Minidomains from evolution for scaffold engineering

Protein engineering is a powerful approach that has enabled the development of novel drugs and biotechnologies. Recent advances in genome annotation and computational prediction have shifted attention toward smaller, non-antibody scaffolds - miniproteins - typically fewer than 100 amino acids. Despite their small size, these molecules exhibit remarkable structural complexity, offering a rich resource for drug discovery but also presenting challenges in distilling this complexity into practical starting points. In this review, we focus on a class of miniproteins known as minidomains: well-defined structural units shaped by evolution that perform specific functions within larger proteins yet can operate independently, making them naturally adapted scaffolds for bioengineering. Using a data-driven approach, we survey proteomes to identify these minidomains and provide a sequence- and structure-informed perspective to guide engineering. To illustrate this approach, we highlight Ig-like C1 domains, the most prevalent minidomain in humans. Finally, we summarize established and emerging strategies for engineering these scaffolds. Together, these advances in technology and design lay the foundation for a promising future for minidomain-based applications.