EventProf. Roman Jerala

Design of molecular origami nanostructures and folding pathways

Roman-Jerala-Abstract-Pics
  • Gradišar H, Božič S, Doles T, Vengust D, Hafner-Bratkovič I, Mertelj A, Webb B, Šali A, Klavžar S, Jerala R. (2013) Nat Chem Biol. 6:362-6.
  • Kočar V, Schreck JS, Čeru S, Gradišar H, Bašić N, Pisanski T, Doye JP, Jerala R. Nat Commun. (2016) 7:10803.
  • Drobnak I, Gradišar H, Ljubetič A, Merljak E, Jerala, R. (2017) Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity. Am.Chem.Soc.139: 8229-8236.
  • Ljubetič, A., Lapenta, F., Gradišar, H., Drobnak, I., Aupič, J., Strmšek, Ž., Lainšček, D., Hafner-Bratkovič, I., Majerle, A., Krivec, N.,  Benčina, M., Pisanski, T., Ćirković Veličković, T., Round, A., Carazo, J.M., Melero, R. and Jerala, R., (2017) Design of in vivo self-assembling coiled-coil protein origami. Nat Biotech, 35:1094-1101.

Proteins are the most advanced nanostructures, defined by the sequence of amino acids. Nature provides a limited number of protein sequences and folds, which have been optimized during evolution. New protein folds are very challenging to design due to the delicate balance of numerous weak long range noncovalent interactions stabilizing proteins structure. Modular design of polypeptide-based polyhedra was inspired by the DNA-based nanostructures. The folding problem of proteins was bypassed by designing de novo coiled-coil protein origami (CCPO) folds by relying on the well-understood specificity of coiled-coil dimers and used them as modules to guide the polypeptide chain between vertices of the selected polyhedral cage. The principle was demonstrated by the construction of a nanoscale protein tetrahedral cage from a single polypeptide chain composed of 12 coiled-coil forming segments1. In this assembly 6 edges of the polyhedron are defined by orthogonal coiled-coil dimers.

Modularity of designed structures could also allow the design of the folding pathway, which is required particularly for the design of topologically knotted structures as the chain needs to be steered through the previously formed loops in a predefined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology only the one with the folding pathway designed according to the “free-end” rule folded efficiently into the target structure2. Besides high folding yields upon slow annealing, this design also folded rapidly.

Introduction of supercharged CC building modules3 and protein origami computational design platform CoCoPOD enabled design of protein origami cages that are able to self-assemble in vivo. Complexity of protein origami structures as extended to more than 700 residue proteins with tetrahedral, four-sided pyramid and triangular prism that fold efficiently, with kinetics and stability comparable to globular proteins4. In vivo folding of protein origami opens prospects for new applications of this new type of protein folds as we demonstrate that they do not trigger any adverse reaction in mammalian cells and in the animals.

About The Speaker

jerala

Prof. Roman Jerala is head of the Department of Synthetic Biology and Immunology at the National Institute of Chemistry in Ljubljana, Slovenia. He is also a full professor at the Faculty of Chemistry and Chemical technology, University of Ljubljana, synthetic biology project director at the Centre of Excellence EN-FIST and EMBO member. His research areas of interest include synthetic biology, designed bionanostructures and molecular mechanism of innate immunity. In 2013, his group published an article in Nature Chemical Biology on designed coiled-coil protein origami (CCPO) cages using reprogrammed bacteria by synthesizing a protein that folds itself into a tetrahedron measuring just 5 nanometres along each edge, which can be used as container for delivering drugs on the nanoscale. That paves a path to designing and producing completely new protein shapes. This work was recently extended by a second generation of CCPOs that are able to self-assemble in vivo, published in the Nature Biotechnology. Dr. Jerala received numerous awards including Pregl award by the National institute of chemistry for outstanding scientific achievements, Zois award for outstanding scientific achievements (the highest national scientific award) and Medal for services by the President of the Republic of Slovenia. He is internationally best known as the leader of Slovenian teams that won the Grand prize at the International Genetically Engineered Machine (iGEM) competition in 2010, 2008, and 2006 in addition to 5 Track winner awards.