Peptide self-assembly for nanomaterials: the old new kid on the block

2015 ◽  
Vol 44 (22) ◽  
pp. 8288-8300 ◽  
Author(s):  
Emiliana De Santis ◽  
Maxim G. Ryadnov
Keyword(s):  
Self Assembly ◽  
Self Assembling ◽  
Peptide Materials

Self-assembling peptide materials are categorised according to main nanomaterial forms in relation to non-peptide materials.

scholarly journals Self-assembling Peptide Discovery: Overcoming Human Bias With Machine Learning

2021 ◽  
Author(s):  
Rohit Batra ◽  
Troy Loeffler ◽  
Henry Chan ◽  
Srilok Sriniva ◽  
Honggang Cui ◽  
...  
Keyword(s):  
Machine Learning ◽  
Self Assembly ◽  
Search Space ◽  
Sequence Length ◽  
Monte Carlo Tree Search ◽  
Self Assembling ◽  
Naturally Occurring ◽  
Peptide Materials ◽  
Dynamics Simulations ◽  
Better Than

Abstract Peptide materials have a wide array of functions from tissue engineering, surface coatings to catalysis and sensing. This class of biopolymer is composed of a sequence, comprised of 20 naturally occurring amino acids whose arrangement dictate the peptide functionality. While it is highly desirable to tailor the amino acid sequence, a small increase in their sequence length leads to dramatic increase in the possible candidates (e.g., from tripeptide = 20^3 or 8,000 peptides to a pentapeptide = 20^5 or 3.2 M). Traditionally, peptide design is guided by the use of structural propensity tables, hydrophobicity scales, or other desired properties and typically yields <10 peptides per study, barely scraping the surface of the search space. These approaches, driven by human expertise and intuition, are not easily scalable and are riddled with human bias. Here, we introduce a machine learning workflow that combines Monte Carlo tree search and random forest, with molecular dynamics simulations to develop a fully autonomous computational search engine (named, AI-expert) to discover peptide sequences with high potential for self-assembly (as a representative target functionality). We demonstrate the efficacy of the AI-expert to efficiently search large spaces of tripeptides and pentapeptides. Subsequent experiments on the proposed peptide sequences are performed to compare the predictability of the AI-expert with those of human experts. The AI performs on-par or better than human experts and suggests several non-intuitive sequences with high self-assembly propensity, outlining its potential to overcome human bias and accelerate peptide discovery.

scholarly journals Heterotypic Supramolecular Hydrogels Formed by Noncovalent Interactions in Inflammasomes

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 77
Author(s):  
Adrianna N. Shy ◽  
Huaimin Wang ◽  
Zhaoqianqi Feng ◽  
Bing Xu
Keyword(s):  
Self Assembly ◽  
Electrostatic Interactions ◽  
Structural Information ◽  
Noncovalent Interactions ◽  
Protein Structures ◽  
Peptide Sequence ◽  
Binding Motifs ◽  
Self Assembling ◽  
Transmission Electron ◽  
Peptide Materials

The advance of structural biology has revealed numerous noncovalent interactions between peptide sequences in protein structures, but such information is less explored for developing peptide materials. Here we report the formation of heterotypic peptide hydrogels by the two binding motifs revealed by the structures of an inflammasome. Specifically, conjugating a self-assembling motif to the positively or negatively charged peptide sequence from the ASCPYD filaments of inflammasome produces the solutions of the peptides. The addition of the peptides of the oppositely charged and complementary peptides to the corresponding peptide solution produces the heterotypic hydrogels. Rheology measurement shows that ratios of the complementary peptides affect the viscoelasticity of the resulted hydrogel. Circular dichroism indicates that the addition of the complementary peptides results in electrostatic interactions that modulate self-assembly. Transmission electron microscopy reveals that the ratio of the complementary peptides controls the morphology of the heterotypic peptide assemblies. This work illustrates a rational, biomimetic approach that uses the structural information from the protein data base (PDB) for developing heterotypic peptide materials via self-assembly.

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.

