Tag: proteins

Hijacking cell’s natural machinery to help treat diseases

Hijacking cell’s natural machinery to help treat diseases

“Molecular glue” could be used to control activity of harmful proteins

Proteins do most of the work in our body’s cells. But when a protein is too active or does not function properly, it can lead to disease or other health problems.

Researchers from the University of Toronto have discovered a molecule, CLEO4-88, that acts as a ‘molecular glue,’ binding together two proteins to inactivate one of them. The finding – enabled by the Canadian Light Source (CLS) at the University of Saskatchewan – points to the possibility of one day treating disease by controlling the activity of harmful proteins.Video: Hijacking cell’s natural machinery to help treat diseases

Molecular glues typically stick together two proteins that would not normally interact, marking one of them for destruction. In this study, researcher Chetan Chana and colleagues discovered that instead marking a protein for destruction, CLEO4-88 inactivated it. The team’s findings are published in the journal Nature Chemical Biology.

The high-powered X-rays at the CLS enabled the researchers to see that CLEO4-88 stuck two proteins together and slowed down the activity of one of them (ACAA1). While ACAA1 – which is involved in breaking down fats inside cells – was not destroyed, its activity was reduced. This mechanism could potentially be leveraged to control some triple negative breast cancers, where ACAA1 activity has been shown to be elevated.

Read more on the CLS website

Image: Molecular glue – crystal

Credit: CLS

New malaria vaccine shows promise in preclinical trials

New malaria vaccine shows promise in preclinical trials

International research team used CLS to map structure of human antibodies bound to their prototype vaccine.

Malaria is caused by a parasite that is spread to humans by infected mosquitoes. In 2024, almost 282 million people worldwide were infected and 610,000 died, according to the World Health Organization. Malaria is a leading cause of death in children under the age of five.

Using the Canadian Light Source (CLS) at the University of Saskatchewan, an international team involving researchers from Canada, the US, and the Netherlands have developed a novel vaccine that is showing considerable promise in preclinical trials.Video: New malaria vaccine shows promise in preclinical trials

“Our long-term goal is to eliminate malaria by designing a vaccine that is more effective than the ones currently on the market,” says lead author Danton Ivanochko, a researcher at the Hospital for Sick Children (SickKids) in Toronto.

When the researchers examined blood samples from people with naturally acquired immunity to malaria, they were able to identify which proteins on the parasite play the largest role in transmission.

Read more on the CLS website

Chemical shifts help track molecules breaking apart in real time

Chemical shifts help track molecules breaking apart in real time

Ultrafast X-ray photoelectron spectroscopy at European XFEL offers a new way to watch reactions, atom by atom.

When molecules fall apart, their electric charge doesn’t stay put—it rearranges as bonds stretch and break. An international team of scientists has now tracked these ultrafast changes in the small molecule fluoromethane (CH₃F). It was the first time that the Small Quantum Systems (SQS) instrument at European XFEL could deliver detailed insights into transient states during chemical reactions. These intermediate states, that only exist temporarily while the reaction is ongoing, are often the key drivers of chemistry and therefore crucial to understand. Over the long term, that kind of insight can support progress in areas such as atmospheric science (where sunlight-driven reactions and fragmentation pathways shape air chemistry), as well as the study of complex molecular systems including biomolecules and proteins, where local excitation and charge transfer can trigger structural change.

In the experiment, the researchers first triggered the reaction with an optical laser pulse. Next, they used the X-ray laser pulses that the European XFEL produces, to eject an electron from the core of either the fluorine or the carbon atom in the molecule. They measured the electron’s kinetic energy, which reveals how strongly it was bound inside the atom. That binding energy is extremely sensitive to the local electrical environment, producing so-called “chemical shifts” that act like a fingerprint of the charge distribution surrounding the atom from which the electron has been ejected. With an overall time resolution of about 35 femtoseconds (trillions of times shorter than the blink of an eye), the team could follow changes separately at two atomic sites, carbon and fluorine, inside the same molecule. The method is called time-resolved X-ray photoelectron spectroscopy (tr‑XPS).

