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Coiled coil protein origami: from modular design principles towards biotechnological applications

Fabio Lapenta, Jana Aupič, Žiga Strmšek, Roman Jerala
2018 Chemical Society Reviews  
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.  ...  the interaction. 45 Orthogonal coiled coil sets The ability to construct complex modular protein assemblies depends on the availability of required building blocks.  ...  The heatmap shows the protein-protein interaction pattern for the orthogonal peptide set reported in ref. 21.  ... 
doi:10.1039/c7cs00822h pmid:29400389 fatcat:hh5zyocwrvhblnwftvjgnetobq

Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo

Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner-Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski (+5 others)
2017 Nature Biotechnology  
Orthogonality of coiled-coil forming peptides The heterodimeric CC-forming segments used in protein origami constructs are based on a previously published orthogonal set, including P3, P4, P5, P6, P7 and  ...  Functional amino-acid residues can be readily incorporated, whereas DNA requires introduction of functional moieties or domains via chemical conjugation 31 .  ... 
doi:10.1038/nbt.3994 pmid:29035374 fatcat:gj5ij2oi3fdwlhffyrndefkt7q

Designing the structure and folding pathway of modular topological bionanostructures

A. Ljubetič, I. Drobnak, H. Gradišar, R. Jerala
2016 Chemical Communications  
[34] [35] [36] [37] [38] Other sets of orthogonal protein-protein binding pairs could in principle also be used to construct topofold proteins, but coiled-coils (and nucleic acid duplexes) have the  ...  The protein tetrahedron recently built 24 using orthogonal coiled-coiled modules is not knotted, as it uses modules shorter than one superhelical turn, but for protein topofold structures constructed from  ... 
doi:10.1039/c6cc00421k pmid:27001947 fatcat:hdya2656nfabdnbq3kcoa7gio4

Self-assembled bionanostructures: proteins following the lead of DNA nanostructures

Helena Gradišar, Roman Jerala
2014 Journal of Nanobiotechnology  
While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically  ...  designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures.  ...  Designed topological protein folds based on interacting coiled-coil modules Recent innovative approach to construct new engineered self-assembled protein nanostructures is based on the concatenated interacting  ... 
doi:10.1186/1477-3155-12-4 pmid:24491139 pmcid:PMC3938474 fatcat:ckweled3a5esbgldvvbaeg6ft4

Designer nucleic acids to probe and program the cell

Yamuna Krishnan, Mark Bathe
2012 Trends in Cell Biology  
The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic  ...  base-pairing and construction rules [3, 4] , where the edges of the polyhedra comprise individual DNA duplexes.  ...  In an important development, a highthroughput approach was delineated [80] that screens endogenous RNA interactions to identify orthogonal mRNA-regulatory RNA pairs.  ... 
doi:10.1016/j.tcb.2012.10.001 pmid:23140833 fatcat:klcvqoia6vavrjmybhxj4z6g3y

A Set of Computationally Designed Orthogonal Antiparallel Homodimers that Expands the Synthetic Coiled-Coil Toolkit

Christopher Negron, Amy E. Keating
2014 Journal of the American Chemical Society  
Currently, a limited number of wellcharacterized protein interaction components are available.  ...  The DFIRE model was then combined with the CLASSY multistate protein design framework to engineer sets of three orthogonal antiparallel homodimeric coiled coils.  ...  Interestingly, they found that most polyhedra require orthogonal antiparallel and parallel dimers.  ... 
doi:10.1021/ja507847t pmid:25337788 pmcid:PMC4277747 fatcat:pm323gz2qrh47krluvwjsyxlmy

New scoring schemes for protein fold recognition based on Voronoi contacts

R. Zimmer, M. Wohler, R. Thiele
1998 Bioinformatics  
Sequence-structure alignment is a basic tool for the identification of model folds for protein sequences and the construction of crude structural models.  ...  Availability: The potentials are made available via the program system ToPLign (URL: http://cartan.gmd.de/ ToPLign.html).  ...  These interactions depend on the chemical properties of amino acid side chains (e.g. charge, polarity and hydrophobicity) and the distance of interacting partners.  ... 
doi:10.1093/bioinformatics/14.3.295 pmid:9614274 fatcat:hccyd22l6bczja4ss7bjqk6w6m

Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications

Rana Jahanban-Esfahlan, Khaled Seidi, Ali Jahanban-Esfahlan, Mehdi Jaymand, Effat Alizadeh, Hassan Majdi, Reza Najjar, Tahereh Javaheri, Peyman Zare
2019 Nanotechnology, Science and Applications  
This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and  ...  , the chemical conjugation of amino-modified DNA oligonucleotides was demonstrated with chlorohexane or benzylguanine groups as orthogonal tags for the genetic modification of proteins of interest fused  ...  Moreover, achieving a therapeutic effect, catalytically self-assembled siRNA-based gene silencing via functionalized DNA dendritic complexes was constructed.  ... 
doi:10.2147/nsa.s227193 pmid:31686793 pmcid:PMC6800557 fatcat:xb7ecjf3urcw7bfuwz2e5zydbq

A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures

Andreja Majerle, San Hadži, Jana Aupič, Tadej Satler, Fabio Lapenta, Žiga Strmšek, Jurij Lah, Remy Loris, Roman Jerala
2021 Proceedings of the National Academy of Sciences of the United States of America 118(17)  
of CC protein origami polyhedra or CC-based bionanomaterials.  ...  Furthermore, we identified a pair of allosteric nanobodies in which the binding to the distant epitopes on the antiparallel homodimeric APH CC is coupled via a strong positive cooperativity.  ...  of CC protein origami polyhedra or CC-based bionanomaterials. nanobody | coiled-coil dimer | coiled-coil protein origami | protein assembly | protein design T he coiled-coil (CC) structural motif is one  ... 
doi:10.3204/pubdb-2021-04334 fatcat:cys3wo3ysbe4hajvvhrxzy6h7a

