A novel technological breakthrough presented by researchers at the European Molecular Biology Laboratory (EMBL) now promises to revolutionize how scientists decode these protein-ligand interactions on a massive scale. In a recent study published in Nature Structural and Molecular Biology, the Savitski Group at EMBL unveiled HT-PELSA, a high-throughput peptide-centric local stability assay. This method not only scales up the classical PELSA workflow but also enhances sensitivity and applicability, allowing the exploration of protein-ligand engagements directly in complex biological mixtures such as crude cell lysates, tissues, and bacteria—a feat previously unattainable with traditional techniques.

The original PELSA methodology emerged only last year as an innovative technique to detect protein-ligand binding events by monitoring local changes in protein stability upon ligand association. Binding typically stabilizes specific protein regions against enzymatic cleavage by proteases such as trypsin, resulting in changes in the abundance of peptide fragments from those regions. Tracking such subtle alterations across the entire proteome allowed researchers to identify previously elusive binding hotspots with remarkable peptide-level resolution. However, PELSA’s labor-intensive nature restricted it to processing only a limited number of samples daily, imposing significant bottlenecks on throughput and sample diversity.

HT-PELSA brilliantly addresses these limitations through a radical shift in sample handling format, transitioning from traditional tubes to a 96-well plate micro-well system optimized for automation. This transformation enables robotic handling and parallel processing of hundreds of samples simultaneously, exponentially boosting throughput without compromising the exquisite sensitivity that made PELSA powerful. As Kejia Li, the pioneering postdoctoral fellow who spearheaded the adaptation at EMBL, explains, this newly developed workflow now allows the analysis of roughly 400 samples per day, compared to a mere 30 with the original method—a remarkable fifteenfold increase in efficiency.

At the core of HT-PELSA’s enhanced workflow lies an ingenious exploitation of the hydrophobic and water-repellant characteristics of proteins relative to their peptide fragments. While trypsin digestion retains its fundamental role, HT-PELSA leverages a novel protein-adsorption surface, which preferentially captures intact proteins while allowing cleaved peptides to remain in solution. This physical separation streamlines sample processing and, crucially, opens the door to investigating membrane proteins—a notoriously difficult class to analyze. Membrane proteins comprise about 60% of all known drug targets and their delicate structures often render them incompatible with conventional methods requiring harsh extraction and purification, which can alter their native conformations.

By enabling the direct study of protein-ligand binding events in unpurified complex biological samples, HT-PELSA offers unprecedented insights into physiologically relevant interactions. This method preserves the native environment of membrane proteins and other challenging targets, allowing researchers to observe how candidate drugs or endogenous molecules engage these proteins under biologically realistic conditions. Such capability is vital for drug discovery pipelines, where understanding the binding specificity and mechanistic impact of small molecules on their intended targets can dramatically improve target validation and lead optimization.

Isabelle Becher, a key contributor to the project and laboratory officer in charge at EMBL’s Savitski Group, emphasizes the profound biological understanding HT-PELSA provides. The method charts an expansive landscape of protein-ligand interactions by revealing dynamic changes in local stability patterns across thousands of proteins simultaneously. This holistic view enhances the ability to decipher underlying molecular mechanisms governing cellular processes and pathologies. Furthermore, identifying selective interactions aids in the rational design of therapeutics tailored to precise protein targets, improving efficacy while minimizing off-target effects, thus advancing safer and more effective medicines.

In addition to its primary focus on ligand binding, the current study showcases HT-PELSA’s capacity to detect modifications in protein-protein interactions induced by ligand association. This dual-sensitivity highlights the method’s versatility in capturing the wider network of molecular interactions that define cellular states and responses. Looking forward, the researchers intend to extend HT-PELSA’s application to assess protein-nucleic acid interactions, further expanding its utility in elucidating the molecular architecture and functional circuitry of cells.

Mikhail Savitski, team leader at EMBL Heidelberg and senior author of the study, remarks that HT-PELSA is a transformative step in proteomics technology, significantly accelerating both fundamental research and applied biomedical science. Beyond its immediate role in protein function characterization, HT-PELSA’s scalability and robustness position it as a cornerstone platform capable of driving large-scale drug screening campaigns. Its integration with advanced mass spectrometry and bioinformatics workflows promises to usher in a new era of molecular precision medicine.

This advancement holds particular promise for the pharmaceutical industry and academic researchers alike. The ability to swiftly assess hundreds of drug candidates across diverse protein targets, including integral membrane components often overlooked previously, represents a monumental stride toward combating complex diseases. Simultaneously, it equips biologists with a powerful tool to dissect proteome dynamics in various tissues and organisms, facilitating a deeper grasp of biology from a systems-level perspective.

In summary, HT-PELSA marks a milestone in the ongoing quest to decode the intricacies of protein-ligand interactions at an unprecedented scale and depth. By marrying the finesse of the original PELSA assay with automation and novel biochemical innovations, this cutting-edge technology unlocks access to challenging protein classes and complex biological samples. It stands as a shining example of how marrying technological ingenuity with biological insight can create transformative tools, primed to accelerate the discovery and optimization of next-generation drugs while enriching our fundamental understanding of life’s molecular underpinnings.

Subject of Research: Protein-ligand interactions; high-throughput proteomics; membrane proteins; drug discovery

Article Title: High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria

News Publication Date: 5-Nov-2025

Web References: 10.1038/s41594-025-01699-y

Image Credits: Daniela Velasco/EMBL

Keywords: Molecular evolution, Proteomics

The breakthrough came from a remarkable collaboration between European Molecular Biology Laboratory (EMBL) Group Leader Gautam Dey, Omaya Dudin—then at EPFL—and scientists Paul Guichard and Virginie Hamel at the University of Geneva. They leveraged the pioneering technology of expansion microscopy, originally developed at MIT, and further optimized it into Ultrastructure Expansion Microscopy (U-ExM). This technique effectively renders otherwise impermeable cell walls porous, enabling fluorescent labeling and imaging of intracellular components that were once inaccessible. When Dudin first applied this to Ichthyosporea, a marine protist linked closely to animals and fungi, they successfully visualized its internal architecture, breaking a longstanding barrier in protistology.

The ambition of this team extended far beyond single species studies. They forged an international collaboration that recently culminated in exploring the cellular organization of over 200 eukaryotic plankton species—a monumental endeavor documented in the journal Cell. This project, part of the Traversing European Coastlines (TREC) expedition and dubbed PlanExM, demonstrates a stunning panorama of ultrastructural diversity across marine microbes. It’s arguably the first comprehensive atlas to detail the microscopic landscapes that underpin life at the cellular level in these enigmatic organisms, opening up new vistas for evolutionary biology and cell science.

One of the key sites fueling this research was the Station Biologique in Roscoff, France, a premier marine research facility housing one of Europe’s most exhaustive culture collections of marine microorganisms. Upon requesting samples for testing expansion microscopy, the researchers were astounded to find access granted to over 200 unique species, far surpassing expectations. According to co-first author Felix Mikus, this “treasure trove” allowed them to fix and prepare samples intensively over several continuous days, marking a pivotal moment in accessing previously hidden cellular intricacies.

Expansion microscopy itself is a technological marvel that circumvents the classical diffraction limits of light microscopy. By embedding biological specimens in a swellable hydrogel, and inducing their physical expansion, spatial resolution is boosted dramatically. This expansion—ranging typically from fourfold to sixteenfold linear increase—preserves the relative positions of biomolecules, allowing structural details at nanometer scales to be resolved with standard light microscopy setups. This technique sidesteps the need for costly super-resolution microscopes and complex optical setups, democratizing access to ultrastructural details across biological disciplines.

Harnessing this technique, researchers homed in on the cytoskeleton, the intricate filamentous network that shapes the interior scaffolding of eukaryotic cells. In particular, they examined microtubules—rigid, hollow tubes vital for cell shape, division, and motility—and centrins, specialized proteins instrumental in organizing microtubule architecture within microtubule-organizing centers. The scope of their investigation, spanning hundreds of species from diverse clades, enabled mapping the variations in cytoskeletal organization, uncovering both conserved and distinctive traits across the eukaryotic domain.