“Core-level photoelectron spectroscopy tells us what is happening at a specific atom,” says Michael Meyer, lead scientist at the Small Quantum Systems (SQS) instrument at European XFEL. “By probing carbon and fluorine independently, we can see when different fragments appear and how the charge distribution evolves during dissociation. 

Read more on the European XFEL website

Image: Illustration of the pump–probe experiment on fluoromethane (CH₃F): Shortly after an ultrashort optical laser pulse (red) has ionized the molecule and triggered bond breaking, a femtosecond X-ray pulse (blue/white) ejects a core electron (green clouds) from the fluorine atom (green ball). By measuring the electron’s kinetic energy, the experiment tracks time-dependent ‘chemical shifts’ that reveal how the local electronic environment changes as the molecule dissociates – in this case the departure of a hydrogen atom (white ball).

Credit: Illustration: European XFEL

Breaking boundaries in biomedicine: APS enables protein design

Breaking boundaries in biomedicine: APS enables protein design

From growth hormones to cancer drugs, small molecules play a crucial role in our health. Monitoring them is essential to keeping us healthy; it enables physicians to calculate dosages and patients to monitor their medical conditions at home, for example.

Monitoring small molecules depends on sensing where they are, and in what concentrations. While scientists have developed sensors to detect some small molecules, these sensors are used primarily in research and drug discovery and can only detect a limited range of molecules with particular qualities. There is a compelling need for sensors that can detect and signal the presence of diverse small molecules of different shapes, sizes, flexibility and polarity. 

Using artificial intelligence (AI), a team of scientists led by Nobel Prize winner David Baker at the University of Washington has created a computational method for generating proteins that bind and signal a wide range of small molecules with great effectiveness. Baker won the 2024 Nobel Prize in Chemistry for computational protein design.

The research described here, published in Science and conducted in part at the Advanced Photon Source (APS), exemplifies that approach. The APS is a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory.

The sensor design problem

Creating a protein sensor for small molecules is very difficult. The protein must first bind to the small molecule, then signal its presence. 

The team solved both problems with modular design strategies. Their AI-generated proteins consist of identical repeating subunits surrounding a central cavity. The cavity holds a pocket where the small molecule binds.

The subunits, being modular, are easily disassembled. In this way, the small molecule binding proteins can be treated like Lego blocks and be connected to well-established signaling proteins (such as split green fluorescent protein, or GFP), to make a full sensing protein device. When a small molecule binds in the pocket, the subunits reassemble, which leads to the signaling module sending a signal that the small molecule is present.

First step: Binding

The team chose a diverse spectrum of ligands (molecules that bind to protein receptors to send signals between cells), including cholic acid, a biomarker for liver disease; methotrexate, a cancer drug, which requires regular monitoring; thyroxine, a human hormone that indicates thyroid conditions; and a cyclic peptide.

The scientists constructed a machine learning algorithm based on AlphaFold2 (a protein structure predictor whose developers, John Jumper and Demis Hassabis, shared the Nobel Prize in Chemistry with Baker) and other machine learning protein design algorithms to generate thousands of proteins to bind the small molecules.

After computational design, the team tested the designed proteins in the laboratory and identified binders to particular ligands, following computational design and using machine learning methods to choose the best designs for experimental tests.

To confirm the accuracy of their design approach, the Baker team turned to the APS. They used the ultrabright X-ray beams to collect data on the atomic structure of the binding proteins. Using the Northeastern Collaborative Access Team (NE-CAT) beamlines at 24-ID at the APS, the team determined the structures of crystals formed from one of the designed proteins. 

“Prediction algorithms are excellent tools, but without verification of the structures, there’s no proof that the predictions match reality,” said Kay Perry of Cornell University, staff scientist at NE-CAT. ​“X-ray crystallography remains one of the best ways to make that confirmation, and the team was able to do so in this case.”

Second step: Signaling

The next challenge was turning the binding proteins into signaling proteins. The scientists took advantage of their modularity to create two different types of signaling events. 

The team built ligand-induced dimerization proteins from the binders. Linna An, the first author of this study, said the technology can be used in many health-related applications, such as regulating the release of drugs in cancer therapies.

