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

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.

scholarly journals Intracellular artificial supramolecules based on de novo designed Y15 peptides

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.

scholarly journals De novo design of self-assembling helical protein filaments

Science ◽  
2018 ◽  
Vol 362 (6415) ◽  
pp. 705-709 ◽  
Author(s):  
Hao Shen ◽  
Jorge A. Fallas ◽  
Eric Lynch ◽  
William Sheffler ◽  
Bradley Parry ◽  
...  
Keyword(s):  
De Novo ◽  
Computational Design ◽  
Building Blocks ◽  
Repeat Units ◽  
Self Assembling ◽  
Wide Range ◽  
Helical Protein ◽  
Monomeric Proteins

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.

scholarly journals Self-assembly of Functional Nanostructures by Short Helical Peptide Building Blocks

2019 ◽  
Vol 26 (2) ◽  
pp. 88-97 ◽  
Author(s):  
Santu Bera ◽  
Ehud Gazit
Keyword(s):  
Self Assembly ◽  
Amyloid Fibrils ◽  
Building Blocks ◽  
Smart Devices ◽  
Helical Peptides ◽  
Functional Roles ◽  
Mesoscale Structures ◽  
Self Assembling ◽  
Wide Range ◽  
Self Assembled

The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.

Biological Assembly of Modular Protein Building Blocks as Sensing, Delivery, and Therapeutic Agents

2020 ◽  
Vol 11 (1) ◽  
pp. 35-62 ◽  
Author(s):  
Emily A. Berckman ◽  
Emily J. Hartzell ◽  
Alexander A. Mitkas ◽  
Qing Sun ◽  
Wilfred Chen
Keyword(s):  
Protein Design ◽  
Biomedical Applications ◽  
De Novo ◽  
Building Blocks ◽  
Specific Protein ◽  
Therapeutic Agents ◽  
Biological Functions ◽  
Functional Protein ◽  
Wide Range ◽  
De Novo Protein Design

Nature has evolved a wide range of strategies to create self-assembled protein nanostructures with structurally defined architectures that serve a myriad of highly specialized biological functions. With the advent of biological tools for site-specific protein modifications and de novo protein design, a wide range of customized protein nanocarriers have been created using both natural and synthetic biological building blocks to mimic these native designs for targeted biomedical applications. In this review, different design frameworks and synthetic decoration strategies for achieving these functional protein nanostructures are summarized. Key attributes of these designer protein nanostructures, their unique functions, and their impact on biosensing and therapeutic applications are discussed.

ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES

2011 ◽  
Vol 03 (04) ◽  
pp. 667-684 ◽  
Author(s):  
LUIS RUIZ ◽  
SINAN KETEN
Keyword(s):  
Hydrogen Bonds ◽  
Large Scale ◽  
Shear Failure ◽  
Cyclic Peptide ◽  
Building Blocks ◽  
Great Promise ◽  
Deformation And Failure ◽  
Self Assembling ◽  
Self Assembled ◽  
Organic Nanotubes

Organic building blocks inspired by biological systems are promising for fabricating nanostructured materials for a broad range of applications such as antimicrobials, biosensors, electronics, and biomaterials. Self-assembling cyclic peptide organic nanotubes have shown great promise for these applications due to their precise structural features, diverse chemical functionalization capabilities and exceptional stability arising from arrangement of hydrogen bonds into cooperative clusters. Mechanical behavior of organic nanotubes is important for various possible applications ranging from subnanoporous selective membranes to molecular templates for electronics. However, large-scale deformation mechanisms of organic nanotubes have not been studied thus far. Here we investigate the mechanisms involved in the large deformation and failure of self-assembled organic nanotubes, focusing on geometry effects characteristic of protein nanostructures. We carry out molecular dynamics simulations to assess the role of hydrogen bonds as weak interactions in the context of deformation and failure processes involving bending and shear loads. Mechanisms of failure are found to depend on the cross-sectional geometry and the deformation rate, where a transition to localized shear failure is observed at high-strain rates. Our results provide important physical insight into the mechanics of organic nanotubes central to emerging applications of self-assembling peptides in biomedicine and biotechnology.