Hiral Shah, an EMBL Postdoctoral Fellow, emphasized how these patterns of tubulin and centrin organization across various groups allow not only a snapshot of structural diversity but also evolutionary predictions. For example, dinoflagellates—a speciose and ecologically critical group in marine environments—displayed distinctive tubulin and centrin structures linked to cell cortical regions and flagella, offering clues to their evolutionary adaptations. Such information was previously unattainable with traditional microscopy, highlighting the transformative potential of combining U-ExM with large-scale biodiversity studies.

Armando Rubio Ramos, also a co-first author and researcher at the University of Geneva, remarked on the paradigm shift enabled by this ultrastructural expansion approach. Integrating U-ExM with high-throughput imaging platforms and computational comparative analyses bridges the gap between molecular sequence data and physical cellular organization. This fusion creates a new dimension for interpreting how subcellular architectures have evolved and diversified, laying a foundation for exploring cellular morphology in an evolutionary context across microbial eukaryotes.

Beyond fundamental biological insights, the research demonstrates the practicality of expansion microscopy for direct analysis of complex environmental samples. The technique’s adaptability to natural plankton collected from marine ecosystems sidesteps challenges posed by cell wall impermeability, heterogeneous cell populations, and operational complexity. This opens the door to broad application prospects, such as monitoring ecological dynamics, assessing biodiversity shifts, and linking cellular physiology with environmental variables in real-time.

The success of this interdisciplinary endeavor has attracted significant support, underscored by securing a CHF 2 million grant from the prestigious Moore Foundation, with contributions from collaborators including Thomas Richards from Oxford University. This funding paves the way for deeper exploration into selected protist species to address fundamental questions about cell division mechanisms, the emergence of multicellularity, and phenotypic diversity underpinning evolutionary transitions. Such studies hold promise for integrating microscopy-derived phenotypes with multiomics datasets, revolutionizing our understanding of life’s cellular foundations at scale.

Gautam Dey envisions expansion microscopy becoming the first high-resolution imaging technology capable of matching the scale and depth of contemporary biodiversity genomics projects. This synergy could facilitate associating genetic and molecular data with detailed cellular physiology across the vast tree of life. The team’s extraordinary journey, from adapting a novel imaging method to developing a planetary atlas of microbial cytoskeletal diversity, heralds an exciting era where microscopic form and function converge to reveal life’s hidden architectures in stunning detail.

With this powerful approach now established, the research community stands at the threshold of unprecedented discovery opportunities. The fusion of expansion microscopy, high-throughput imaging, and evolutionary biology promises to unravel the deepest secrets of microbial eukaryotes, elucidating how cellular complexity evolved, diversified, and impacts ecosystems worldwide. As the project moves forward, it symbolizes a landmark shift in the visualization and understanding of the invisible majority of life beneath the waves.

Subject of Research: Cells
Article Title: Charting the landscape of cytoskeletal diversity in microbial eukaryotes.
News Publication Date: 31-Oct-2025
Web References:

• TREC Expedition
• Moore Foundation Grant Announcement
  References:
• DOI: 10.1016/j.cell.2025.09.027
  Image Credits: Felix Mikus/EMBL
  Keywords: Molecular biology, Cell biology

Recent advancements in microscopy and biophysical techniques have unlocked new avenues for exploring chromosomal behavior during cell division. Leading this charge are researchers at the European Molecular Biology Laboratory (EMBL), who have introduced a groundbreaking chromatin tracing method that directly visualizes the intricate processes involved in chromosome compaction and organization at high resolution. Within this new framework, the research elucidates how lengthy strands of DNA intricately weave together to form nested loops during the division, driven by a remarkable interplay of forces between these DNA elements.

For decades, the existence of DNA loops has been theorized to play a pivotal role in shaping chromosomal architecture. Since their initial identification in the 1990s, condensins, which are large protein complexes that bind with DNA during cell division, have come under scrutiny. They perform the critical function of extruding DNA to create loops of varying dimensions, facilitating the appropriate packing of chromosomes. Past work by EMBL scientists has significantly contributed to understanding the structural mechanics of these processes, convincing researchers of the extraordinary importance of condensins in safeguarding chromosome integrity during cell division.

Mutations within condensin structures have dire consequences, leading to catastrophic chromosome segregation anomalies that can trigger cell death, foster cancerous developments, or give rise to rare yet debilitating genetic disorders known as "condensinopathies." Therefore, a closer examination of the dynamic looping mechanism has the potential to unveil keys to preventing such severe consequences. Despite this recognition of the loops’ importance, real-time observations of looping dynamics at the cellular level have proven challenging. Traditional imaging techniques often employ harsh chemical treatments and elevated temperatures, yielding insights at the cost of disrupting the native state of the DNA structures being examined.

To circumvent this dilemma, Kai Beckwith, an innovative former postdoc working under the guidance of EMBL’s Ellenberg Group, devised a novel approach to delicately extract one strand of DNA from cellular environments at various phases of division. This method preserves the integrity of chromosome structures while enabling the application of targeted DNA-binding labels to visualize and probe the nanoscale organization of the exposed DNA strand. Calibrated with a technique known as LoopTrace, the researchers could directly monitor the progressive unfolding of DNA as it transitioned through pivotal structural formations in the cell division cycle.

As these researchers meticulously gathered and interpreted their data, they discovered that the looping of DNA occurs in a two-phased manner during cellular replication. Initially, stable large loops emerge, subsequently subdividing into smaller, transient loops that intricately enhance the compaction of the chromosomes. It became apparent that two distinct types of condensin protein complexes drive this orchestrated looping effect. To forge a comprehensive understanding of how this ambient looping leads to the formation of definitive rod-shaped chromosomes, the researchers architected a computational model predicated on two cardinal assumptions: First, the presence of overlapping loops—both large and small—formed through condensin activity; and second, the natural tendency of these loops to repel each other.

The results sourced from their computational model proved enlightening, as the scientists realized that the preceding assumptions were fundamental in revealing the native structure of mitotic chromosomes. The large condensin-driven loops exceeded previously held dimensions, significantly overlapping as they simultaneously facilitated intricate cellular architectures. These loop dynamics and interactions possess paramount relevance in elucidating the mechanisms behind successful chromosome segregation during exploitation, a concept that had long remained theoretical.

In light of these findings, the researchers plan to further dissect this multilayered process while considering additional molecular regulators that may influence the compaction of chromosomal structures. Building on this excitement, Jan Ellenberg and his research team were recently awarded a notable ERC Advanced Grant worth €3.1 million, affirming their commitment to deciphering the nuanced folding principles that govern chromosomal assemblies during and after cell division.

Upon reflection, Jan Ellenberg, Senior Scientist at EMBL Heidelberg, heralded their latest publication in the esteemed journal "Cell" as a monumental step forward in the quest to unravel the cellular mechanics underlying chromosomal packaging. The discoveries from this work form a foundational understanding of the molecular orchestration at play within cellular inheritance, offering bright prospects for devising strategies to mitigate errors that could precipitate various human diseases.

As this line of inquiry continues to evolve, researchers are keenly attuned to the implications of their work extending beyond the immediate realms of chromosome architecture. A companion study led by Andreas Brunner recently unveiled parallel insights into other aspects of cellular dynamics, demonstrating that the same principles governing nested loop formation during cell division persist in a cell’s growth phase, facilitated by alternative protein complexes known as cohesins.

Surprisingly, investigators noted the fundamental continuity of the looping mechanisms, suggesting that both condensins and cohesins share core principles in orchestrating sequential DNA loop formation. However, they also highlighted subtle, yet crucial, mechanistic differences that dictate how DNA is tightly packed into accessible entities during division. These findings open new avenues for investigation, emphasizing the potential to decipher the underlying principles governing not just the physical architecture of chromosomes but also the broader biological implications that stem from these central processes in life.

Through advanced methodologies, EMBL scientists have taken an unprecedented leap toward unveiling the underpinnings of cellular replication processes, transitioning from abstract theorization to observable evidence. The ramifications of this research extend far beyond the lab, potentially setting the stage for groundbreaking discoveries in medical science, genetics, and our understanding of fundamental biological processes.

As investigations continue to deepen, the confluence of technology and biological curiosity promises not only to demystify the inner workings of cells but also to illuminate pathways toward innovative strategies for health preservation and disease prevention.