In a different type of signaling event, the scientists fused the binding proteins to a newly designed nanopore, a protein creating a channel allowing ion flow. The fused unit was constructed in such a way that when a small molecule blocked the binding pocket, the whole nanopore was blocked, preventing the flow of ions and loss of current. Loss of current signaled the presence of the small molecule. 

Read more on APS website

Image: The crystal structure of CHD_r1 (gray) is very similar to the computational design model (colored).

Credit: Linna An, et al., Science.

Scientists visualise the paths controlling heart performance

Scientists visualise the paths controlling heart performance

Scientists have found the role of two proteins in the functioning of the heart. The results could help better design targeted strategies to treat certain cardiomyopathies. The results are out in PNAS.

The heart works using tiny muscle filaments, and two main steps control how they interact: first calcium signals cause changes in the thin filament (actin), allowing it to connect with myosin motors. Then myosin motors on the thick filament switch from “off” (inactive) to “on” (active), so they can pull on actin and create force and shortening. The thick filament can sense how much force is needed and adjust how many motors to turn on, but scientists are still figuring out exactly how this works.

Cardiomyopathies take place when these mechanisms regulating the contraction-relaxation cycle of the heart malfunction. This is due to mutations in the contractile proteins (myosin and actin) but also in accessory proteins (Myosin-binding protein-C and titin). Broadly, MyBP-C and titin ensure together that the heart contracts effectively while maintaining responsiveness to changes in demand.

A team from the University of Firenze (Italy) used small-angle X-ray diffraction at the ESRF’s ID02 beamline back in 2017 and showed that, during muscle contraction, myosin motors move outward from the thick filament, enabling interaction with actin based on the load, which in the cardiac ventricle is the arterial pressure against which blood must be pumped (Reconditi et al. PNAS 2017). Evidence from other laboratories also suggested that thick filament activation is modulated by regulatory domains in the myosin motor itself and by accessory proteins like MyBP-C and titin. However, their specific function in cardiac performance was not known in detail.

Now the same team has found the role that MyBP-C and titin play in the functioning of the heart, at beamline ID02. “The beamline ID02 is ideal thanks to its camera length, so we can have the detector closer or further to the samples in a range from 0.5 to 31 m. This lets us explore the contractile proteins as well as the sarcomere, the unit cell of muscle, which is crucial for our research”, says Massimo Reconditi, scientist at the University of Firenze and corresponding author of the paper. “With EBS, thanks to its low divergence, we can observe on the same diffraction pattern a high number of reflections together with their fine structure”, he adds. 

Read more on ESRF website

Image: Theyencheri Narayanan, scientist in charge of ID02, on the beamline.

Credit: S. Candé. 

MCB JU researchers discovered a mechanism regulating the essential process of hypusination

MCB JU researchers discovered a mechanism regulating the essential process of hypusination

A research team from the Malopolska Centre of Biotechnology at Jagiellonian University (MCB UJ), led by dr hab. Przemysław Grudnik, in collaboration with scientists from the Medical College of Wisconsin, has uncovered an unusual role of the ERK1/2 kinases in the regulation of a unique post translational modification, hypusination. This breakthrough not only bridges a gap in our understanding of the mechanisms controlling hypusination, an essential process for the human body, but also reveals a surprising function of ERK1/2. These findings have recently been published in the scientific journal “Cell Reports”.

Hypusination is a highly specific modification of eukaryotic translation factor 5A (eIF5A), and deoxyhypusine synthase (DHPS)  is responsible for catalyzing the first and limiting step of this process. Hypusination enables eIF5A to facilitate the synthesis of other proteins in the cells, which is a fundamental process. Despite its critical function in cellular homeostasis, the regulation of hypusination remains elusive. Researchers at MCB have started to unravel the mechanisms controlling hypusination and have shown the new unexpected finding that the extracellular signal regulated kinases 1/2 (ERK1/2) perform a non kinase function by directly interacting with DHPS to regulate hypusination. ERK1/2 are key enzymes in a signaling pathway, which is crucial in regulating cell growth, differentiation, and cell survival in human bodies. Until now, these proteins have been studied for their enzymatic (kinase) activity, which allows them to activate other proteins through phosphorylation (adding phosphate groups).

