, has made it possible to determine the three-dimensional structures of a large number of proteins and protein complexes in great detail and without the need for crystallisation. More recently, advances in computing and artificial intelligence are further accelerating the generation of new knowledge.
As explained by Nogales, “we are fearlessly using mature techniques and are going all out, exploring what we can do. What is still under development is that dynamic part. Every time you watch one of these films it is inspiring, because someone has achieved this milestone in the system they are studying and you think: now I could use it in mine”.
Nogales is referring to the study of the wide range of molecular machinery that performs numerous tasks in the life of the cell: “Biological complexes work based on a set of laws that are the same in all organisms; they are the same physical and chemical principles, the same evolutionary rules, so learning about one system gives insights into how it might work in another. The systems may be different, but they are not aliens”.
Protein-machines that read genetic information
A central theme at the congress was the molecular machinery that interacts with DNA. Every cell in an organism contains DNA molecules that store genetic information, which drives the functioning of the cell. DNA is therefore an instruction manual that hundreds of proteins, working as tiny molecular machines, turn into biological actions.
DNA is copied into messenger RNA (mRNA) molecules so that the instructions can be used without touching the original; these RNAs must be cut and rearranged, and their information needs to be read. The DNA itself must be duplicated before cell division. Investigating how the proteins responsible for these processes work is a burning issue in today’s science.
How the epigenetic information –the lifestyle marks– is copied
One of the advances presented referred to the assembly of epigenetic marks, biochemical signals that are added to genes to regulate their activity and that change depending on the environment, such as diet and lifestyle.
Alessandro Costa, from the Crick Institute in London, addressed a totally new problem: how to transfer the epigenetic information to new DNA when the cell is divided.
Fernández-Leiro explains: “DNA has the famous double helix structure, which also folds into more complex structures; when DNA is copied, everything has to be disassembled and reassembled in the ‘daughter’ DNA molecules. In this process, we are copying genetic information, which we are already well aware of. However, the way in which epigenetic information is transferred to the new DNA is not yet known in detail”.
In practice, it is a question of understanding in depth how the organism reacts to its environment throughout its life.
The immense diversity of antibodies
Several researchers discussed how variability in antibodies is generated. The cell must be able to randomly produce an infinite number of different antibodies in order to detect any enemy, and according to Llorca, “it has been really impressive and exciting to see the huge advances in understanding such processes at the molecular level, as presented in the talks by Wei Yang, from the American National Institutes of Health, and Yuan He, from Johns Hopkins University in the USA”.
“Antibodies that are capable of recognising and neutralising almost any previously unseen invading agent need to be generated”, he explains. “The cell solves this problem by designing antibodies that are built like Lego, assembling a number of small pieces in different ways. This enables a huge repertoire of different combinations to be generated, resulting in a wide variety of antibodies ready to recognise almost any agent. Part of the machinery responsible for assembling these pieces is the same as that which repairs DNA breaks”.
New drugs
One of the most immediate applications of advances in structural biology is the design of new drugs. It is explained by Nogales: “Knowledge of the structure has steered drug creation for a long time but now our techniques are far more powerful, enabling us to target complex pharmacological systems that used to be very difficult to visualise”.
In other words, “I now have a vision of the shape of the protein complex, of its chemistry, and I can understand how a mutation changes it and prevents it from functioning as a molecular machine”, adds Nogales. “I can see the keyholes in that molecule, so I can design a key to open, break or change it. This is related to drug development”. Examples of potential new antibiotics were presented at the congress.
Eva Nogales is a pioneer in the use of cryo electron microscopy to reveal how gene transcription occurs. In 2023, she won the Shaw Prize in Life Science and Medicine for her research into how the transcription of information written in genes is initiated. She has just been elected as a Fellow of the Royal Society.
Llorca, who heads the Macromolecular Complexes in DNA Damage Response Group at the CNIO, spoke about one of his latest projects, the discovery of the mechanism that helps virus such as monkey pox to block and evade a human cellular defence system. His group has also published the first atomic-scale ‘movie’ of microtubules under construction, a key process for cell division.
Fernández-Leiro, Head of the Genomic Integrity and Structural Biology Junior Group at CNIO, focused on mitochondrial DNA replication, a process that differs from nuclear DNA replication, about which very little is known.
The three organisers highlighted the role of young researchers at the congress: “The contribution of PhD students and postdoctoral researchers has been essential. Seeing them present their work is inspiring and gives us new energy”, said Nogales.
The CNIO-CaixaResearch Frontiers Meetings are prestigious international conferences on cutting-edge topics in cancer research. At these meetings, around twenty guest speakers from all around the world present their latest findings. Another hundred experts selected due to the interest of their contributions also participate through posters or short presentations.