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Coiled coil protein origami: from modular design principles towards biotechnological applications
2018
Chemical Society Reviews
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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
2017
Nature Biotechnology
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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
2016
Chemical Communications
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[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
2014
Journal of Nanobiotechnology
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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
2012
Trends in Cell Biology
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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
2014
Journal of the American Chemical Society
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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
1998
Bioinformatics
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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
2019
Nanotechnology, Science and Applications
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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
2021
Proceedings of the National Academy of Sciences of the United States of America 118(17)
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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
2006
Biophysical Journal
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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
2014
Journal of Polymer Science Part B: Polymer Physics
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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]
2010
Lecture Notes in Computer Science
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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
2021
Nature Communications
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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
2019
Journal of the American Chemical Society
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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
2021
Proceedings of the National Academy of Sciences of the United States of America
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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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