Researchers at MCB employed cryo-electron microscopy (cryo EM) to study the structure of the DHPS ERK2 complex. The data revealed that ERK2 binds to DHPS at the entrance to its active site, effectively blocking access for eIF5A. The findings also highlight how cellular signaling via the Raf/MEK/ERK pathway modulates ERK1/2 association with DHPS. When this pathway is activated, the interaction between ERK1/2 and DHPS decreases, allowing eIF5A to be hypusinated. Moreover, ERK1/2’s kinase activity controls how much DHPS and eIF5A the cell produces. This discovery provides fresh insights into how cells regulate essential processes such as protein synthesis in response to external signals.

Read more on the SOLARIS website

Image: Dr hab. Przemysław Grudnik (on the right) and Paweł Kochanowski (on the left) are holding a model of the DHPS-ERK2 complex.

Unlocking the secrets of proteins

Unlocking the secrets of proteins

This year’s Nobel Prize in Chemistry goes to three researchers who have made a decisive contribution to cracking the code of proteins – important building blocks of life. However, developing applications from this knowledge, for example in medicine, requires research institutes such as PSI. 

This year’s Nobel Prize in Chemistry came as a surprise in several respects. Firstly, only one of the three scientists chosen, David Baker, is a member of an academic research institution. The other two, Demis Hassabis and John Jumper, work at the Google subsidiary DeepMind. Secondly, the award is based on artificial intelligence (AI). And thirdly, the achievement being recognised draws on an Open Science project that would not have been possible without comprehensive, high-quality, open databases provided by the global scientific community – to which the Paul Scherrer Institute PSI is an important contributor. Given these unusual circumstances, it is easy to overlook the actual reason for awarding the prize. Yet that itself is revolutionary enough: The Nobel Committee is paying tribute to the three scientists for a breakthrough in protein research. Working at the company DeepMind, two of them developed an AI called AlphaFold which is able to predict the spatial structure of a protein with astonishing precision. This structure is a result of the way the molecule is folded, which in turn depends on the sequence of amino acids it contains.

Spatial folding is crucial

It is difficult to assess the full extent of the new possibilities offered by AlphaFold. Proteins and their spatial folding form the central basis of all biological systems – disrupting them can have fatal consequences. The form, function and activity of every single cell are controlled by proteins. This also holds true for the 30 trillion or more cells that make up the human body, or course, including the cells of the immune system and the brain, but also pathologically modified cancer cells. Some extra-cellular structures produced by cells are also made from proteins. These include collagen, which gives skin, bones, tendons and connective tissue their structure and strength. However, until recently scientists were often puzzled as to how the sequence of amino acids, which is relatively easy to determine, gives rise to the three-dimensional configuration.

To determine the spatial structure of proteins, which is crucial for their biological function, researchers had to resort to highly complex X-ray crystallography experiments, which often took years. Only in recent years has it become possible to achieve this by means of a particularly high-resolution form of electron microscopy. X-ray crystallography was first successfully used to determine the structure of a protein in 1959; the protein in question was myoglobin, the mussel protein which is responsible for intramuscular oxygen transport. The scientists led by Max Perutz, who was awarded the Nobel Prize for Chemistry in 1962, turned the protein into a crystal and sent monochromatic X-rays through it, similar to the radiation produced by Swiss Light Source SLS at PSI. The resulting diffraction pattern can be used to determine the folding of the protein chain – and thus provide information about the function of the protein. The location of active centres, for example, which interact with small molecules. 

At the time that AlphaFold was developed, the structure of some 140,000 proteins had been determined experimentally. These are all listed in the Protein Data Bank (PDB), established in 1971, which is freely accessible to scientists and the general public. “More than five percent of the data it contains comes from the Swiss Light Source SLS at PSI,” says Jörg Standfuss, Head of the Laboratory of Biomolecular Research, which focuses on structural biology at the PSI Centre for Life Sciences. Most of the rest comes from other research centres that operate a high-quality X-ray source.

