De Novo Designed Peptide and Protein Hairpins Self-assemble into Sheets and Nanoparticles

AbstractThe design and assembly of peptide based materials has advanced considerably, leading to a variety of fibrous, sheet and nanoparticle structures. A remaining challenge is to account for and control different possible supramolecular outcomes accessible to the same or similar peptide building blocks. Here we present a de novo peptide system that forms nanoparticles or sheets depending on the strategic placement of a ‘disulfide pin’ between two elements of secondary structure that drive self-assembly. Specifically, we join homodimerizing and homotrimerizing de novo coiled-coil α-helices with a flexible linker to generate a series of linear peptides. The helices are pinned back-to-back, constraining them as hairpins by a disulfide bond placed either proximal or distal to the linker. Computational modeling and advanced microscopy show that the proximally pinned hairpins self-assemble into nanoparticles, whereas the distally pinned constructs form sheets. These peptides can be made synthetically or recombinantly to allow both chemical modifications and the introduction of whole protein cargoes as required.

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Interfacial zippering-up of coiled-coil protein filaments

Physical Chemistry Chemical Physics ◽

10.1039/c5cp05938k ◽

2015 ◽

Vol 17 (46) ◽

pp. 31055-31060 ◽

Cited By ~ 6

Author(s):

Emiliana De Santis ◽

Valeria Castelletto ◽

Maxim G. Ryadnov

Keyword(s):

Self Assembly ◽

De Novo ◽

Coiled Coil ◽

Morphological Control

A de novo self-assembly topology for engineering protein nanostructures under morphological control is reported.

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Beyond icosahedral symmetry in packings of proteins in spherical shells

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1706825114 ◽

2017 ◽

Vol 114 (34) ◽

pp. 9014-9019 ◽

Cited By ~ 17

Author(s):

Majid Mosayebi ◽

Deborah K. Shoemark ◽

Jordan M. Fletcher ◽

Richard B. Sessions ◽

Noah Linden ◽

...

Keyword(s):

Self Assembly ◽

De Novo ◽

Multiple Scales ◽

Building Blocks ◽

Icosahedral Symmetry ◽

Protein Cages ◽

Natural Systems ◽

Wide Range ◽

Stable Arrangement ◽

Symmetric Structures

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.

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DNA-dependent macromolecular condensation drives self-assembly of the meiotic DNA break machinery

10.1101/2020.02.21.960245 ◽

2020 ◽

Cited By ~ 3

Author(s):

Corentin Claeys Bouuaert ◽

Stephen Pu ◽

Juncheng Wang ◽

Dinshaw J. Patel ◽

Scott Keeney

Keyword(s):

Self Assembly ◽

Chromosome Structure ◽

Coiled Coil ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Dna Breakage ◽

And Control

Formation of meiotic DNA double-strand breaks (DSBs) by Spo11 is tightly regulated and tied to chromosome structure, but the higher-order assemblies that execute and control DNA breakage are poorly understood. We address this question through molecular characterization of Saccharomyces cerevisiae RMM proteins (Rec114, Mei4 and Mer2)—essential, conserved components of the DSB machinery. Each subcomplex of Rec114–Mei4 (2:1 heterotrimer) or Mer2 (homotetrameric coiled coil) is monodisperse in solution, but they independently condense with DNA into dynamic, reversible nucleoprotein clusters that share properties with phase-separated systems. Multivalent interactions drive condensation, which correlates with DSB formation in vivo. Condensates fuse into mixed Rec114–Mei4–Mer2 clusters that further recruit Spo11 complexes. Our data show how the DSB machinery self-assembles on chromosome axes to create centers of DSB activity. We propose that multilayered control of Spo11 arises from recruitment of regulatory components and modulation of biophysical properties of the condensates.

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Functional self-assembling polypeptide bionanomaterials

Biochemical Society Transactions ◽

10.1042/bst20120025 ◽

2012 ◽

Vol 40 (4) ◽

pp. 629-634 ◽

Cited By ~ 11

Author(s):

Tibor Doles ◽

Sabina Božič ◽

Helena Gradišar ◽

Roman Jerala

Keyword(s):

Self Assembly ◽

Biological Systems ◽

Three Dimensional ◽

Coiled Coil ◽

Chemical Properties ◽

Building Blocks ◽

External Signal ◽

Form Complex ◽

Cell Factories ◽

Self Assembling

Bionanotechnology seeks to modify and design new biopolymers and their applications and uses biological systems as cell factories for the production of nanomaterials. Molecular self-assembly as the main organizing principle of biological systems is also the driving force for the assembly of artificial bionanomaterials. Protein domains and peptides are particularly attractive as building blocks because of their ability to form complex three-dimensional assemblies from a combination of at least two oligomerization domains that have the oligomerization state of at least two and three respectively. In the present paper, we review the application of polypeptide-based material for the formation of material with nanometre-scale pores that can be used for the separation. Use of antiparallel coiled-coil dimerization domains introduces the possibility of modulation of pore size and chemical properties. Assembly or disassembly of bionanomaterials can be regulated by an external signal as demonstrated by the coumermycin-induced dimerization of the gyrase B domain which triggers the formation of polypeptide assembly.

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DNA nanotubes and helical nanotapes via self-assembly of ssDNA-amphiphiles

Soft Matter ◽

10.1039/c4sm01332h ◽

2015 ◽

Vol 11 (1) ◽

pp. 109-117 ◽

Cited By ~ 18

Author(s):

Timothy R. Pearce ◽

Efrosini Kokkoli

Keyword(s):

Secondary Structure ◽

Self Assembly ◽

Building Blocks ◽

The Self ◽

Hydrophobic Tail ◽

Dna Nanotubes ◽

Assembly Behavior

ssDNA-amphiphiles with three building blocks, a hydrophobic tail, a polycarbon spacer and different ssDNA headgroups that were created to explore the effect of DNA length and secondary structure on the self-assembly behavior of the amphiphiles, formed bilayer nanotapes that transitioned from twisted nanotapes, to helical nanotapes to nanotubes.

