scholarly journals Beyond icosahedral symmetry in packings of proteins in spherical shells

2017 ◽  
Vol 114 (34) ◽  
pp. 9014-9019 ◽  
Author(s):  
Majid Mosayebi ◽  
Deborah K. Shoemark ◽  
Jordan M. Fletcher ◽  
Richard B. Sessions ◽  
Noah Linden ◽  
...  
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Multiple Scales ◽  
Building Blocks ◽  
Icosahedral Symmetry ◽  
Protein Cages ◽  
Natural Systems ◽  
Wide Range ◽  
Stable Arrangement ◽  
Symmetric Structures

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.

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.

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.

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 Modification of a Single Atom Affects the Physical Properties of Double Fluorinated Fmoc-Phe Derivatives

2021 ◽  
Vol 22 (17) ◽  
pp. 9634
Author(s):  
Moran Aviv ◽  
Dana Cohen-Gerassi ◽  
Asuka A. Orr ◽  
Rajkumar Misra ◽  
Zohar A. Arnon ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physical Properties ◽  
Self Assembly ◽  
Deep Understanding ◽  
Building Blocks ◽  
The Self ◽  
Single Atom ◽  
Supramolecular Organization ◽  
Assembly Process ◽  
Wide Range

Supramolecular hydrogels formed by the self-assembly of amino-acid based gelators are receiving increasing attention from the fields of biomedicine and material science. Self-assembled systems exhibit well-ordered functional architectures and unique physicochemical properties. However, the control over the kinetics and mechanical properties of the end-products remains puzzling. A minimal alteration of the chemical environment could cause a significant impact. In this context, we report the effects of modifying the position of a single atom on the properties and kinetics of the self-assembly process. A combination of experimental and computational methods, used to investigate double-fluorinated Fmoc-Phe derivatives, Fmoc-3,4F-Phe and Fmoc-3,5F-Phe, reveals the unique effects of modifying the position of a single fluorine on the self-assembly process, and the physical properties of the product. The presence of significant physical and morphological differences between the two derivatives was verified by molecular-dynamics simulations. Analysis of the spontaneous phase-transition of both building blocks, as well as crystal X-ray diffraction to determine the molecular structure of Fmoc-3,4F-Phe, are in good agreement with known changes in the Phe fluorination pattern and highlight the effect of a single atom position on the self-assembly process. These findings prove that fluorination is an effective strategy to influence supramolecular organization on the nanoscale. Moreover, we believe that a deep understanding of the self-assembly process may provide fundamental insights that will facilitate the development of optimal amino-acid-based low-molecular-weight hydrogelators for a wide range of applications.

Artificial protein assemblies with well-defined supramolecular protein nanostructures

2021 ◽  
Author(s):  
Suyeong Han ◽  
Yongwon Jung
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
Building Blocks ◽  
Protein Assembly ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Wide Range ◽  
Array Structures ◽  
Small Chemical ◽  
Artificial Protein

Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.

Nanoparticles and self-organisation: the emergence of hierarchical properties from the nanoparticle soup (i.e., the small is getting bigger). Concluding remarks for Faraday Discussion: Nanoparticle Synthesis and Assembly.

2015 ◽  
Vol 181 ◽  
pp. 481-487 ◽  
Author(s):  
David J. Schiffrin
Keyword(s):  
Self Assembly ◽  
Optical Materials ◽  
Nanoparticle Synthesis ◽  
Hierarchical Structures ◽  
Building Blocks ◽  
Main Theme ◽  
Colloid Science ◽  
Wide Range ◽  
Properties Of Materials ◽  
Discussion Format

Some four years ago, one of the participants in this Discussion (Prof. Nicholas Kotov) predicted that: “within five years we shall see multiple examples of electronic, sensor, optical and other devices utilizing self-assembled superstructures” (N. A. Kotov, J. Mater. Chem., 2011, 21, 16673–16674). Although this prediction came partially to fruition, we have witnessed an unprecedented interest in the properties of materials at the nanoscale. The point highlighted by Kotov, however, was the importance of self-assembly of structures from well characterised building blocks to yield hierarchical structures, hopefully with predictable properties, a concept that is an everyday pursuit of synthetic chemists. This Discussion has brought together researchers from a wide range of disciplines, i.e., colloid science, modelling, nanoparticle synthesis and organisation, magnetic and optical materials, and new imaging methods, within the excellent traditional Faraday Discussion format, to discuss advances in areas relevant to the main theme of the meeting.

Deciphering the route to cyclic monoterpenes in Chrysomelina leaf beetles: source of new biocatalysts for industrial application?

