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.

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 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.

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.

scholarly journals Advances in emergent biological recognition elements and bioelectronics for diagnosing COVID-19

2021 ◽  
Vol 4 (1) ◽  
pp. 231-247
Author(s):  
Praopim Limsakul ◽  
Krit Charupanit ◽  
Chochanon Moonla ◽  
Itthipon Jeerapan
Keyword(s):  
Biological Recognition ◽  
Recognition Elements

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 Accurate long-read de novo assembly evaluation with Inspector

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Chen ◽  
Yixin Zhang ◽  
Amy Y. Wang ◽  
Min Gao ◽  
Zechen Chong
Keyword(s):  
Genome Assembly ◽  
De Novo Assembly ◽  
In Silico ◽  
Large Scale ◽  
De Novo ◽  
Small Scale ◽  
De Novo Genome Assembly ◽  
Consensus Sequences ◽  
Assembly Evaluation ◽  
Long Read

AbstractLong-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors.

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

Self Assembled Monolayers and Carbon Nanotubes: A Significant Tool’s for Modification of Electrode Surface

2020 ◽  
Vol 18 (9) ◽  
pp. 669-685
Author(s):  
Padmaker Pandey ◽  
Anamika Pandey ◽  
Shruti Singh ◽  
Nikhil Kant Shukla
Keyword(s):  
Carbon Nanotubes ◽  
Volume Ratio ◽  
Biological Molecules ◽  
Self Assembled Monolayers ◽  
Self Assembling ◽  
Biological Surfaces ◽  
Biological Recognition ◽  
Monomolecular Films ◽  
Assembled Monolayers ◽  
Interfacial Surfaces

A compromising and well-organized model system is needed for investigating the molecular behaviour of biomolecules as many transduction processes and biological recognition occur at biological surfaces. The application of techniques in interfacial surfaces like one molecule thick films has made a feasible and significant tool for modern scientific studies. Self Assembling Monolayers (SAMs) technology is a very useful means for producing monomolecular films of various biological molecules on different substrates. Carbon Nanotubes (CNTs) have length-to-diameter aspect ratio property which provides a large surface-to-volume ratio, making it an intensely capable material for biomolecular attachments. The incorporation of Carbon Nanotubes (CNTs) with biological systems forming functional assemblies has shown an explored area of research. Organo-sulfur mainly alkanethiol (CnH2n+1–SH) molecules get adsorbed onto CNTs. This phenomenon has grabbed a lot of attention because Self Assembling Monolayers (SAMs) of organo-sulfur compound acts as an example system for understanding important chemical, physical or biological processes.

scholarly journals Analysis of DDT Isomers with Enzyme-Linked Immunosorbent Assay and Optical Immunosensor Based on Rat Monoclonal Antibodies as Biological Recognition Elements

2010 ◽  
Vol 93 (1) ◽  
pp. 44-58 ◽  
Author(s):  
Petra M Krämer ◽  
Cristina M Weber ◽  
Stephan Forster ◽  
Peter Rauch ◽  
Elisabeth Kremmer
Keyword(s):  
Monoclonal Antibodies ◽  
Enzyme Linked Immunosorbent Assay ◽  
Lambda Light Chain ◽  
Optical Readout ◽  
Biological Recognition ◽  
Optical Immunosensor ◽  
Recognition Elements ◽  
Field Excitation ◽  
Phosphate Buffered Saline ◽  
Surface Water Samples

Abstract New rat monoclonal antibodies (mAbs) for DDT [1,1,1-trichloro-2,2-bis (4-chlorophenyl) ethane], namely DDT 7C12, DDT 1C1, and DDT 1B2, were developed, characterized, and applied in ELISA both in coating antigen and in enzyme-tracer format. The latter used horseradish peroxidase (HRP) or glucose oxidase as enzymes. The lowest concentration of p,p-DDT was determined with mAb DDT 7C12 and DDT-hapten HRP, with a test midpoint (IC50) of 0.5 ± 0.2 µg/L (n = 10) in 40 mM PBS (phosphate-buffered saline). The mouse anti-rat immunoglobulin lambda-light chain mAb LA1B12 was used as capture mAb. The best IC50 for o,p´-DDT in 40 mM PBS was 1.0 ± 0.3 µg/L (n = 12) and was obtained with mAb DDT 1C1 and DDT-hapten HRP, whereas mAb DDT 1B2 was very selective for p,p-DDT with an IC50 of 4.2 ± 1.6 µg/L (in 40 mM PBS, n = 9). An optical immunosensor was optimized and applied for the analysis of DDT (or DDT equivalents). This immunosensor consists of a bench-top optical readout device and disposable sensor chips, which include the fluidic system. Evanescent field excitation and emission of the fluorophore Oyster<sup/>-645 was used. An IC50 for p,p´-DDT [in 5 (v/v) isopropanol in 40 mM PBS] of 4 µg/L was obtained using DDT 7C12-Oyster-645. ELISA and immunosensor were used for the analysis of p,p-DDT in unspiked and spiked surface water samples. Within the working ranges of these immunotechniques, recoveries ranged from 80 to 120.

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