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Factors Affecting Molecular Self-Assembly and Its Mechanism

Scientific Research Journal ◽

10.24191/srj.v9i1.9414 ◽

2012 ◽

Vol 9 (1) ◽

pp. 43

Author(s):

Huey Ling Tan

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Molecular Engineering ◽

Molecular Structures ◽

Polymer Science ◽

Factors Affecting ◽

Dna Structures ◽

Self Assembling ◽

Wide Range ◽

And Control

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use of peptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study of biological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi- and tri-block copolymers to DNA structures as well as simple and complex proteins and peptides. The ultimate goal is to harness molecular self-assembly such that design and control of bottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes of life and non-life science applications. Such aspirations can be achieved through understanding the fundamental principles behind the self organisation and self-synthesis processes exhibited by biological systems.

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Segregation and activation of myosin IIB creates a rear in migrating cells

The Journal of Cell Biology ◽

10.1083/jcb.200806030 ◽

2008 ◽

Vol 183 (3) ◽

pp. 543-554 ◽

Cited By ~ 145

Author(s):

Miguel Vicente-Manzanares ◽

Margaret A. Koach ◽

Leanna Whitmore ◽

Marcelo L. Lamers ◽

Alan F. Horwitz

Keyword(s):

Self Assembly ◽

De Novo ◽

Coiled Coil ◽

Myosin Isoforms ◽

C Terminus ◽

Filament Bundles ◽

A Cell ◽

Myosin Iia ◽

And Function ◽

Migrating Cells

We have found that MLC-dependent activation of myosin IIB in migrating cells is required to form an extended rear, which coincides with increased directional migration. Activated myosin IIB localizes prominently at the cell rear and produces large, stable actin filament bundles and adhesions, which locally inhibit protrusion and define the morphology of the tail. Myosin IIA forms de novo filaments away from the myosin IIB–enriched center and back to form regions that support protrusion. The positioning and dynamics of myosin IIA and IIB depend on the self-assembly regions in their coiled-coil C terminus. COS7 and B16 melanoma cells lack myosin IIA and IIB, respectively; and show isoform-specific front-back polarity in migrating cells. These studies demonstrate the role of MLC activation and myosin isoforms in creating a cell rear, the segregation of isoforms during filament assembly and their differential effects on adhesion and protrusion, and a key role for the noncontractile region of the isoforms in determining their localization and function.

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Porous coordination polymers constructed from anisotropic metal–carboxylate–pyridyl clusters

Pure and Applied Chemistry ◽

10.1351/pac-con-12-06-08 ◽

2012 ◽

Vol 85 (2) ◽

pp. 405-416 ◽

Cited By ~ 12

Author(s):

Yue-Biao Zhang ◽

Jie-Peng Zhang

Keyword(s):

Coordination Polymers ◽

Self Assembly ◽

Rational Design ◽

Building Blocks ◽

Metal Carboxylate ◽

Porous Coordination Polymers ◽

Isotropic Metal ◽

And Control ◽

Anisotropic Metal

While isotropic metal–carboxylate clusters as secondary building blocks have enabled the rational design of porous coordination polymers (PCPs) with predictable topologies, augmented metal–carboxylate–pyridyl clusters can be used as anisotropic secondary building blocks to facilitate the construction of higher-connectivity frameworks and control over structural directionality in self-assembly.

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Flexible, symmetry-directed approach to assembling protein cages

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1606013113 ◽

2016 ◽

Vol 113 (31) ◽

pp. 8681-8686 ◽

Cited By ~ 60

Author(s):

Aaron Sciore ◽

Min Su ◽

Philipp Koldewey ◽

Joseph D. Eschweiler ◽

Kelsey A. Diffley ◽

...

Keyword(s):

Large Scale ◽

Analytical Ultracentrifugation ◽

De Novo ◽

Coiled Coil ◽

Building Blocks ◽

Structural Features ◽

Biological Properties ◽

Protein Subunits ◽

Linker Sequence ◽

Protein Cage

The assembly of individual protein subunits into large-scale symmetrical structures is widespread in nature and confers new biological properties. Engineered protein assemblies have potential applications in nanotechnology and medicine; however, a major challenge in engineering assemblies de novo has been to design interactions between the protein subunits so that they specifically assemble into the desired structure. Here we demonstrate a simple, generalizable approach to assemble proteins into cage-like structures that uses short de novo designed coiled-coil domains to mediate assembly. We assembled eight copies of a C3-symmetric trimeric esterase into a well-defined octahedral protein cage by appending a C4-symmetric coiled-coil domain to the protein through a short, flexible linker sequence, with the approximate length of the linker sequence determined by computational modeling. The structure of the cage was verified using a combination of analytical ultracentrifugation, native electrospray mass spectrometry, and negative stain and cryoelectron microscopy. For the protein cage to assemble correctly, it was necessary to optimize the length of the linker sequence. This observation suggests that flexibility between the two protein domains is important to allow the protein subunits sufficient freedom to assemble into the geometry specified by the combination of C4 and C3 symmetry elements. Because this approach is inherently modular and places minimal requirements on the structural features of the protein building blocks, it could be extended to assemble a wide variety of proteins into structures with different symmetries.

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