Local structural flexibility drives oligomorphism in computationally designed protein assemblies.

Area of Science:

• Protein engineering
• Structural biology
• Biophysics

Background:

• Naturally occurring protein assemblies exhibit dynamic structures for specialized functions, like clathrin coats adapting to cargo.
• Current computational protein design methods primarily focus on creating static structures with high precision.

Approach:

• Characterized three computationally designed protein assemblies using cryo-electron microscopy (cryo-EM) single-particle reconstruction and native mass spectrometry.
• Employed structural modeling and molecular dynamics simulations to investigate the source of observed structural diversity.

Key Points:

• Designed protein assemblies formed multiple, unanticipated architectures, deviating from static design goals.
• Structural flexibility in specific subunit regions was identified as the key driver of this architectural diversity.
• Constrained flexibility within building blocks explained the formation of a defined range of architectures, preventing non-specific aggregation.

Conclusions:

• Deliberately incorporating structural flexibility into protein design principles opens new avenues for exploring previously inaccessible structural and functional spaces.
• This approach enables the creation of novel, adaptable protein assemblies with tailored functionalities.