Explanation of the Stability of Thermophilic Proteins Based on Unique Micromorphology

Simone Melchionna, Raffaele Sinibaldi, Giuseppe Briganti
2006 Biophysical Journal  
By analyzing the simulation data via the Voronoi space tessellation, we have found that the two proteins have the same macromolecular packing, while the water-exposed surface area is larger for the thermophile  ...  From an enthalpic point of view, the thermophile shows a larger number of intramolecular hydrogen bonds, stronger electrostatic interactions, and a flatter free-energy landscape.  ...  We compute the volume occupied by the solutes and the protein-water interfacial region by employing the Voronoi construction to partition the space into atom-based polyhedra (46, 47) .  ... 
doi:10.1529/biophysj.105.078972 pmid:16533850 pmcid:PMC1459513 fatcat:ax6rsp5o7jhohmenjenqmp37ye

Giant surfactants based on molecular nanoparticles: Precise synthesis and solution self-assembly

Xinfei Yu, Yiwen Li, Xue-Hui Dong, Kan Yue, Zhiwei Lin, Xueyan Feng, Mingjun Huang, Wen-Bin Zhang, Stephen Z. D. Cheng
2014 Journal of Polymer Science Part B: Polymer Physics  
Micelle formation is affected not only by their primary chemical structures, but also by the experimental conditions.  ...  INTRODUCTION Amphiphiles contain chemically distinct parts (e.g., hydrophilic and hydrophobic parts) connected via primary chemical bonds.  ...  MNPs provide a library of essential building blocks to construct various "giant molecules," 34 such as molecular Janus particles, 38-42 giant polyhedra, 34 and giant surfactants. 17, 18 Fullerene Fullerenes  ... 
doi:10.1002/polb.23571 fatcat:5sbc7vdskneujm3cvk4y5rtknq

Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms [chapter]

Frederic Cazals
2010 Lecture Notes in Computer Science  
Our implementation of the model allows an analysis of protein-water contacts that highlights the role of structural water molecules at protein-protein interfaces.  ...  We developed a model of macromolecular interfaces based on the Voronoi diagram and the related alpha-complex, and we tested its properties on a set of 96 protein-protein complexes taken from the Protein  ...  Chemical composition, accessibility, and interactions Chemical groups The chemical composition of the facets that form the AB interfaces is given in Table 4 : 58% of the facets involve a nonpolar (carbon-containing  ... 
doi:10.1007/978-3-642-16001-1_36 fatcat:3z2rolrtibcv7kowesx5saiugi

Designed folding pathway of modular coiled-coil-based proteins

Jana Aupič, Žiga Strmšek, Fabio Lapenta, David Pahovnik, Tomaž Pisanski, Igor Drobnak, Ajasja Ljubetič, Roman Jerala
2021 Nature Communications  
Designed coiled-coil protein origami (CCPO) cages are distinct from natural compact proteins, since their fold is prescribed by discrete long-range interactions between orthogonal pairwise-interacting  ...  The number of orthogonal modules required for constructing a CCPO tetrahedron can be reduced from six to as little as three different CC modules.  ...  Proteins were fluorescently labelled with Sulfo-cy3 and Sulfo-cy5 (Lumiprobe, MD, USA) via thiol-maleimide coupling.  ... 
doi:10.1038/s41467-021-21185-5 pmid:33574262 fatcat:3dh52t5peffotjoeoonantxqma

Combining Synthesis and Self-Assembly in One Pot to Construct Complex 2D Metallo-Supramolecules Using Terpyridine and Pyrylium Salts

Heng Wang, Yiming Li, Hao Yu, Bo Song, Shuai Lu, Xin-Qi Hao, Yuan Zhang, Ming Wang, Saw-Wai Hla, Xiaopeng Li
2019 Journal of the American Chemical Society  
Multicomponent self-assembly in one pot provides an efficient way for constructing complex architectures using multiple types of building blocks with different levels of interactions orthogonally.  ...  Here, we developed a multicomponent synthesis/self-assembly strategy, which combined covalent interaction (C-N bond, formed through condensation of pyrylium salt with primary amine) and metal-ligand interaction  ...  However, rational design of different levels of interactions in an orthogonal manner to minimize unwanted products is still full of challenges in the multicomponent system, and thus limits the complexity  ... 
doi:10.1021/jacs.9b05682 pmid:31345024 pmcid:PMC6852697 fatcat:6edgmeipzncbno5lt24wcrjqzu

A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures

Andreja Majerle, San Hadži, Jana Aupič, Tadej Satler, Fabio Lapenta, Žiga Strmšek, Jurij Lah, Remy Loris, Roman Jerala
2021 Proceedings of the National Academy of Sciences of the United States of America  
of CC protein origami polyhedra or CC-based bionanomaterials.  ...  Furthermore, we identified a pair of allosteric nanobodies in which the binding to the distant epitopes on the antiparallel homodimeric APH CC is coupled via a strong positive cooperativity.  ...  of CC protein origami polyhedra or CC-based bionanomaterials. nanobody | coiled-coil dimer | coiled-coil protein origami | protein assembly | protein design T he coiled-coil (CC) structural motif is one  ... 
doi:10.1073/pnas.2021899118 pmid:33893235 pmcid:PMC8092592 fatcat:lvvoyiv72zhkrpu4uv5pmfxr64
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