Self-assembled artificial viral capsids bearing coiled-coils at the surface

We demonstrated a simple strategy for constructing enveloped artificial viral capsids by self-assembly of anionic artificial viral capsid and lipid bilayer containing cationic lipid.

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Molecular design of stapled pentapeptides as building blocks of self-assembled coiled coil–like fibers

Science Advances ◽

10.1126/sciadv.abd0492 ◽

2021 ◽

Vol 7 (4) ◽

pp. eabd0492

Author(s):

Yixiang Jiang ◽

Wan Zhang ◽

Fadeng Yang ◽

Chuan Wan ◽

Xiang Cai ◽

...

Keyword(s):

Self Assembly ◽

Molecular Design ◽

Chemical Space ◽

Coiled Coil ◽

Building Blocks ◽

Coiled Coils ◽

Computational Method ◽

Side Chain ◽

Chain Flexibility ◽

Self Assembled

Peptide self-assembly inspired by natural superhelical coiled coils has been actively pursued but remains challenging due to limited helicity of short peptides. Side chain stapling can strengthen short helices but is unexplored in design of self-assembled helical nanofibers as it is unknown how staples could be adapted to coiled coil architecture. Here, we demonstrate the feasibility of this design for pentapeptides using a computational method capable of predicting helicity and fiber-forming tendency of stapled peptides containing noncoded amino acids. Experiments showed that the best candidates, which carried an aromatically substituted staple and phenylalanine analogs, displayed exceptional helicity and assembled into nanofibers via specific head-to-tail hydrogen bonding and packing between staple and noncoded side chains. The fibers exhibited sheet-of-helix structures resembling the recently found collapsed coiled coils whose formation was sensitive to side chain flexibility. This study expands the chemical space of coiled coil assemblies and provides guidance for their design.

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A Photoresponsive Artificial Viral Capsid Self-Assembled from an Azobenzene-Containing β-Annulus Peptide

International Journal of Molecular Sciences ◽

10.3390/ijms22084028 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4028

Author(s):

Kazunori Matsuura ◽

Seiya Fujita

Keyword(s):

Uv Irradiation ◽

Structural Changes ◽

Solid Phase ◽

Viral Capsid ◽

Trans Form ◽

Peptide Backbone ◽

Viral Capsids ◽

Azobenzene Moiety ◽

Self Assembled ◽

Peptide Materials

Photoinduced structural changes in peptides can dynamically control the formation and dissociation of supramolecular peptide materials. However, the existence of photoresponsive viral capsids in nature remains unknown. In this study, we constructed an artificial viral capsid possessing a photochromic azobenzene moiety on the peptide backbone. An azobenzene-containing β-annulus peptide derived from the tomato bushy stunt virus was prepared through solid-phase synthesis using Fmoc-3-[(3-aminomethyl)-phenylazo]phenylacetic acid. The azobenzene-containing β-annulus (β-Annulus-Azo) peptide showed a reversible trans/cis isomerization property. The β-annulus-azo peptide self-assembled at 25 μM into capsids with the diameters of 30–50 nm before UV irradiation (trans-form rich), whereas micrometer-sized aggregates were formed after UV irradiation (cis-form rich). The artificial viral capsid possessing azobenzene facilitated the encapsulation of fluorescent-labeled dextrans and their photoinduced release from the capsid.

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Coiled-coil networking shapes cell molecular machinery

Molecular Biology of the Cell ◽

10.1091/mbc.e12-05-0396 ◽

2012 ◽

Vol 23 (19) ◽

pp. 3911-3922 ◽

Cited By ~ 44

Author(s):

Yongqiang Wang ◽

Xinlei Zhang ◽

Hong Zhang ◽

Yi Lu ◽

Haolong Huang ◽

...

Keyword(s):

Protein Interactions ◽

Critical Role ◽

Coiled Coil ◽

Coiled Coils ◽

Protein Protein Interactions ◽

Full Spectrum ◽

Kinetochore Assembly ◽

Genome Wide ◽

Molecular Machinery ◽

Systematic Understanding

The highly abundant α-helical coiled-coil motif not only mediates crucial protein–protein interactions in the cell but is also an attractive scaffold in synthetic biology and material science and a potential target for disease intervention. Therefore a systematic understanding of the coiled-coil interactions (CCIs) at the organismal level would help unravel the full spectrum of the biological function of this interaction motif and facilitate its application in therapeutics. We report the first identified genome-wide CCI network in Saccharomyces cerevisiae, which consists of 3495 pair-wise interactions among 598 predicted coiled-coil regions. Computational analysis revealed that the CCI network is specifically and functionally organized and extensively involved in the organization of cell machinery. We further show that CCIs play a critical role in the assembly of the kinetochore, and disruption of the CCI network leads to defects in kinetochore assembly and cell division. The CCI network identified in this study is a valuable resource for systematic characterization of coiled coils in the shaping and regulation of a host of cellular machineries and provides a basis for the utilization of coiled coils as domain-based probes for network perturbation and pharmacological applications.