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

2020 ◽  
Vol 27 (9) ◽  
pp. 923-929
Author(s):  
Gaurav Pandey ◽  
Prem Prakash Das ◽  
Vibin Ramakrishnan
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Light Scattering ◽  
Chain Length ◽  
Self Assembly ◽  
The Self ◽  
Ionic Charge ◽  
Self Assembling ◽  
Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

Self-assembling behaviour of a modified aromatic amino acid in competitive medium

Soft Matter ◽  
2020 ◽  
Vol 16 (28) ◽  
pp. 6599-6607 ◽  
Author(s):  
Pijush Singh ◽  
Souvik Misra ◽  
Nayim Sepay ◽  
Sanjoy Mondal ◽  
Debes Ray ◽  
...  
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Aromatic Amino Acid ◽  
Photophysical Properties ◽  
Solvent Mixture ◽  
The Self ◽  
Solvent Ratio ◽  
Self Assembling

The self-assembly and photophysical properties of 4-nitrophenylalanine (4NP) are changed with the alteration of solvent and final self-assembly state of 4NP in competitive solvent mixture and are dictated by the solvent ratio.

Sticky ends in a self-assembling ABA triblock copolymer: the role of ureas in stimuli-responsive hydrogels

2019 ◽  
Vol 4 (1) ◽  
pp. 91-102 ◽  
Author(s):  
Ryan T. Shafranek ◽  
Joel D. Leger ◽  
Song Zhang ◽  
Munira Khalil ◽  
Xiaodan Gu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Viscoelastic Properties ◽  
Triblock Copolymer ◽  
Thermal Response ◽  
Stimuli Responsive ◽  
Self Assembling ◽  
Polymeric Hydrogels ◽  
Aba Triblock Copolymer ◽  
Responsive Hydrogels

Directed self-assembly in polymeric hydrogels allows tunability of thermal response and viscoelastic properties.

scholarly journals A New Hope: Self-Assembling Peptides with Antimicrobial Activity

Pharmaceutics ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 166 ◽  
Author(s):  
Lucia Lombardi ◽  
Annarita Falanga ◽  
Valentina Del Genio ◽  
Stefania Galdiero
Keyword(s):  
Self Assembly ◽  
Biomedical Applications ◽  
High Specificity ◽  
Antibacterial Activities ◽  
Mechanisms Of Action ◽  
Great Promise ◽  
Functional Nanomaterials ◽  
Self Assembling ◽  
Low Toxicity ◽  
Bio Compatibility

Peptide drugs hold great promise for the treatment of infectious diseases thanks to their novel mechanisms of action, low toxicity, high specificity, and ease of synthesis and modification. Naturally developing self-assembly in nature has inspired remarkable interest in self-assembly of peptides to functional nanomaterials. As a matter of fact, their structural, mechanical, and functional advantages, plus their high bio-compatibility and bio-degradability make them excellent candidates for facilitating biomedical applications. This review focuses on the self-assembly of peptides for the fabrication of antibacterial nanomaterials holding great interest for substituting antibiotics, with emphasis on strategies to achieve nano-architectures of self-assembly. The antibacterial activities achieved by these nanomaterials are also described.

scholarly journals Multiscale additive manufacturing of polymers using 3D photo-printable self-assembling ionic liquid monomers

2019 ◽  
Vol 4 (3) ◽  
pp. 580-585 ◽  
Author(s):  
Bineh G. Ndefru ◽  
Bryan S. Ringstrand ◽  
Sokhna I.-Y. Diouf ◽  
Sönke Seifert ◽  
Juan H. Leal ◽  
...  
Keyword(s):  
Ionic Liquid ◽  
Additive Manufacturing ◽  
Self Assembly ◽  
Low Cost ◽  
Low Resolution ◽  
Top Down ◽  
Bottom Up ◽  
Cost Approach ◽  
Self Assembling ◽  
Nanoscale Features

Combining bottom-up self-assembly with top-down 3D photoprinting affords a low cost approach for the introduction of nanoscale features into a build with low resolution features.