Subject of Research: Chromosomal dynamics during cell division
Article Title: Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes
News Publication Date: 24-Mar-2025
Web References: Link to the article
References: Not available
Image Credits: Daniela Velasco Lozano/EMBL

Keywords: Chromosome structure, DNA looping, Cell division, Condensins, Cohesins, Nanoscale imaging, EMBL, Genome integrity, Cell biology, Biophysics.

The research elucidated the complexities of glycosylation, a vital biochemical process that regulates diverse cellular activities, including cell adhesion, motility, and intercellular communication. Despite its importance, glycosylation has posed substantial challenges to researchers; traditionally, it has been difficult to study on a systemic scale due to the limited number of glycosylated proteins within a biological sample. This study, however, introduced an innovative methodology referred to as DQGlyco, which significantly enhances the ability to analyze glycosylation dynamics with high resolution and specificity.

DQGlyco leverages readily accessible laboratory materials to isolate and analyze glycosylated proteins from complex biological samples. By employing functionalized silica beads, the researchers successfully enriched samples, leading to an extraordinary identification of over 150,000 unique glycosylated protein forms. This discovery underscores the method’s capability to provide insights into glycosylation patterns at a previously unattainable scale, revealing the intricacies of protein modification.

One of the notable applications of this method was its use to investigate the glycosylation profiles in brain tissues of mice. The research team meticulously compared the glycosylation signatures from mice with gut bacteria to those of germ-free mice, which were raised in sterile conditions devoid of microbiota. The results indicated significant differences in glycosylation patterns, particularly in proteins associated with neural function, such as those involved in cognitive processes and axon guidance.

The implications of these findings are profound, as they suggest that gut bacteria may play a crucial role in modulating not only physical health but also cognitive and neural function through biochemical pathways. The connection between the gut microbiome and the brain, often referred to as the gut-brain axis, has gained increasing attention in recent years, with studies indicating that the microbial composition can influence behavior, mood, and even neurological diseases. This research contributes a vital piece to the puzzle, offering mechanistic insights into how gut bacteria can induce molecular changes in the brain via glycosylation.

In light of these findings, the researchers have initiated efforts to make their datasets publicly accessible through a dedicated application tailored for fellow scientists. The goal of this initiative is twofold: to foster collaboration within the research community and to enable other scientists to leverage the findings to investigate glycosylation patterns across different biological contexts and species.

Moreover, the researchers have expressed interest in using machine learning technologies, including AlphaFold, to predict the variability of glycosylation sites in diverse organisms. This advancement could potentially revolutionize the understanding of glycosylation and its evolutionary implications across species. The integration of AI and computational tools into biological research signifies a paradigm shift that may yield novel insights and applications in the field.

The overarching objective of this innovative study and its subsequent methodological advancements transcends mere academic inquiry; it strives to unravel the functional roles of glycosylation in cellular physiology and its larger implications for health and disease. Glycosylation’s involvement in various pathologies, including neurodegenerative disorders and cancer, reinforces the necessity for sophisticated techniques that can adequately address these complex biochemical phenomena.

As the EMBL team continues to build upon their findings, they are poised to explore the functional consequences of glycosylation changes instigated by the gut microbiome. This line of inquiry not only aims to enhance understanding of biochemical processes but also to unveil potential therapeutic targets for conditions exacerbated by dysbiosis—a disruption in the gut microbiota.

In summary, the research conducted at EMBL marks a notable entry into the evolving discourse surrounding the gut-brain axis, contributing vital insights into how gut microbiota can shape molecular landscapes within the brain through the intricate process of glycosylation. As the scientific community continues to probe the depths of this relationship, the future appears promising for uncovering the underlying mechanisms that connect our microbial inhabitants with cerebral function and overall health.

Subject of Research: The impact of gut bacteria on protein glycosylation in the brain.
Article Title: Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco).
News Publication Date: 10-Feb-2025
Web References: Nature Structural & Molecular Biology
References: None available.
Image Credits: Daniela Velasco Lozano/EMBL

Keywords: Glycosylation, Protein Dynamics, Gut Microbiota, Brain Function, Molecular Biology, EMBL, DQGlyco, Neurobiology, Microbial Ecosystems, Glycoprofiling, Machine Learning, AlphaFold.