Recent advances in the fabrication and bio-medical applications of self-assembled dipeptide nanostructures

Nanomedicine ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. 139-163
Author(s):  
Sonika Chibh ◽  
Jibanananda Mishra ◽  
Avneet Kour ◽  
Virander S Chauhan ◽  
Jiban J Panda
Keyword(s):  
Significant Role ◽  
Self Assembly ◽  
Biomedical Applications ◽  
Building Blocks ◽  
Natural Phenomenon ◽  
Medical Applications ◽  
Self Assembling ◽  
Recent Advances ◽  
Potential Applications ◽  
Self Assembled

Molecular self-assembly is a widespread natural phenomenon and has inspired several researchers to synthesize a compendium of nano/microstructures with widespread applications. Biomolecules like proteins, peptides and lipids are used as building blocks to fabricate various nanomaterials. Supramolecular peptide self-assembly continue to play a significant role in forming diverse nanostructures with numerous biomedical applications; however, dipeptides offer distinctive supremacy in their ability to self-assemble and produce a variety of nanostructures. Though several reviews have articulated the progress in the field of longer peptides or polymers and their self-assembling behavior, there is a paucity of reviews or literature covering the emerging field of dipeptide-based nanostructures. In this review, our goal is to present the recent advancements in dipeptide-based nanostructures with their potential applications.

scholarly journals De Novo Design of a pH-triggered Self-assembled β-hairpin Nano Peptide for the Dual Biological Function of Antibacterial and Entrapment

2021 ◽  
Author(s):  
Qiuke Li ◽  
Jinze Li ◽  
Weikang Yu ◽  
Zhihua Wang ◽  
Jiawei Li ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
De Novo ◽  
Ph Regulation ◽  
Membrane Integrity ◽  
Intestinal Flora ◽  
Building Blocks ◽  
Self Assembled ◽  
High Concentrations

Abstract BackgroundAcid-tolerant enteric pathogens could evade small intestinal acid barriers, colonizing and infecting the intestinal tract. Whereas broad-spectrum antibiotics are not the best therapeutic strategy because of the disruption of intestinal flora caused by its indiscriminate antimicrobial activity against beneficial and harmful bacteria. So that is what inspired us to combine pH regulation with nanotechnology to develop a pH-triggered site-targeted antimicrobial peptide with entrapping function. ResultsAccording to the features of amino-acid building blocks and the diagonal cation–π interaction principle, a self-assembled peptide (SAP) was designed, and the results showed that changes in pH conditions could trigger the transformation of the microstructure of the nanopeptide, which has great antimicrobial activity against Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, and Bacillus cereus under acidic conditions by disrupting bacterial membrane integrity, and great biocompatibility in vivo and in vitro and high tolerance. Moreover, SAP at high concentrations showed the entrapment property, which plays an important role in phagocytic clearance in the infection forces.ConclusionsOur study revealed the antibacterial activity of a short β-hairpin forming self-assembled peptide and establishes an innovative design strategy for peptide-based nanomaterials and a new treatment strategy for gastrointestinal bacterial infection.

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

2019 ◽  
Vol 141 (22) ◽  
pp. 8891-8895 ◽  
Author(s):  
Zibo Chen ◽  
Matthew C. Johnson ◽  
Jiajun Chen ◽  
Matthew J. Bick ◽  
Scott E. Boyken ◽  
...  
Keyword(s):  
De Novo ◽  
Building Blocks ◽  
Self Assembling ◽  
2D Arrays

scholarly journals De novo design of a pH-triggered self-assembled β-hairpin nanopeptide with the dual biological functions for antibacterial and entrapment

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiuke Li ◽  
Jinze Li ◽  
Weikang Yu ◽  
Zhihua Wang ◽  
Jiawei Li ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Bacterial Infections ◽  
De Novo ◽  
Ph Regulation ◽  
Membrane Integrity ◽  
Intestinal Flora ◽  
Building Blocks ◽  
Self Assembled

Abstract Background Acid-tolerant enteric pathogens can evade small intestinal acid barriers, colonize and infect the intestinal tract. However, broad-spectrum antibiotics are not the best therapeutic strategy because of the disruption of intestinal flora caused by its indiscriminate antimicrobial activity against beneficial and harmful bacteria. So that is what inspired us to combine pH regulation with nanotechnology to develop a pH-triggered site-targeted antimicrobial peptide with entrapping function. Results A pH-triggered dual biological functional self-assembled peptide (SAP) was designed according to the features of amino-acid building blocks and the diagonal cation–π interaction principle. The results of characterization experiments showed that changes in pH conditions could trigger microstructural transformation of the nanopeptide from nanospheres to nanofibers. The subsequent antibacterial and toxicity experiments determined that SAP had great antimicrobial activity against Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, and Bacillus cereus above 15.6 μg/mL under acidic conditions by disrupting bacterial membrane integrity, excellent biocompatibility in vitro even at 250 μg/mL and high tolerance in physical environment. Moreover, at peptide concentrations greater than 62.5 μg/mL, SAP showed the entrapment property, which played an important role in phagocytic clearance in infection forces. Meanwhile, the in vivo results revealed that SAP possessed excellent therapeutic effect and good biosafety. Conclusions Our study revealed the antibacterial activity of a short β-hairpin forming self-assembled peptide, and established an innovative design strategy for peptide-based nanomaterials and a new treatment strategy for gastrointestinal bacterial infections. Graphic Abstract

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

2003 ◽  
Vol 773 ◽  
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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