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Projects / Programmes source: ARIS

SYNTHETIC POLYPEPTIDE NANOSTRUCTURES FOR BIOTECHNOLOGICAL APPLICATIONS

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Research activity

Code Science Field Subfield
4.06.02  Biotechnical sciences  Biotechnology  Bio-engineering 

Code Science Field
T490  Technological sciences  Biotechnology 

Code Science Field
2.09  Engineering and Technology  Industrial biotechnology 
Keywords
bionanomaterials, selfassembly, polypeptides, designed nanostructures
Evaluation (rules)
source: COBISS
Evaluation of bibliographic research performance indicators according to ARIS methodology
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (16)
no. Code Name and surname Research area Role Period No. of publications
1.  15686  PhD Gregor Anderluh  Biochemistry and molecular biology  Researcher  2014 - 2016  968 
2.  14360  PhD Mojca Benčina  Biotechnology  Researcher  2013 - 2016  392 
3.  33301  Tibor Doles  Biochemistry and molecular biology  Technical associate  2013 - 2014  41 
4.  32254  PhD Rok Gaber  Biotechnology  Researcher  2013 - 2015  52 
5.  17915  PhD Helena Gradišar  Biotechnology  Researcher  2013 - 2016  130 
6.  23563  PhD Iva Hafner Bratkovič  Neurobiology  Researcher  2014 - 2016  211 
7.  06628  PhD Roman Jerala  Biochemistry and molecular biology  Head  2013 - 2016  1,190 
8.  34520  PhD Vid Kočar  Pharmacy  Junior researcher  2013 - 2015  35 
9.  34252  Tina Lebar  Biochemistry and molecular biology  Technical associate  2013 - 2016  67 
10.  32984  PhD Jan Lonzarić  Biochemistry and molecular biology  Technical associate  2014 - 2016  46 
11.  17917  PhD Andreja Majerle  Biotechnology  Researcher  2013 - 2016  92 
12.  17280  Darija Oven    Technical associate  2014 - 2015  4 
13.  26500  PhD Nina Pirher  Biotechnology  Researcher  2013 - 2014  42 
14.  32874  Mojca Seručnik  Biotechnology  Technical associate  2016  31 
15.  31967  PhD Simona Sitar  Chemistry  Researcher  2014  56 
16.  12318  PhD Ema Žagar  Materials science and technology  Researcher  2014  484 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  20,997 
2.  2992  EN-FIST CENTRE OF EXCELLENCE  Ljubljana  3664830  2,837 
Abstract
Proteins are versatile natural nanomachines that perform most functions in all living organisms. Unlike DNA-based nanostructures, where we can construct different nanostructures based on the base pairing complementarity, artificial protein structures are much more challenging to design de novo, therefore designed proteins have been up to now mainly limited to homologues of known protein folds. An engineering approach to polypeptide-based nanostructure design is to construct the polypeptide scaffold from modular polypeptide building blocks such as coiled-coils, which are widespread structural elements in natural proteins whose folding and specificity are quite well understood. We recently devised a strategy to design self-assembling polypeptide nanostructures, based on modular building elements, consisting of orthogonal coiled-coil dimer forming segments. We designed a nanoscale hollow tetrahedron that self-assembled from a single polypeptide chain comprising 12 concatenated coiled-coil-dimer-forming peptide segments separated by flexible peptide hinges. Those segments were selected among the natural and designed coiled-coil dimers. Self-assembly of the recombinant polypeptide chain connecting vertices of a tetrahedron was guided by the defined order of segments and their pairwise interactions that form 6 rigid edges of the tetrahedron composed from coiled-coil dimers, each measuring approximately 5 nm. Creation of this new protein fold is an important achievement, but will have much more significant impact on the progress of biotechnology if this approach can be extended beyond this single example. The topological analysis indicated that in principle any polyhedral structure could be made from the polypeptide chain comprising correctly ordered orthogonal dimeric segments. Within the project we plan to develop and extend this technological platform by 1) creation of more complex designed polypeptide polyhedra such as a tetragonal pyramid and trigonal bipyramid consisting of 8 and 9 edges, respectively, 2) expand the length of coiled-coil edges to vary the size and shape of polypeptide polyhedra, 3) investigate the hierarchical self-assembly of polypeptide nanostructures from several polypeptide chains, 4) expand the set of orthogonal coiled-coil building elements, which will support the design of increasingly complex artificial nanostructures achievable by this innovative approach and 5) functionalize the designed bionanostructures by introduction of cysteine residues into the selected sites to increase stability, allow position-specific coupling of cargo and assembly of nano-polyhedra. Polypeptides will be designed based on the topological and computational analysis and will be produced in E. coli transformed with synthetic genes. Self-assembled polypeptide nanostructures and their properties will be analyzed by circular dichroism, dynamic light scattering, determination of zeta potential, fluorescence of reconstituted split fluorescent proteins, atomic force microscopy and transmission electron microscopy. The aim of the project is therefore creation of additional new polypeptide folds that do not exist in nature. We expect that the results of this project will establish solid foundations for this technological platform and explore its potentials for the future biotechnological applications.
Significance for science
Modular protein nanostructures based on modules that form a helix gimped represent one of the most interesting and original principles the assembly of new protein structures. Within the project we have developed and new building blocks as well as new principles and assembly of modular biomimetic structures that will allow the formation of major planned structure. With the formation of several new patterns of protein folding process has been moved limit the reach of our designer platform that will allow researchers to prepare more complex structures with new and interesting features.
Significance for the country
The study is important for the implementation of Slovenian science in the world, build a national interdisciplinary expertise in the field of biomimetic nanomaterials and synthetic biology. PI has been since 2013 invited as invited speaker to three different Gordon Research Conferences, on peptides (Ventura, C, 2014), bioinspired nanomaterials (Sunday River, VT, 2014) and on Physical virology (Il Ciocco, IT, 2017). An important result of the project is the training of researchers at various levels of training, from students to mature researchers. Some of the success of the project were presented to the general public, which is improving the image of Slovenian science and motivate the younger generation to parts of science. The platform developed under this project are already beginning to be used for biotechnological applications, such as vaccines.
Most important scientific results Annual report 2013, 2014, 2015, final report
Most important socioeconomically and culturally relevant results Annual report 2013, 2014, 2015, final report
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