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.

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.

scholarly journals A bottom-up approach for the de novo design of functional proteins

2020 ◽  
Author(s):  
Che Yang ◽  
Fabian Sesterhenn ◽  
Jaume Bonet ◽  
Eva van Aalen ◽  
Leo Scheller ◽  
...  
Keyword(s):  
Protein Design ◽  
Mammalian Cells ◽  
De Novo ◽  
Protein Structures ◽  
Functional Protein ◽  
Regular Secondary Structure ◽  
Bottom Up ◽  
Binding Motifs ◽  
Wide Range ◽  
Novel Protein

AbstractDe novo protein design has enabled the creation of novel protein structures. To design novel functional proteins, state-of-the-art approaches use natural proteins or first design protein scaffolds that subsequently serve as templates for the transplantation of functional motifs. In these approaches, the templates are function-agnostic and motifs have been limited to those with regular secondary structure. Here, we present a bottom-up approach to build de novo proteins tailored to structurally complex functional motifs. We applied a bottom-up strategy to design scaffolds for four different binding motifs, including one bi-functionalized protein with two motifs. The de novo proteins were functional as biosensors to quantify epitope-specific antibody responses and as orthogonal ligands to activate a signaling pathway in engineered mammalian cells. Altogether, we present a versatile strategy for the bottom-up design of functional proteins, applicable to a wide range of functional protein design challenges.

scholarly journals Expression of non-muscle type myosin heavy polypeptide 9 (MYH9) in mammalian cells

10.4081/845 ◽  
2009 ◽  
Vol 47 (4) ◽  
pp. 345 ◽  
Author(s):  
T Takubo ◽  
S Wakui ◽  
K Daigo ◽  
K Kurokata ◽  
T Ohashi ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Actin Polymerization ◽  
Fluorescent Protein ◽  
Myosin Ii ◽  
Type I ◽  
Myosin Heavy Chains ◽  
Functional Protein ◽  
Heavy Chains ◽  
Myosin I ◽  
Muscle Myosin

Myosin is a functional protein associated with cellular movement, cell division, muscle contraction and other functions. Members of the myosin super-family are distinguished from the myosin heavy chains that play crucial roles in cellular processes. Although there are many studies of myosin heavy chains in this family, there are fewer on non-muscle myosin heavy chains than of muscle myosin heavy chains. Myosin is classified as type I (myosin I) or type II (myosin II). Myosin I, called unconventional myosin or mini-myosin, has one head, while myosin II, called conventional myosin, has two heads. We transfected myosin heavy polypeptide 9 (MYH9) into HeLa cells as a fusion protein with enhanced green fluorescent protein (EGFP) and analyzed the localization and distribution of MYH9 in parallel with those of actin and tubulin. The results indicate that MYH9 colocalizes with actin stress fibers. Since it has recently been shown by genetic analysis that autosomal dominant giant platelet syndromes are MYH9-related disorders, our development of transfected EGFP-MYH9 might be useful for predicting the associations between the function of actin polymerization, the MYH9 motor domain, and these disorders.

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.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
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.

Artificial protein assemblies with well-defined supramolecular protein nanostructures

2021 ◽  
Author(s):  
Suyeong Han ◽  
Yongwon Jung
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
Building Blocks ◽  
Protein Assembly ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Wide Range ◽  
Array Structures ◽  
Small Chemical ◽  
Artificial Protein

Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.

Deciphering the route to cyclic monoterpenes in Chrysomelina leaf beetles: source of new biocatalysts for industrial application?

2017 ◽  
Vol 72 (9-10) ◽  
pp. 417-427 ◽  
Author(s):  
Antje Burse ◽  
Wilhelm Boland
Keyword(s):  
De Novo ◽  
Sustainable Use ◽  
Building Blocks ◽  
Leaf Beetle ◽  
Industrial Applications ◽  
Metabolic Diversity ◽  
Leaf Beetles ◽  
Wide Range ◽  
Extreme Habitats ◽  
Plant Sources

AbstractThe drastic growth of the population on our planet requires the efficient and sustainable use of our natural resources. Enzymes are indispensable tools for a wide range of industries producing food, pharmaceuticals, pesticides, or biofuels. Because insects constitute one of the most species-rich classes of organisms colonizing almost every ecological niche on earth, they have developed extraordinary metabolic abilities to survive in various and sometimes extreme habitats. Despite this metabolic diversity, insect enzymes have only recently generated interest in industrial applications because only a few metabolic pathways have been sufficiently characterized. Here, we address the biosynthetic route to iridoids (cyclic monoterpenes), a group of secondary metabolites used by some members of the leaf beetle subtribe Chrysomelina as defensive compounds against their enemies. The ability to produce iridoids de novo has also convergently evolved in plants. From plant sources, numerous pharmacologically relevant structures have already been described. In addition, in plants, iridoids serve as building blocks for monoterpenoid indole alkaloids with broad therapeutic applications. As the commercial synthesis of iridoid-based drugs often relies on a semisynthetic approach involving biocatalysts, the discovery of enzymes from the insect iridoid route can account for a valuable resource and economic alternative to the previously used enzymes from the metabolism of plants. Hence, this review illustrates the recent discoveries made on the steps of the iridoid pathway in Chrysomelina leaf beetles. The findings are also placed in the context of the studied counterparts in plants and are further discussed regarding their use in technological approaches.

scholarly journals Beyond icosahedral symmetry in packings of proteins in spherical shells

2017 ◽  
Vol 114 (34) ◽  
pp. 9014-9019 ◽  
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.

HeLa cells as a model to study the invasiveness and biology ofLegionella pneumophila

1998 ◽  
Vol 44 (5) ◽  
pp. 430-440 ◽  
Author(s):  
Rafael A Garduño ◽  
Frederick D Quinn ◽  
Paul S Hoffman
Keyword(s):  
Hela Cells ◽  
Legionella Pneumophila ◽  
Mammalian Cells ◽  
Actin Polymerization ◽  
De Novo ◽  
Model System ◽  
Invasion Mechanisms ◽  
Virulent Strains ◽  
Host Parasite ◽  
Bacterial Protein Synthesis

HeLa cells were established as a model system to study the invasiveness and biology of Legionella pneumophila. In this model, invasion could be distinguished from adherence; virulent strains of L. pneumophila were adherent and invasive, whereas nonvirulent strains were adherent but poorly invasive. Invasion was rapid and did not require de novo bacterial protein synthesis, suggesting that the invasion factor is constitutively expressed by virulent strains. Entry into HeLa cells required actin polymerization and an intact microtubule cytoskeleton and was only moderately inhibited by the presence of 100 mM glucose or galactose. Intracellular replication of virulent L. pneumophila took place in ribosome-studded complex endosomes and led to the formation of free bacteria-laden vesicles presumably released from lysed HeLa cells, These free vesicles (referred to as mature vesicles) were isolated in continuous density gradients of Percoll. The bacteria contained in the isolated mature vesicles had a unique envelope structure and were highly adherent to HeLa cells, characteristics that correlated with a bright red appearance after the Giménez stain (Giménez positive). Plate-grown legionellae and replicating legionellae, harboured in complex endosomes, displayed a typical Gram-negative envelope and stained green after the Giménez stain (Giménez negative). Chronically infected cultures of HeLa cells were also established that may be a useful tool for studying long-term interactions between virulent L. pneumophila and mammalian cells. HeLa cells constitute a valuable model system that offers unique opportunities to study parasite-directed endocytosis, as well as stage specific host-parasite interactions.Key words: Legionella pneumophila, HeLa cells, invasion mechanisms, intracellular pathogens.

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