De novo supraparticle construction by a self-assembled Janus cyclopeptide to tame hydrophilic microRNA and hydrophobic molecule for anti-tumor cocktail therapy and augmented immunity

2020 ◽  
Vol 401 ◽  
pp. 126080
Author(s):  
Junjun She ◽  
Yaguang Li ◽  
Siqi Yan ◽  
Yuwei Yan ◽  
Dan Liu ◽  
...  
Keyword(s):  
De Novo ◽  
Hydrophobic Molecule ◽  
Self Assembled

De novo synthesis of pH-responsive, self-assembled, and targeted polypeptide nano-micelles for enhanced delivery of doxorubicin

2021 ◽  
Author(s):  
Longbao Zhu ◽  
Wen-liang Xu ◽  
Weiwei Zhang ◽  
Ming-cai Wu ◽  
Wanzhen Li ◽  
...  
Keyword(s):  
De Novo ◽  
Ph Responsive ◽  
De Novo Synthesis ◽  
Self Assembled

scholarly journals MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

2020 ◽  
Vol 48 (9) ◽  
pp. 5135-5146 ◽  
Author(s):  
Christopher Maffeo ◽  
Aleksei Aksimentiev
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Dna Nanotechnology ◽  
Equilibrium Structure ◽  
Molecular Graphics ◽  
Structure And Dynamics ◽  
Self Assembled ◽  
Actual Shape ◽  
And Function ◽  
Assembly Principles

Abstract Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

scholarly journals Comprehensive Fitness Landscape of a Multi-Geometry Protein Capsid Informs Machine Learning Models of Assembly

2021 ◽  
Author(s):  
Daniel D. Brauer ◽  
Celine B. Santiago ◽  
Zoe N. Merz ◽  
Esther McCarthy ◽  
Danielle Tullman-Ercek ◽  
...  
Keyword(s):  
Machine Learning ◽  
In Silico ◽  
Quaternary Structure ◽  
De Novo ◽  
Fitness Landscape ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Particle Assembly ◽  
Complex Particle ◽  
Self Assembled

Virus-like particles (VLPs) are non-infections viral-derived nanomaterials poised for biotechnological applications due to their well-defined, modular self-assembling architecture. Although progress has been made in understanding the complex effects that mutations may have on VLPs, nuanced understanding of the influence particle mutability has on quaternary structure has yet to be achieved. Here, we generate and compare the apparent fitness landscapes of two capsid geometries (T=3 and T=1 icosahedral) of the bacteriophage MS2 VLP. We find significant shifts in mutability at the symmetry interfaces of the T=1 capsid when compared to the wildtype T=3 assembly. Furthermore, we use the generated landscapes to benchmark the performance of in silico mutational scanning tools in capturing the effect of missense mutation on complex particle assembly. Finding that predicted stability effects correlated relatively poorly with assembly phenotype, we used a combination of de novo features in tandem with in silico results to train machine learning algorithms for the classification of variant effects on assembly. Our findings not only reveal ways that assembly geometry affects the mutable landscape of a self-assembled particle, but also establish a template for the generation of predictive mutational models of self-assembled capsids using minimal empirical training data.

De novo design of Self-assembly Hydrogels based on Fmoc-diphenylalanine Providing with Drug Release

2021 ◽  
Author(s):  
Xiang Li ◽  
Huijun Zhang ◽  
Lingyan Liu ◽  
Chunyan Cao ◽  
Peng Wei ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Drug Delivery System ◽  
Delivery System ◽  
Self Assembly ◽  
De Novo ◽  
De Novo Design ◽  
Short Peptides ◽  
Self Assembled

The short peptides with self-assembled nanostructures are widely applied in the areas of drug delivery system and biomaterials. In this article, we create a new peptide-based hydrogelator (Fmoc-FFRRVR) based on...

Supramolecular Structure and Stability of the GNNQQNY β-Sheet Bilayer Filament: A Computational Study

2007 ◽  
Author(s):  
Jiyong Park ◽  
Byungnam Kahng ◽  
Wonmuk Hwang
Keyword(s):  
Self Assembly ◽  
Amyloid Fibrils ◽  
De Novo ◽  
Structural Information ◽  
Computational Study ◽  
Molecular Structures ◽  
Theoretical Approaches ◽  
Self Assembled ◽  
Β Sheet

Self-assembly of β-sheet forming peptides into filaments has drawn great interests in biomedical applications [1,2]; Hydrogels formed by filaments self-assembled from de novo designed peptides possess potential applications for cell culture scaffolds [3]. On the other hand, peptides derived from amyloidogenic proteins in neurodegenerative diseases such as Alzheimer’s and Parkinson’s also form similar β-sheet filaments in vitro. They share little sequence homology, yet filaments formed by these self-assembling peptides commonly have the cross-β structure, the key signature of the amyloid fibril. Detailed structural information of the self-assembled β-sheet filaments has been limited partly due to the difficulty in preparing ordered filament samples, and it has been only recently that solid-state nuclear magnetic resonance and x-ray techniques have revealed their molecular structure at the atomic level [4,5]. Although molecular structures of amyloid fibrils are becoming available, physical principles governing their self-assembly and the properties of the filaments are not well-understood, for which computational as well as theoretical approaches are desirable [6].

scholarly journals Design and synthesis of nanofibers of self-assembled de novo glycoconjugates towards mucosal lining restoration and anti-inflammatory drug delivery

Tetrahedron ◽  
2016 ◽  
Vol 72 (40) ◽  
pp. 6078-6083 ◽  
Author(s):  
Jie Zhou ◽  
Michael O'Keeffe ◽  
Gongxian Liao ◽  
Fan Zhao ◽  
Cox Terhorst ◽  
...  
Keyword(s):  
Drug Delivery ◽  
De Novo ◽  
Inflammatory Drug ◽  
Design And Synthesis ◽  
Mucosal Lining ◽  
Anti Inflammatory ◽  
Self Assembled

De Novo Design of Self-Assembled Hexapeptides as β-Amyloid (Aβ) Peptide Inhibitors

2014 ◽  
Vol 5 (10) ◽  
pp. 972-981 ◽  
Author(s):  
Qiuming Wang ◽  
Guizhao Liang ◽  
Mingzhen Zhang ◽  
Jun Zhao ◽  
Kunal Patel ◽  
...  
Keyword(s):  
De Novo ◽  
De Novo Design ◽  
Peptide Inhibitors ◽  
Aβ Peptide ◽  
Amyloid Aβ ◽  
Β Amyloid ◽  
Self Assembled

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.

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