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ARCIMBOLDOon coiled coils

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317017582 ◽

2018 ◽

Vol 74 (3) ◽

pp. 194-204 ◽

Cited By ~ 14

Author(s):

Iracema Caballero ◽

Massimo Sammito ◽

Claudia Millán ◽

Andrey Lebedev ◽

Nicolas Soler ◽

...

Keyword(s):

Coiled Coil ◽

Coiled Coils ◽

Translational Symmetry ◽

Command Line ◽

Phase Problem ◽

Final Solution ◽

Resolution Limit ◽

Helical Structures ◽

Small Model ◽

Test Pool

ARCIMBOLDOsolves the phase problem by combining the location of small model fragments usingPhaserwith density modification and autotracing usingSHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers.ARCIMBOLDO_LITEhas been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures usingARCIMBOLDO. Features fromPhaserv.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification andSHELXEautotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode withinARCIMBOLDOfor the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) orARCIMBOLDO_LITEtask interface inCCP4i.

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α/β coiled coils

eLife ◽

10.7554/elife.11861 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 14

Author(s):

Marcus D Hartmann ◽

Claudia T Mendler ◽

Jens Bassler ◽

Ioanna Karamichali ◽

Oswin Ridderbusch ◽

...

Keyword(s):

Repeat Unit ◽

Coiled Coil ◽

Coiled Coils ◽

Heptad Repeat ◽

Protein Fold ◽

Local Formation ◽

Unexpected Formation ◽

New Type ◽

Backbone Structure ◽

Level Of Understanding

Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be described by parametric equations. This level of understanding has allowed their manipulation in unprecedented detail. They do not seem a likely source of surprises, yet we describe here the unexpected formation of a new type of fiber by the simple insertion of two or six residues into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the supercoil to the breaking point, causing the local formation of short β-strands, which move the path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains only one backbone hydrogen bond per repeat unit from the parent coiled coil. Our results show that a substantially novel backbone structure is possible within the allowed regions of the Ramachandran space with only minor mutations to a known fold.

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Integration of Rotation and Piston Motions in Coiled-Coil Signal Transduction

Journal of Bacteriology ◽

10.1128/jb.00459-07 ◽

2007 ◽

Vol 189 (16) ◽

pp. 6048-6056 ◽

Cited By ~ 22

Author(s):

Rong Gao ◽

David G. Lynn

Keyword(s):

Coiled Coil ◽

Dynamic Environment ◽

Coiled Coils ◽

Signal Integration ◽

Signaling Mechanisms ◽

Protein Receptor ◽

Single Protein ◽

Environmental Responses ◽

Multiple Signaling ◽

Host Signals

ABSTRACT A coordinated response to a complex and dynamic environment requires an organism to simultaneously monitor and interpret multiple signaling cues. In bacteria and some eukaryotes, environmental responses depend on the histidine autokinases (HKs). For example, VirA, a large integral membrane HK from Agrobacterium tumefaciens, regulates the expression of virulence genes in response to signals from multiple molecular classes (phenol, pH, and sugar). The ability of this pathogen to perceive inputs from different known host signals within a single protein receptor provides an opportunity to understand the mechanisms of signal integration. Here we exploited the conserved domain organization of the HKs and engineered chimeric kinases to explore the signaling mechanisms of phenol sensing and pH/sugar integration. Our data implicate a piston-assisted rotation of coiled coils for integration of multiple inputs and regulation of critical responses during pathogenesis.

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Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures

International Journal of Molecular Sciences ◽

10.3390/ijms21103584 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3584 ◽

Cited By ~ 1

Author(s):

Won Min Park

Keyword(s):

Modular Design ◽

Coiled Coil ◽

Molecular Complexes ◽

Building Blocks ◽

Structural Features ◽

Coiled Coils ◽

Design Strategies ◽

Protein Motifs ◽

Self Assembling ◽

Current Design

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.

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