Precise assembly of complex beta sheet topologies from de novo designed building blocks

Area of Science:

• Protein engineering and computational biology.
• Structural biology and molecular evolution.

Background:

• Designing complex alpha-beta protein topologies is difficult due to numerous possible packing arrangements.
• Evolutionary emergence of large, complex protein topologies may have faced similar design challenges.

Purpose of the Study:

• To demonstrate the design of novel protein topologies with six- and seven-stranded beta sheets.
• To explore a potential mechanism for the evolution of complex beta sheets in proteins.

Main Methods:

• Insertion of a de novo designed beta sheet protein into another to merge their beta sheets.
• Amino acid sequence optimization at newly formed interfaces (strand-strand, strand-helix, helix-helix).
• Validation through crystal structure determination and comparison with computational models.
• Database searches (SCOP) for structurally similar proteins.

Main Results:

• Successful design and structural validation of two novel protein topologies with extended beta sheets.
• Crystal structures closely matched computational design predictions.
• Weak structural matches found in databases, differing in beta sheet connectivity.

Conclusions:

• De novo protein design can create complex topologies by merging beta sheets.
• The beta sheet fusion mechanism may have played a role in the natural evolution of complex protein structures.