Self-Assembling 2D Arrays with de Novo Protein Building Blocks

We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

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Intracellular artificial supramolecules based on de novo designed Y15 peptides

Nature Communications ◽

10.1038/s41467-021-23794-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Takayuki Miki ◽

Taichi Nakai ◽

Masahiro Hashimoto ◽

Keigo Kajiwara ◽

Hiroshi Tsutsumi ◽

...

Keyword(s):

Mammalian Cells ◽

Actin Polymerization ◽

Fluorescent Protein ◽

De Novo ◽

Adaptor Protein ◽

Building Blocks ◽

Vaccine Adjuvants ◽

Functional Protein ◽

Self Assembling ◽

Wide Range

AbstractDe novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms β-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles into fibrils and is observed as fluorescent puncta in mammalian cells. Y15 self-assembly is validated by fluorescence anisotropy and pull-down assays. By using the Y15 platform, we demonstrate intracellular reconstitution of Nck assembly, a Src-homology 2 and 3 domain-containing adaptor protein. The artificial clusters of Nck induce N-WASP (neural Wiskott-Aldrich syndrome protein)-mediated actin polymerization, and the functional importance of Nck domain valency and density is evaluated.

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Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans

International Journal of Molecular Sciences ◽

10.3390/ijms23020676 ◽

2022 ◽

Vol 23 (2) ◽

pp. 676

Author(s):

Shin Irumagawa ◽

Keiko Hiemori ◽

Sayoko Saito ◽

Hiroaki Tateno ◽

Ryoichi Arai

Keyword(s):

De Novo ◽

Building Blocks ◽

Cell Labeling ◽

Carbohydrate Binding ◽

Specific Cell ◽

High Avidity ◽

Functional Protein ◽

Self Assembling ◽

Self Assembled ◽

Binding Avidity

Lectins, carbohydrate-binding proteins, are attractive biomolecules for medical and biotechnological applications. Many lectins have multiple carbohydrate recognition domains (CRDs) and strongly bind to specific glycans through multivalent binding effect. In our previous study, protein nano-building blocks (PN-blocks) were developed to construct self-assembling supramolecular nanostructures by linking two oligomeric proteins. A PN-block, WA20-foldon, constructed by fusing a dimeric four-helix bundle de novo protein WA20 to a trimeric foldon domain of T4 phage fibritin, self-assembled into several types of polyhedral nanoarchitectures in multiples of 6-mer. Another PN-block, the extender PN-block (ePN-block), constructed by tandemly joining two copies of WA20, self-assembled into cyclized and extended chain-type nanostructures. This study developed novel functional protein nano-building blocks (lectin nano-blocks) by fusing WA20 to a dimeric lectin, Agrocybe cylindracea galectin (ACG). The lectin nano-blocks self-assembled into various oligomers in multiples of 2-mer (dimer, tetramer, hexamer, octamer, etc.). The mass fractions of each oligomer were changed by the length of the linkers between WA20 and ACG. The binding avidity of the lectin nano-block oligomers to glycans was significantly increased through multivalent effects compared with that of the original ACG dimer. Lectin nano-blocks with high avidity will be useful for various applications, such as specific cell labeling.

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Combinatorial Peptide Libraries for Selecting Inorganic-Binding Proteins: A Step in Molecular Biomimetics

MRS Proceedings ◽

10.1557/proc-773-n8.1 ◽

2003 ◽

Vol 773 ◽

Cited By ~ 1

Author(s):

C. Tamerler ◽

S. Dinçer ◽

D. Heidel ◽

N. Karagûler ◽

M. Sarikaya

Keyword(s):

Binding Proteins ◽

Building Blocks ◽

Molecular Engineering ◽

Inorganic Materials ◽

Combinatorial Peptide Libraries ◽

Self Assembling ◽

Complex Functions ◽

Recent Developments ◽

Specific Proteins ◽

Molecular Biomimetics

AbstractProteins, one of the building blocks in organisms, not only control the assembly in biological systems but also provide most of their complex functions. It may be possible to assemble materials for practical technological applications utilizing the unique advantages provided by proteins. Here we discuss molecular biomimetic pathways in the quest for imitating biology at the molecular scale via protein engineering. We use combinatorial biology protocols to select short polypeptides that have affinity to inorganic materials and use them in assembling novel hybrid materials. We give an overview of some of the recent developments of molecular engineering towards this goal. Inorganic surface specific proteins were identified by using cell surface and phage display technologies. Examples of metal and metal oxide specific polypeptides were represented with an emphasis on certain level of specificities. The recognition and self assembling characteristics of these inorganic-binding proteins would be employed in develeopment of hybrid multifunctional materials for novel bio- and nano-technological applications.

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Factors Affecting Molecular Self-Assembly and Its Mechanism

Scientific Research Journal ◽

10.24191/srj.v9i1.5385 ◽

2012 ◽

Vol 9 (1) ◽

pp. 43 ◽

Cited By ~ 1

Author(s):

Hueyling Tan

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Molecular Engineering ◽

Molecular Structures ◽

Polymer Science ◽

New Approach ◽

Factors Affecting ◽

Dna Structures ◽

Self Assembling ◽

Wide Range

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 ofpeptides 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 ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

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Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

Nature Communications ◽

10.1038/s41467-020-20689-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Fengbin Wang ◽

Ordy Gnewou ◽

Charles Modlin ◽

Leticia C. Beltran ◽

Chunfu Xu ◽

...

Keyword(s):

Structural Analysis ◽

Synthetic Peptide ◽

Quaternary Structure ◽

De Novo ◽

Rational Approach ◽

Lateral Interactions ◽

Protein Assemblies ◽

Self Assembling ◽

Arginine Residues ◽

Insight Into

AbstractThe exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

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