Photosynthesis is one of nature’s most remarkable process: it captures sunlight and transforms it into chemical energy that sustains nearly all life on Earth. Yet sunlight is a double-edged sword. When it becomes too intense, it can damage the very machinery that enables this conversion. Marine microalgae such as diatoms have evolved to master this challenge. These highly diverse organisms inhabit some of the planet’s harshest environments, constantly moving between dim ocean depths and bright surface waters where light intensity constantly shifts. Despite these fluctuations, diatoms thrive, producing about one-fifth of Earth’s oxygen. How do they manage to both harness and protect themselves from light? Our recent study, “Conformational Plasticity Enables Functional Switching in Diatom Light-Harvesting Complexes,” explores this question at the molecular level. What began as a routine molecular dynamics study of proteins from two diatom species (P. tricornutum and C. gracilis) revealed how flexible protein scaffolds allow diatoms to toggle between two modes: one optimized for efficient energy harvesting and another that safely dissipates excess light as heat.
A Shape-Shifting Light Harvester
At the heart of diatom photosynthesis are proteins that capture blue-green light underwater. Over the past few years, advances in cryo-electron microscopy (cryo-EM) have provided detailed snapshots of these proteins in different diatom species. Yet, while diverse, these snapshots are static - frozen moments of systems that are anything but rigid. When I am showing simulations of protein motion to colleagues in structural biology or biochemistry, I often get surprised looks; they kind of say, “Oh, they really do move!” That sense of motion is what drew me to biomolecules in the first place; the astonishing choreography of thousands of atoms working in concert to sustain life. Every biochemistry lecture reminds us that proteins move and breathe, yet the images we see in textbooks show them as still. What if we could combine knowledge from all those experimentally resolved static structures to predict how they actually move? To explore this idea, we downloaded all known diatom light-harvesting protein structures from scientific repositories. Their diversity was immediately clear, yet beneath that variety we found a shared structural core, like a kind of mathematical common denominator. Even more strikingly, all these proteins shifted between only a few distinct shapes. It was like taking a series of still photographs of people at a party, then using artificial intelligence (AI) to turn them into a movie and discover that everyone breathes, no matter the setting. The key difference among the diatom proteins was how much their scaffolds expanded or contracted, in terms of a subtle, breathing-like motion. Supercomputer simulations of just a couple of these proteins confirmed this: they too transitioned among the same distinct shapes.
Structure Meets Function
Using machine learning, we discovered that this “breathing” motion was strongly and linearly correlated with changes in how efficiently energy travels within the protein as a critical parameter that determines whether light energy is converted into chemical energy or safely dissipated as heat. In essence, the protein’s motion acts like a molecular dimmer switch, fine-tuning the flow of energy depending on light conditions. We then asked whether this flexibility was an intrinsic property of these proteins or merely a side effect of environmental conditions. To test this, we turned to deep-learning protein design tools. By slightly varying amino acid sequences, we examined whether each observed conformation could, in principle, be stabilized. The answer was yes. This means the adaptability is built into the protein’s architecture itself. Different amino acid sequences, shifts in acidity, or interactions with regulatory proteins can bias the protein toward one conformation or another.
Why This Matters Beyond Academic Curiosity
This kind of molecular versatility is not just fascinating, but it’s globally significant. Diatoms perform roughly 20% of all photosynthesis on Earth, a contribution comparable to that of the world’s rainforests. Their extraordinary efficiency and resilience help regulate atmospheric carbon dioxide and sustain marine food webs. By uncovering the shape-shifting nature of diatom light-harvesting proteins, we may have identified a key to engineering photosynthetic systems that are as adaptable as life itself. Imagine bioengineered crops or algae that can exert increased resilience to fluctuating light and therefore enhancing carbon capture to help the fight against climate change. Moreover, the identified patterns could inform the design of synthetic light-harvesting systems for renewable energy.
Behind the Scenes and Conclusions
Months of supercomputer simulations produced terabytes of data, but the real challenge lay in detecting meaningful patterns within the complex molecular motion. Humans are natural pattern seekers, and the turning point came when we realized that all known diatom light-harvesting proteins, across multiple species, could be described by just a few interconverting states. That universality suggested a fundamental design principle. We are now working toward experimental validation, to correlate this molecular breathing with measurable physical properties. Of course, what we have identified is a simplified motif present in all experimentally resolved diatom light harvesting proteins so far. We remain open to refining our understanding as new evidence from light harvesting structures emerges, as life endures not by resisting change, but by mastering it to adapt.
Collaborative work
The lab of Biomolecular Dynamics and Engineering (Prof. Vangelis Daskalakis) focused on identifying and characterizing the structural patterns and dynamic motions of the proteins, while the Computational Physics and Biophysics Group (Prof. Ulrich Kleinekathöfer) analyzed how energy flows within these same proteins. Together, we revealed how structural flexibility governs light harvesting and protection in diatoms. Researchers were financially funded by the Hellenic Foundation for Research & Innovation (H.F.R.I) in the context of the call “Basic Research Financing (Horizontal support for all Sciences), National Recovery and Resilience Plan (Greece 2.0) for the project number 014775, with acronym “SUNDIAL” (Theofani-Iosifina Sousani) and from the European Union’s Horizon Europe Research and Innovation Program under the Marie Skłodowska-Curie grant agreement No 101119442 (Boutheina Zender; Sayan Maity).