scholarly journals Self-assembling Supramolecular Complex Nanostructures Constructed from de Novo Protein Nanobuilding Blocks

2018 ◽  
Vol 58 (6) ◽  
pp. 313-315
Author(s):  
Naoya KOBAYASHI ◽  
Ryoichi ARAI
Keyword(s):  
De Novo ◽  
Supramolecular Complex ◽  
Self Assembling ◽  
Nanobuilding Blocks ◽  
Complex Nanostructures

Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks

2018 ◽  
Vol 7 (5) ◽  
pp. 1381-1394 ◽  
Author(s):  
Naoya Kobayashi ◽  
Kouichi Inano ◽  
Kenji Sasahara ◽  
Takaaki Sato ◽  
Keisuke Miyazawa ◽  
...  
Keyword(s):  
De Novo ◽  
Self Assembling ◽  
Nanobuilding Blocks

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

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.

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 Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
George Ueda ◽  
Aleksandar Antanasijevic ◽  
Jorge A Fallas ◽  
William Sheffler ◽  
Jeffrey Copps ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
De Novo ◽  
Viral Glycoprotein ◽  
Influenza Hemagglutinin ◽  
Self Assembling ◽  
Cryo Electron Microscopy ◽  
Viral Glycoproteins ◽  
Protein Nanoparticles ◽  
New Generation ◽  
Tailored Design

Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first de novo designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.

De novo synthesis and properties of analogues of the self-assembling chlorosomal bacteriochlorophylls

2011 ◽  
Vol 35 (11) ◽  
pp. 2671 ◽  
Author(s):  
Olga Mass ◽  
Dinesh R. Pandithavidana ◽  
Marcin Ptaszek ◽  
Koraliz Santiago ◽  
Joseph W. Springer ◽  
...  
Keyword(s):  
De Novo ◽  
The Self ◽  
De Novo Synthesis ◽  
Self Assembling

scholarly journals Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160214 ◽  
Author(s):  
Nathan H. Joh ◽  
Gevorg Grigoryan ◽  
Yibing Wu ◽  
William F. DeGrado
Keyword(s):  
Protein Folding ◽  
Membrane Protein ◽  
Protein Design ◽  
De Novo ◽  
Cell Signalling ◽  
Membrane Protein Folding ◽  
Cellular Processes ◽  
Membrane Pores ◽  
Self Assembling ◽  
And Function

Ion transporters and channels are able to identify and act on specific substrates among myriads of ions and molecules critical to cellular processes, such as homeostasis, cell signalling, nutrient influx and drug efflux. Recently, we designed Rocker, a minimalist model for Zn 2+ /H + co-transport. The success of this effort suggests that de novo membrane protein design has now come of age so as to serve a key approach towards probing the determinants of membrane protein folding, assembly and function. Here, we review general principles that can be used to design membrane proteins, with particular reference to helical assemblies with transport function. We also provide new functional and NMR data that probe the dynamic mechanism of conduction through Rocker. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

Self-Assembling Nanostructures: Recognition and Ordered Assembly in Protein-Based Materials

1992 ◽  
Vol 292 ◽  
Author(s):  
Kevin P. McGrath ◽  
David L. Kaplan
Keyword(s):  
De Novo ◽  
Specific Interaction ◽  
Rational Approach ◽  
New Approach ◽  
Consensus Sequences ◽  
Specific Recognition ◽  
Self Assembling ◽  
Biological Recognition ◽  
Recognition Elements ◽  
Recombinant Polypeptides

AbstractA new approach to materials design is presented, utilizing specific recognition and assembly at the molecular level. The approach described exploits the control over polymer chain microstructure afforded by biosynthesis to produce proteinbased materials with precisely defined physical properties. Incorporated into these materials are recognition elements that stringently control the placement and organization of each chain within higher order superstructures. The proteins, designated Recognin A2 through Recognin E2, are recombinant polypeptides designed de novo from both natural consensus sequences and an appreciation of the physical principles governing biological recognition. These materials are designed to examine the forces involved in specific recognition and complexation. through control of charge identity and placement, a pattern for specific interaction can be introduced. A subset of these materials are programmed to spontaneously assemble into complex, multicomponent structures and represent the first step in a rational approach to nanometer-scale structural design.

Beyond the heteroepitaxial quantum dot: Self-assembling complex nanostructures controlled by strain and growth kinetics

2005 ◽  
Vol 72 (15) ◽  
Author(s):  
J. L. Gray ◽  
R. Hull ◽  
Chi-Hang Lam ◽  
P. Sutter ◽  
J. Means ◽  
...  
Keyword(s):  
Quantum Dot ◽  
Growth Kinetics ◽  
Self Assembling ◽  
Complex Nanostructures

Peptide α-helices for synthetic nanostructures

2007 ◽  
Vol 35 (3) ◽  
pp. 487-491 ◽  
Author(s):  
M.G. Ryadnov
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Three Dimensional ◽  
Functional Materials ◽  
Protein Assemblies ◽  
Helical Peptides ◽  
Design Rules ◽  
Natural Protein ◽  
Self Assembling ◽  
Recent Developments

Supramolecular structures arising from a broad range of chemical archetypes are of great technological promise. Defining such structures at the nanoscale is crucial to access principally new types of functional materials for applications in bionanotechnology. In this vein, biomolecular self-assembly has emerged as an efficient approach for building synthetic nanostructures from the bottom up. The approach predominantly employs the spontaneous folding of biopolymers to monodisperse three-dimensional shapes that assemble into hierarchically defined mesoscale composites. An immediate interest here is the extraction of reliable rules that link the chemistry of biopolymers to the mechanisms of their assembly. Once established these can be further harnessed in designing supramolecular objects de novo. Different biopolymer classes compile a rich repertoire of assembly motifs to facilitate the synthesis of otherwise inaccessible nanostructures. Among those are peptide α-helices, ubiquitous folding elements of natural protein assemblies. These are particularly appealing candidates for prescriptive supramolecular engineering, as their well-established and conservative design rules give unmatched predictability and rationale. Recent developments of self-assembling systems based on helical peptides, including fibrous systems, nanoscale linkers and reactors will be highlighted herein.

scholarly journals A de novo self-assembling peptide hydrogel biosensor with covalently immobilised DNA-recognising motifs

2016 ◽  
Vol 52 (40) ◽  
pp. 6697-6700 ◽  
Author(s):  
Patrick J. S. King ◽  
Alberto Saiani ◽  
Elena V. Bichenkova ◽  
Aline F. Miller
Keyword(s):  
De Novo ◽  
External Surface ◽  
Rna Sequences ◽  
Fluorescence Response ◽  
Self Assembling ◽  
Recognition Elements ◽  
Peptide Hydrogel

The conjugate co-assemblies within the peptide-rich fibres leaving oligonucleotide recognition elements exposed on the external surface of the peptide fibre to ‘fish out’ DNA/RNA sequences, leading to a fluorescence response.

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