Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein AncHLD-RLuc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of AncHLD-RLuc challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins.

Department of Biochemistry University of Cambridge Cambridge UK

Department of Biotechnology and Enzyme Catalysis Institute of Biochemistry University of Greifswald Greifswald Germany

International Clinical Research Center St Anne's University Hospital Brno Brno Czech Republic

Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of Science Masaryk University Brno Czech Republic

Research Centre for Applied Molecular Oncology Masaryk Memorial Cancer Institute Brno Czech Republic

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Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis

Illuminating the mechanism and allosteric behavior of NanoLuc luciferase

Machine Learning-Guided Protein Engineering

SBILib: a handle for protein modeling and engineering

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering

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figshare
10.6084/m9.figshare.14453700.v1