Read more on PSI website

Image: Proteins are involved in all life processes. They are made up of amino acid chains that form complex structures. This structure is crucial to the function of the proteins. That is why being able to predict the structure of a protein based on its amino acid sequence using AI is so important for understanding life and for innovation in medicine and biology.

Credit: hotspianiegra – stock.adobe.com

Fundamentally different

Fundamentally different

Large research facilities at PSI such as the X-ray free-electron laser SwissFEL and the Swiss Light Source SLS – especially after the upgrade SLS 2.0 – deliver unimaginably vast amounts of data. Artificial intelligence is helping to evaluate data efficiently and exploit the facilities’ full potential for research.

Proteins are the workhorses of life. As tiny molecular machines, they are found in every cell and have a role in nearly all biological processes – from metabolism to cellular communication. Their diversity is enormous, because in the human body alone there are hundreds of thousands of different proteins, each with its own function. Proteins are important targets for drugs, and understanding their structure and function is an important task in biological research. One challenge in drug development is to find, if possible, an active agent that interacts with just one type of protein, to the exclusion of all the rest.

To achieve such a feat, one must first understand the language of proteins. The basis of this protein language is a kind of alphabet. It essentially consists of 20 building blocks analogous to letters. In proteins, however, it’s not about letters, but rather amino acids. Each protein is built up from a certain sequence of these amino acids; the sequence in turn largely determines its properties. Researchers would now like to know which protein sequence leads to which property. This is where so-called large language models such as GPT4 come into play. The AI chatbot ChatGPT, which has been causing a stir since 2022, is based on GPT4. Both were developed by the company OpenAI. ChatGPT uses an extensive dataset of texts created by humans to learn the patterns and structures of language. When the user enters a question or task, the model produces a response based on its understanding of the contexts and patterns that it learned during training. In this way it can write poems, novels and even programming code.

Flurin Hidber, a doctoral candidate supervised by Xavier Deupi, an expert in bioinformatics and protein structure at PSI, uses AI in protein research. Hidber uses a sophisticated model similar to ChatGPT that is trained to predict amino acids in protein sequences, instead of generating human-like language. This unique ability does not merely mimic the predictive capabilities of language models in AI, but rather provides valuable insights into the structure and function of proteins. Pharmaceutical researchers could use these to tailor medications and significantly shorten the process of trial and error in the laboratory, which in the end yields only a small proportion of drug candidates with promising properties.

An ambitious goal

Deupi and Hidber are working towards an ambitious goal: being able to determine the precise amino acid sequence that leads to a desired protein property. One focus of their research is light-sensitive proteins, a speciality of Deupi’s group and a research subject at SwissFEL. These proteins occur in many organisms, from microbes to humans, and have medical potential. Hidber’s use of AI to predict the properties of light-sensitive proteins solely on the basis of the sequence of their building blocks represents a significant advance in this field.

Through the precise prediction of the light-absorption properties of proteins, Hidber’s work could pave the way for the development of molecules with tailored properties – a step that could have a profound impact on optogenetics. This scientific technique employs light to control and monitor the activity of certain cells in living organisms, such as nerve cells in the brain. Researchers insert genes for light-sensitive proteins into these cells so they can precisely influence the cells’ behaviour by irradiating them with light.

This technology could contribute to the understanding and treatment of neurological diseases, since it provides a tool that can be used to investigate and control the activity of specific brain cells with unprecedented precision. For the future, Deupi and Hidber have set themselves the goal of reversing this process. They want to design new proteins with properties tailored to meet specific requirements, for example proteins that react to light of a particular colour. This blueprint could then be checked experimentally, and hopefully confirmed by colleagues in the laboratory.

The topic of protein dynamics is also at the heart of Cecilia Casadei’s research. The physicist has developed a new algorithm that enables more efficient evaluation of measurements at X-ray free-electron laser facilities such as SwissFEL. The building blocks of life often perform ultrafast movements. Investigating these with precision is crucial to gain a better understanding of proteins. In the long run, this can provide valuable information about disease processes and enable the development of novel medical approaches.

Read more on PSI website

Image: Xavier Deupi (left) and Flurin Hidber from the research group for Condensed Matter Theory want to better understand how the function of proteins is related to their structure. They are targeting light-sensitive proteins in particular. 

Credit:  Paul Scherrer Institute/Markus Fischer; KI image generation: Studio HübnerBraun/Midjourney

Tiny proteins found across the animal kingdom play a key role in cancer spread

Tiny proteins found across the animal kingdom play a key role in cancer spread

Researchers from McGill University have made an exciting discovery about specific proteins involved in the spread of certain cancers.

Dr. Kalle Gehring, professor of biochemistry and founding director of the McGill Centre for Structural Biology, and his team have focused on unravelling the mystery around phosphatases of regenerating liver (PRLs). These proteins are found in all kinds of animals and insects — from humans to fruit flies – and play a unique role in the growth of cancerous tumours and the spread of cancer throughout the body.

“It’s important for us to study PRLs because they are so important in cancer,” said Gehring, “In some cancers, like metastatic colorectal cancer, the proteins are overexpressed up to 300-fold.”

This overexpression of PRLs makes cancer cells more metastatic and drives the spread to other organs.

In his most recent paper, published in the Journal of Biological Chemistry, Gehring and his colleagues confirmed that PRLs exist in all kinds of single- and multi-cell animals. Data collected at the Canadian Light Source (CLS) at the University of Saskatchewan confirmed the role of PRLs in binding magnesium transporters, helping to further the understanding of how these proteins influence human disease.

Read more on the Canadian Light Source website

Attacking cancer cells from the inside out

Attacking cancer cells from the inside out

Researchers from the University of Toronto (U of T) are harnessing the power of proteins to stop cancer cells in their tracks.

“Proteins are the workhorses of the cell,” said Walid A. Houry, professor of biochemistry at U of T. “They define the cell and allow it to divide or migrate if needed.”

The team is especially interested in proteases, enzymes that chew up old or misfolded proteins and act as cellular quality control. Houry and his colleagues used the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan to identify key compounds affecting these quality control mechanisms that cause cell dysfunction and, ultimately, cell death. Their research paper was recently published in Structure.

“Let’s say you have a small puppy and when you leave it in the room, it starts chewing your sofa, your carpet; it’s just hyper and eating everything up,” Houry said. The compounds cause the proteases to act like the puppy, “and the cell cannot handle this type of disruption to its machinery.”

By targeting the cell’s self-destruct button, Houry’s team, including collaborators at Madera Therapeutics, is designing a new approach to cancer therapy. Synchrotron techniques allowed the researchers to visualize the interaction between their compounds and the proteases.

Houry said hard-to-treat cancers like glioblastomas and certain types of breast cancers are good candidates for this new approach.

“Instead of inhibiting a protease, we are hyperactivating the protease, and that is unique.”

The CLS is crucial to the team’s work.

“Synchrotron technology is extremely important for us and our structure-based drug design,” he said. “We want to know why the protein is going wild when we add our compound.”

Read more on the CLS website

Image: Houry research team

MAX IV research contributes to the development of new cancer drugs

MAX IV research contributes to the development of new cancer drugs

In the battle against cancer, scientists from the drug discovery company Sprint Bioscience and researchers from MAX IV have taken important steps together toward developing new and more efficient cancer drugs with the help of fragment screening by X-ray crystallography.

Cancer accounts for nearly one out of six deaths yearly. It begins when one or more genes in a cell mutate, creating an abnormal protein or preventing a protein’s formation.

Therefore, you need to start at the protein level to fight cancer.

Sprint Bioscience is working to develop new drug candidates by identifying small molecules (fragments) that can bind targeted cancer proteins. In collaboration with researchers from the FragMAX team at MAX IV during 2019 and 2020, Sprint Bioscience optimised and developed a protein crystallisation system corresponding to a cancer protein chosen by the company.

Read more on MAX IV website

Image: Crystal incubated with fragment XB00143 mounted on the BioMAX beamline during the screening campaign.

Credit: Sprint Bioscience/BioMAX