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.

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 On the dynamics of some small structural motifs in rRNA upon ligand binding

2008 ◽  
Vol 73 (1) ◽  
pp. 41-53
Author(s):  
Aleksandra Rakic ◽  
Petar Mitrasinovic
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Binding Sites ◽  
De Novo ◽  
Reference Structure ◽  
Base Pairs ◽  
Rna Sequences ◽  
Conformational Model ◽  
Thermodynamic Variables ◽  
Dynamics Simulations

The present study characterizes using molecular dynamics simulations the behavior of the GAA (1186-1188) hairpin triloops with their closing c-g base pairs in large ribonucleoligand complexes (PDB IDs: 1njn, 1nwy, 1jzx). The relative energies of the motifs in the complexes with respect to that in the reference structure (unbound form of rRNA; PDB ID: 1njp) display the trends that agree with those of the conformational parameters reported in a previous study1 utilizing the de novo pseudotorsional (?,?) approach. The RNA regions around the actual RNA-ligand contacts, which experience the most substantial conformational changes upon formation of the complexes were identified. The thermodynamic parameters, based on a two-state conformational model of RNA sequences containing 15, 21 and 27 nucleotides in the immediate vicinity of the particular binding sites, were evaluated. From a more structural standpoint, the strain of a triloop, being far from the specific contacts and interacting primarily with other parts of the ribosome, was established as a structural feature which conforms to the trend of the average values of the thermodynamic variables corresponding to the three motifs defined by the 15-, 21- and 27-nucleotide sequences. From a more functional standpoint, RNA-ligand recognition is suggested to be presumably dictated by the types of ligands in the complexes.

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 Trypsin Pre‐Treatment Combined With Growth Factor Functionalized Self‐Assembling Peptide Hydrogel Improves Cartilage Repair in Rabbit Model

2019 ◽  
Vol 37 (11) ◽  
pp. 2307-2315 ◽  
Author(s):  
Gustavo Zanotto ◽  
Paul Liebesny ◽  
Myra Barrett ◽  
Hannah Zlotnick ◽  
Alan Grodzinsky ◽  
...  
Keyword(s):  
Growth Factor ◽  
Cartilage Repair ◽  
Rabbit Model ◽  
Self Assembling ◽  
Pre Treatment ◽  
Peptide Hydrogel

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 Investigating the In Vivo Antimicrobial Activity of a Self-Assembling Peptide Hydrogel Using a Galleria mellonella Infection Model

ACS Omega ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 2584-2589 ◽  
Author(s):  
Alice P. McCloskey ◽  
Merissa Lee ◽  
Julianne Megaw ◽  
Judith McEvoy ◽  
Sophie M. Coulter ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Galleria Mellonella ◽  
Infection Model ◽  
Self Assembling ◽  
Peptide Hydrogel
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