Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions

De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.

Automated summary

De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context, reproducing reactions and uncovering biophysical principles difficult to extract from natural proteins. Natural proteins can bind ligands with high levels of specificity and affinity. Recent studies have focused on small molecules, nucleic acids, and protein-protein interactions, with advancements in structural design and computational modeling approaches.