Self Assembling Nanostructured Delivery Vehicles for Biochemically Reactive Pairs

1994 ◽  
Vol 351 ◽  
Author(s):  
Nir Kossovsky ◽  
A. Gelman ◽  
H.J. Hnatyszyn ◽  
E. Sponsler ◽  
G.-M. Chow
Keyword(s):  
Physical Properties ◽  
Self Assembly ◽  
Materials Science ◽  
Technology Development ◽  
Biological Behavior ◽  
X Ray Diffraction ◽  
Self Assembling ◽  
Transmission Electron ◽  
Carbon Ceramic

ABSTRACTIntrigued by the deceptive simplicity and beauty of macromolecular self-assembly, our laboratory began studying models of self-assembly using solids, glasses, and colloidal substrates. These studies have defined a fundamental new colloidal material for supporting members of a biochemically reactive pair.The technology, a molecular transportation assembly, is based on preformed carbon ceramic nanoparticles and self assembled calcium-phosphate dihydrate particles to which glassy carbohydrates are then applied as a nanometer thick surface coating. This carbohydrate coated core functions as a dehydroprotectant and stabilizes surface immobilized members of a biochemically reactive pair. The final product, therefore, consists of three layers. The core is comprised of the ceramic, the second layer is the dehydroprotectant carbohydrate adhesive, and the surface layer is the biochemically reactive molecule for which delivery is desired.We have characterized many of the physical properties of this system and have evaluated the utility of this delivery technology in vitro and in animal models. Physical characterization has included standard and high resolution transmission electron microscopy, electron and x-ray diffraction and ζ potential analysis. Functional assays of the ability of the system to act as a nanoscale dehydroprotecting delivery vehicle have been performed on viral antigens, hemoglobin, and insulin. By all measures at present, the favorable physical properties and biological behavior of the molecular transportation assembly point to an exciting new interdisciplinary area of technology development in materials science, chemistry and biology.

scholarly journals A Self-Assembling Amphiphilic Peptide Dendrimer-Based Drug Delivery System for Cancer Therapy

Pharmaceutics ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1092
Author(s):  
Dandan Zhu ◽  
Huanle Zhang ◽  
Yuanzheng Huang ◽  
Baoping Lian ◽  
Chi Ma ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Drug Delivery ◽  
Drug Resistance ◽  
Cancer Therapy ◽  
Self Assembly ◽  
Cancer Drug ◽  
Acquired Drug Resistance ◽  
Self Assembling ◽  
Amphiphilic Peptide ◽  
Peptide Dendrimer

Despite being a mainstay of clinical cancer treatment, chemotherapy is limited by its severe side effects and inherent or acquired drug resistance. Nanotechnology-based drug-delivery systems are widely expected to bring new hope for cancer therapy. These systems exploit the ability of nanomaterials to accumulate and deliver anticancer drugs at the tumor site via the enhanced permeability and retention effect. Here, we established a novel drug-delivery nanosystem based on amphiphilic peptide dendrimers (AmPDs) composed of a hydrophobic alkyl chain and a hydrophilic polylysine dendron with different generations (AmPD KK2 and AmPD KK2K4). These AmPDs assembled into nanoassemblies for efficient encapsulation of the anti-cancer drug doxorubicin (DOX). The AmPDs/DOX nanoformulations improved the intracellular uptake and accumulation of DOX in drug-resistant breast cancer cells and increased permeation in 3D multicellular tumor spheroids in comparison with free DOX. Thus, they exerted effective anticancer activity while circumventing drug resistance in 2D and 3D breast cancer models. Interestingly, AmPD KK2 bearing a smaller peptide dendron encapsulated DOX to form more stable nanoparticles than AmPD KK2K4 bearing a larger peptide dendron, resulting in better cellular uptake, penetration, and anti-proliferative activity. This may be because AmPD KK2 maintains a better balance between hydrophobicity and hydrophilicity to achieve optimal self-assembly, thereby facilitating more stable drug encapsulation and efficient drug release. Together, our study provides a promising perspective on the design of the safe and efficient cancer drug-delivery nanosystems based on the self-assembling amphiphilic peptide dendrimer.

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