Protein engineering holds the key to solving some of humanity's most pressing challenges, from developing novel therapeutics and vaccines to creating sustainable industrial enzymes. Yet, for decades, progress has been constrained by a central dogma: that a protein's core—its densely packed hydrophobic interior—is a fragile, immutable structure. This "house of cards" model suggested that even minor changes to the core would lead to catastrophic misfolding, forcing engineers to focus on conservative, surface-level modifications. A recent study is now dismantling this long-held belief, revealing a far more robust and programmable reality.
The journey of protein engineering has been one of incrementally expanding our ability to modify function. Early methods like directed evolution allowed scientists to select for desired traits but offered little insight into the underlying design principles. A significant conceptual leap came from work identifying "sectors"—networks of co-evolving amino acids that connect distant sites to a protein's active site, often mediating allosteric communication [2]. This revealed that function could be tuned from afar, but the core itself remained largely off-limits, a black box approached with extreme caution. The prevailing strategy remained one of making small, careful edits, a paradigm that inherently limited the scope of innovation [4]. The field needed a systematic way to test the core's true tolerance for change, but the sheer scale of the combinatorial sequence space made this experimentally prohibitive—until now.
A landmark paper in Science by Escobedo et al., "Genetics, energetics, and allostery in proteins with randomized cores and surfaces," provides the first large-scale, systematic interrogation of this forbidden territory [1]. The research team directly confronted the "fragile core" hypothesis by taking a small, well-understood protein domain (the human FYN-SH3 domain) and performing a radical experiment: they systematically randomized its core and surface sequences and synthesized tens of thousands of variants. Using a high-throughput assay, they then measured which of these massively altered sequences could still fold into a stable, functional protein.
The results were stunning and counterintuitive. They found that a vast number of different amino acid combinations could successfully form a stable protein core. Instead of a fragile house of cards, the protein structure behaved more like a set of Lego bricks, where many different pieces could fit together to build a stable whole. This finding alone fundamentally alters our understanding of protein stability.
Even more profoundly, the study revealed why many of these stable variants were non-functional. It wasn't because of structural collapse, as previously assumed. Instead, the changes in the core disrupted the protein's function through subtle, long-range allosteric effects—indirectly altering the shape or dynamics of the distant ligand-binding site. This decouples the problem of stability from the problem of function, showing that allostery, not instability, is the primary constraint on the evolution of protein cores.
To validate this, the researchers developed simple, additive energy models based on their experimental data. Remarkably, these models, trained on a single protein, could accurately predict the stability of natural SH3 domains from organisms separated by over a billion years of evolution [1, 3]. This suggests that the fundamental "rules" of protein folding are far simpler and more universal than previously imagined.
The implications of this work are transformative, signaling a paradigm shift in biological engineering.
While future work will need to explore how these principles scale to larger, multi-domain proteins and complex assemblies [6], the path forward is clear. We are moving from an era of discovering what nature has evolved to an era of designing what biology can become. By revealing the simple, elegant rules hidden within the complexity of the protein core, this research has not just added a new chapter to the textbook—it has given us a new language to write the future of biology.
Ailurus Bio is a pioneering company building bioprograms, which are genetic codes that act as living software to instruct biology. We develop foundational DNAs and libraries to turn lab-grown cells into living instruments that streamline complex procedures in biological research and production. We offer these bioprograms to scientists and developers worldwide, empowering a diverse spectrum of scientific discovery and applications. Our mission is to make biology a general-purpose technology, as easy to use and accessible as modern computers, by constructing a biocomputer architecture for all.