2017 ◽  
Vol 72 (9-10) ◽  
pp. 417-427 ◽  
Author(s):  
Antje Burse ◽  
Wilhelm Boland
Keyword(s):  
De Novo ◽  
Sustainable Use ◽  
Building Blocks ◽  
Leaf Beetle ◽  
Industrial Applications ◽  
Metabolic Diversity ◽  
Leaf Beetles ◽  
Wide Range ◽  
Extreme Habitats ◽  
Plant Sources

AbstractThe drastic growth of the population on our planet requires the efficient and sustainable use of our natural resources. Enzymes are indispensable tools for a wide range of industries producing food, pharmaceuticals, pesticides, or biofuels. Because insects constitute one of the most species-rich classes of organisms colonizing almost every ecological niche on earth, they have developed extraordinary metabolic abilities to survive in various and sometimes extreme habitats. Despite this metabolic diversity, insect enzymes have only recently generated interest in industrial applications because only a few metabolic pathways have been sufficiently characterized. Here, we address the biosynthetic route to iridoids (cyclic monoterpenes), a group of secondary metabolites used by some members of the leaf beetle subtribe Chrysomelina as defensive compounds against their enemies. The ability to produce iridoids de novo has also convergently evolved in plants. From plant sources, numerous pharmacologically relevant structures have already been described. In addition, in plants, iridoids serve as building blocks for monoterpenoid indole alkaloids with broad therapeutic applications. As the commercial synthesis of iridoid-based drugs often relies on a semisynthetic approach involving biocatalysts, the discovery of enzymes from the insect iridoid route can account for a valuable resource and economic alternative to the previously used enzymes from the metabolism of plants. Hence, this review illustrates the recent discoveries made on the steps of the iridoid pathway in Chrysomelina leaf beetles. The findings are also placed in the context of the studied counterparts in plants and are further discussed regarding their use in technological approaches.

scholarly journals Discovering multiscale and self-similar structure with data-driven wavelets

2020 ◽  
Vol 118 (1) ◽  
pp. e2021299118
Author(s):  
Daniel Floryan ◽  
Michael D. Graham
Keyword(s):  
Multiple Scales ◽  
Spatial Scales ◽  
Building Blocks ◽  
Biological Tissues ◽  
Data Driven ◽  
Model Free ◽  
Starting Point ◽  
Wide Range ◽  
Direct Model ◽  
Self Similar

Many materials, processes, and structures in science and engineering have important features at multiple scales of time and/or space; examples include biological tissues, active matter, oceans, networks, and images. Explicitly extracting, describing, and defining such features are difficult tasks, at least in part because each system has a unique set of features. Here, we introduce an analysis method that, given a set of observations, discovers an energetic hierarchy of structures localized in scale and space. We call the resulting basis vectors a “data-driven wavelet decomposition.” We show that this decomposition reflects the inherent structure of the dataset it acts on, whether it has no structure, structure dominated by a single scale, or structure on a hierarchy of scales. In particular, when applied to turbulence—a high-dimensional, nonlinear, multiscale process—the method reveals self-similar structure over a wide range of spatial scales, providing direct, model-free evidence for a century-old phenomenological picture of turbulence. This approach is a starting point for the characterization of localized hierarchical structures in multiscale systems, which we may think of as the building blocks of these systems.

scholarly journals Design of complicated all-α protein structures

2021 ◽  
Author(s):  
Koya Sakuma ◽  
Naohiro Kobayashi ◽  
Toshihiko Sugiki ◽  
Toshio Nagashima ◽  
Toshimichi Fujiwara ◽  
...  
Keyword(s):  
De Novo ◽  
Protein Structures ◽  
Building Blocks ◽  
Helical Structures ◽  
Helix Loop Helix ◽  
Naturally Occurring ◽  
Wide Range ◽  
Helical Protein ◽  
Helical Proteins ◽  
The Universe

A wide range of de novo protein structure designs have been achieved, but the complexity of naturally occurring protein structures is still far beyond these designs. To expand the diversity and complexity of de novo designed protein structures, we sought to develop a method for designing 'difficult-to-describe' α-helical protein structures composed of irregularly aligned α-helices, such as globins. Backbone structure libraries consisting of a myriad of α-helical structures with 5- or 6- helices were generated by combining 18 helix-loop-helix motifs and canonical α-helices, and five distinct topologies were selected for de novo design. The designs were found to be monomeric with high thermal stability in solution and fold into the target topologies with atomic accuracy. This study demonstrated that complicated α-helical proteins are created using typical building blocks. The method we developed would enable us to explore the universe of protein structures for designing novel functional proteins.

Sign in / Sign up

Export Citation Format

Share Document