scholarly journals Computationally designed peptides for self-assembly of nanostructured lattices

2016 ◽  
Vol 2 (9) ◽  
pp. e1600307 ◽  
Author(s):  
Huixi Violet Zhang ◽  
Frank Polzer ◽  
Michael J. Haider ◽  
Yu Tian ◽  
Jose A. Villegas ◽  
...  
Keyword(s):  
Self Assembly ◽  
Noncovalent Interactions ◽  
Building Blocks ◽  
Covalent Modification ◽  
Amino Acid Sequences ◽  
Peptide Sequence ◽  
Self Assembling ◽  
Transmission Electron ◽  
Wide Range ◽  
Micrometer Scale

Folded peptides present complex exterior surfaces specified by their amino acid sequences, and the control of these surfaces offers high-precision routes to self-assembling materials. The complexity of peptide structure and the subtlety of noncovalent interactions make the design of predetermined nanostructures difficult. Computational methods can facilitate this design and are used here to determine 29-residue peptides that form tetrahelical bundles that, in turn, serve as building blocks for lattice-forming materials. Four distinct assemblies were engineered. Peptide bundle exterior amino acids were designed in the context of three different interbundle lattices in addition to one design to produce bundles isolated in solution. Solution assembly produced three different types of lattice-forming materials that exhibited varying degrees of agreement with the chosen lattices used in the design of each sequence. Transmission electron microscopy revealed the nanostructure of the sheetlike nanomaterials. In contrast, the peptide sequence designed to form isolated, soluble, tetrameric bundles remained dispersed and did not form any higher-order assembled nanostructure. Small-angle neutron scattering confirmed the formation of soluble bundles with the designed size. In the lattice-forming nanostructures, the solution assembly process is robust with respect to variation of solution conditions (pH and temperature) and covalent modification of the computationally designed peptides. Solution conditions can be used to control micrometer-scale morphology of the assemblies. The findings illustrate that, with careful control of molecular structure and solution conditions, a single peptide motif can be versatile enough to yield a wide range of self-assembled lattice morphologies across many length scales (1 to 1000 nm).

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.

scholarly journals Biocatalysis of d,l-Peptide Nanofibrillar Hydrogel

Molecules ◽  
2020 ◽  
Vol 25 (13) ◽  
pp. 2995 ◽  
Author(s):  
Tiziano Carlomagno ◽  
Maria C. Cringoli ◽  
Slavko Kralj ◽  
Marina Kurbasic ◽  
Paolo Fornasiero ◽  
...  
Keyword(s):  
Self Assembly ◽  
Solid Phase ◽  
Building Blocks ◽  
Cd Spectroscopy ◽  
Tem Analysis ◽  
Design Rules ◽  
Self Assembling ◽  
Transmission Electron ◽  
Oscillatory Rheometry ◽  
The Many

Self-assembling peptides are attracting wide interest as biodegradable building blocks to achieve functional nanomaterials that do not persist in the environment. Amongst the many applications, biocatalysis is gaining momentum, although a clear structure-to-activity relationship is still lacking. This work applied emerging design rules to the heterochiral octapeptide sequence His–Leu–DLeu–Ile–His–Leu–DLeu–Ile for self-assembly into nanofibrils that, at higher concentration, give rise to a supramolecular hydrogel for the mimicry of esterase-like activity. The peptide was synthesized by solid-phase and purified by HPLC, while its identity was confirmed by 1H-NMR and electrospray ionization (ESI)-MS. The hydrogel formed by this peptide was studied with oscillatory rheometry, and the supramolecular behavior of the peptide was investigated with transmission electron microscopy (TEM) analysis, circular dichroism (CD) spectroscopy, thioflavin T amyloid fluorescence assay, and attenuated total reflectance (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The biocatalytic activity was studied by monitoring the hydrolysis of p-nitrophenyl acetate (pNPA) at neutral pH, and the reaction kinetics followed an apparent Michaelis–Menten model, for which a Lineweaver–Burk plot was produced to determine its enzymatic parameters for a comparison with the literature. Finally, LC–MS analysis was conducted on a series of experiments to evaluate the extent of, if any, undesired peptide acetylation at the N-terminus. In conclusion, we provide new insights that allow gaining a clearer picture of self-assembling peptide design rules for biocatalysis.

scholarly journals The Human LL-37(17-29) Antimicrobial Peptide Reveals a Functional Supramolecular Nanostructure

2020 ◽  
Author(s):  
Yizhaq Engelberg ◽  
Meytal Landau
Keyword(s):  
Lipid Bilayers ◽  
Self Assembly ◽  
Amyloid Fibrils ◽  
Biological Activities ◽  
Building Blocks ◽  
Bacterial Cells ◽  
Bacterial Membranes ◽  
Self Assembling ◽  
Wide Ribbon ◽  
Wide Range

Protein fibrils that perform biological activities present attractive biomaterials. Here we demonstrate, by crystal structures, the self-assembly of the antibacterial human LL-37 active core (residues 17-29) into a stable structure of densely packed helices. The surface of the fibril encompasses alternating hydrophobic and positively charged zigzagged belts, which likely underlie interactions with and subsequent disruption of negatively charged lipid bilayers, such as bacterial membranes. LL-3717-29 correspondingly formed wide, ribbon-like, thermostable fibrils in solution, which co-localized with bacterial cells, and structure-guided mutagenesis analyses supported the role of self-assembly in antibacterial activity. LL-3717-29 resembled, in sequence and in the ability to form amphipathic helical fibrils, the bacterial cytotoxic PSMα3 peptide that assembles into cross-α amyloid fibrils. This suggests helical, self-assembling, basic building blocks across kingdoms of life and point to potential structural mimicry mechanisms. The findings offer a scaffold for functional and durable nanostructures for a wide range of medical and technological applications.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43
Author(s):  
Huey Ling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range ◽  
And Control

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 of peptides 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 of biological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi- and tri-block copolymers to DNA structures as well as simple and complex proteins and peptides. The ultimate goal is to harness molecular self-assembly such that design and control of bottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes of life and non-life science applications. Such aspirations can be achieved through understanding the fundamental principles behind the self­ organisation and self-synthesis processes exhibited by biological systems.

Self-Assembly of Peptide Amphiphiles: Molecularly Engineered Bionanomaterials

2015 ◽  
Vol 1113 ◽  
pp. 586-593 ◽  
Author(s):  
Hamizah Shamsudeen ◽  
Huey Ling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Significant Advance ◽  
Polymer Science ◽  
New Approach ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has now emerged as a new approach in chemical synthesis, engineering, nanotechnology, polymer science, and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in the 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 of peptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. Today, the study of biological self-assembly systems represent a significant advance in the molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi-and tri-block copolymers to complex DNA structures as well as simple and complex proteins and peptides. The attractiveness of such bottom-up processes lies in their capability to build uniform, functional units or arrays and the possibility to exploit such structures at meso-and macroscopic scale for life and non-life science applications.

scholarly journals Self-assembly of Functional Nanostructures by Short Helical Peptide Building Blocks

2019 ◽  
Vol 26 (2) ◽  
pp. 88-97 ◽  
Author(s):  
Santu Bera ◽  
Ehud Gazit
Keyword(s):  
Self Assembly ◽  
Amyloid Fibrils ◽  
Building Blocks ◽  
Smart Devices ◽  
Helical Peptides ◽  
Functional Roles ◽  
Mesoscale Structures ◽  
Self Assembling ◽  
Wide Range ◽  
Self Assembled

The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.

Controllable Synthesis of Cobalt Porphyrin Nanocrystals through Micelle Confinement Self-Assembly

MRS Advances ◽  
2020 ◽  
Vol 5 (42) ◽  
pp. 2147-2155
Author(s):  
Sudi Chen ◽  
Xitong Ren ◽  
Shufang Tian ◽  
Jiajie Sun ◽  
Feng Bai
Keyword(s):  
Self Assembly ◽  
Water Oxidation ◽  
Separation Efficiency ◽  
Noncovalent Interactions ◽  
Building Blocks ◽  
The Self ◽  
Hexagonal Prism ◽  
Assembly Process ◽  
Surfactant Micelles ◽  
Cobalt Porphyrin

AbstractThe self-assembly of optically active building blocks into functional nanocrystals as high-activity photocatalysts is a key in the field of photocatalysis. Cobalt porphyrin with abundant catalytic properties is extensively studied in photocatalytic water oxidation and CO2 reduction. Here, we present the fabrication of cobalt porphyrin nanocrystals through a surfactant-assisted interfacial self-assembly process using Co-tetra(4-pyridyl) porphyrin as building block. The self-assembly process relies on the combined noncovalent interactions such as π-π stacking and axial Co-N coordination between individual porphyrin molecules within surfactant micelles. Tuning different reaction conditions (temperature, the ratio of co-solvent DMF) and types of surfactant, various nanocrystals with well-defined 1D to 3D morphologies such as nanowires, nanorods and nano hexagonal prism were obtained. Due to the ordered accumulation of molecules, the nanocrystals exhibit the properties of the enhanced capability of visible light capture and can conduce to improve the transport and separation efficiency of the photogenerated carriers, which is important for photocatalysis. Further studies of photocatalytic CO2 reduction are being performed to address the relationship between the size and shape of the nanocrystals with the photocatalytic activity.

Zeolates: A Coordination Chemistry View of Metal-Ligand Bonding in Intrazeolite MOCVD Type Precursors and Semiconductor Nanoclusters

1992 ◽  
Vol 277 ◽  
Author(s):  
Geoffrey A. Ozin ◽  
Carol L. Bowes ◽  
Mark R. Steele
Keyword(s):  
Self Assembly ◽  
Materials Science ◽  
Zeolite Y ◽  
Chemical Vapour ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Organic Chemical ◽  
Wide Range ◽  
Shape Selective

ABSTRACTVarious MOCVD (metal-organic chemical vapour deposition) type precursors and their self-assembled semiconductor nanocluster products [1] have been investigated in zeolite Y hosts. From analysis of in situ observations (FTIR, UV-vis reflectance, Mössbauer, MAS-NMR) of the reaction sequences and structural features of the precursors and products (EXAFS and Rietveld refinement of powder XRD data) the zeolite is viewed as providing a macrospheroidal, multidendate coordination environment towards encapsulated guests. By thinking about the α- and β-cages of the zeolite Y host effectively as a zeolate ligand composed of interconnected aluminosilicate “crown ether-like” building blocks, the materials chemist is able to better understand and exploit the reactivity and coordination properties of the zeolite internal surface for the anchoring and self-assembly of a wide range of encapsulated guests. This approach helps with the design of synthetic strategies for creating novel guest-host inclusion compounds having possible applications in areas of materials science such as nonlinear optics, quantum electronics, and size/shape selective catalysis.

scholarly journals A Structurally Variable Hinged Tetrahedron Framework from DNA Origami

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
David M. Smith ◽  
Verena Schüller ◽  
Carsten Forthmann ◽  
Robert Schreiber ◽  
Philip Tinnefeld ◽  
...  
Keyword(s):  
Self Assembly ◽  
Gel Electrophoresis ◽  
Imaging Techniques ◽  
Building Blocks ◽  
Dna Origami ◽  
Microscopy Technique ◽  
Wire Frame ◽  
Wide Range ◽  
Potential Applications ◽  
Linker Molecules

Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT.

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