Download MendeleyDe Novo Design of Proteins for Autocatalytic Isopeptide Bond Formation.
Srisantitham, S., Walker, A.L., Markel, U., Tezcan, F.A.(2025) J Am Chem Soc 147: 12338-12346
- PubMed: 40138671
- DOI: https://doi.org/10.1021/jacs.5c03319
- Primary Citation of Related Structures:
9MXW, 9MXX - PubMed Abstract:
Isopeptide bonds (IPBs)─formed between the amine group of a Lys residue and the carboxamide/carboxy group of Asn/Gln or Asp/Glu─play essential roles in many biological processes, ranging from cellular signaling and regulation to blood clotting and bacterial pathogenesis. The formation of IPBs is not a spontaneous process and requires enzymatic machinery that provides a specialized active site environment to enable this challenging catalytic reaction. Here we report the de novo design and characterization of two proteins (dnIPB-1 and dnIPB-2) capable of autocatalytic IPB formation. While these designed proteins preserve the key active-site residues of their structural template (the bacterial pilin protein RrgA), they possess less than 31% sequence identity to RrgA. Extensive structural and Ala-scanning analyses indicate that IPB formation requires a solvent-protected core motif composed of several critical residues, yet there is also a large tolerance to different protein topologies and overall protein sizes in terms of accommodating an IPB-forming motif. Notably, the structural insights gained from the study of dnIPB-1 and dnIPB-2 also guided the redesign of an initially failed construct (dnIPB-3) and enabled it to form an IPB, highlighting the value of de novo design in examining sequence-structure-function relationships not explored in natural evolution. Our study highlights the versatility of IPBs as designable elements which can be used to construct functional proteins or protein-based materials with enhanced chemical, thermal, and mechanical stabilities.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.
Organizational Affiliation:
