scholarly journals Rational design of peptide-based building blocks for nanoscience and synthetic biology

2009 ◽  
Vol 143 ◽  
pp. 305 ◽  
Author(s):  
Craig T. Armstrong ◽  
Aimee L. Boyle ◽  
Elizabeth H. C. Bromley ◽  
Zahra N. Mahmoud ◽  
Lisa Smith ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Building Blocks

Probing the Substrate Promiscuity of Isopentenyl Phosphate Kinase as a Platform for Hemiterpene Analogue Production

2019 ◽  
Author(s):  
Sean Lund ◽  
Taylor Courtney ◽  
Gavin Williams
Keyword(s):  
Synthetic Biology ◽  
Building Blocks ◽  
Isoprenoid Biosynthesis ◽  
Thermoplasma Acidophilum ◽  
Substrate Promiscuity ◽  
Enzymatic Pathways ◽  
First Time ◽  
Rate Limiting ◽  
Alcohol Dependent ◽  
Isopentenyl Phosphate

Isoprenoids are a large class of natural products with wide-ranging applications. Synthetic biology approaches to the manufacture of isoprenoids and their new-to-nature derivatives are limited due to the provision in Nature of just two hemiterpene building blocks for isoprenoid biosynthesis. To address this limitation, artificial chemo-enzymatic pathways such as the alcohol-dependent hemiterpene pathway (ADH) serve to leverage consecutive kinases to convert exogenous alcohols to pyrophosphates that could be coupled to downstream isoprenoid biosynthesis. To be successful, each kinase in this pathway should be permissive of a broad range of substrates. For the first time, we have probed the promiscuity of the second enzyme in the ADH pathway, isopentenyl phosphate kinase from Thermoplasma acidophilum, towards a broad range of acceptor monophosphates. Subsequently, we evaluate the suitability of this enzyme to provide non-natural pyrophosphates and provide a critical first step in characterizing the rate limiting steps in the artificial ADH pathway.<br>

scholarly journals Anisotropic nanocrystal shape and ligand design for co-assembly

2021 ◽  
Vol 7 (23) ◽  
pp. eabf9402
Author(s):  
Katherine C. Elbert ◽  
William Zygmunt ◽  
Thi Vo ◽  
Corbin M. Vara ◽  
Daniel J. Rosen ◽  
...  
Keyword(s):  
Rational Design ◽  
Ligand Design ◽  
Building Blocks ◽  
Two Dimensional ◽  
Secondary System ◽  
Assembly Design ◽  
Ligand Shell ◽  
Powerful Approach ◽  
Anisotropic Systems ◽  
Direct Materials

The use of nanocrystal (NC) building blocks to create metamaterials is a powerful approach to access emergent materials. Given the immense library of materials choices, progress in this area for anisotropic NCs is limited by the lack of co-assembly design principles. Here, we use a rational design approach to guide the co-assembly of two such anisotropic systems. We modulate the removal of geometrical incompatibilities between NCs by tuning the ligand shell, taking advantage of the lock-and-key motifs between emergent shapes of the ligand coating to subvert phase separation. Using a combination of theory, simulation, and experiments, we use our strategy to achieve co-assembly of a binary system of cubes and triangular plates and a secondary system involving two two-dimensional (2D) nanoplates. This theory-guided approach to NC assembly has the potential to direct materials choices for targeted binary co-assembly.

Evolving protocells to prototissues: rational design of a missing link

2013 ◽  
Vol 41 (5) ◽  
pp. 1159-1165 ◽  
Author(s):  
Shiksha Mantri ◽  
K. Tanuj Sapra
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Structural Elements ◽  
Bottom Up ◽  
Missing Link ◽  
Hierarchical Assembly ◽  
Artificial Cell

Realization of a functional artificial cell, the so-called protocell, is a major challenge posed by synthetic biology. A subsequent goal is to use the protocellular units for the bottom-up assembly of prototissues. There is, however, a looming chasm in our knowledge between protocells and prototissues. In the present paper, we give a brief overview of the work on protocells to date, followed by a discussion on the rational design of key structural elements specific to linking two protocellular bilayers. We propose that designing synthetic parts capable of simultaneous insertion into two bilayers may be crucial in the hierarchical assembly of protocells into a functional prototissue.

scholarly journals Stacking-engineered ferroelectricity in bilayer boron nitride

Science ◽  
2021 ◽  
pp. eabd3230
Author(s):  
Kenji Yasuda ◽  
Xirui Wang ◽  
Kenji Watanabe ◽  
Takashi Taniguchi ◽  
Pablo Jarillo-Herrero
Keyword(s):  
Boron Nitride ◽  
Nonvolatile Memory ◽  
Rational Design ◽  
Parent Compound ◽  
High Mobility ◽  
Building Blocks ◽  
Electric Polarization ◽  
Experimental Realization ◽  
Polar Crystal ◽  
Memory Applications

2D ferroelectrics with robust polarization down to atomic thicknesses provide building blocks for functional heterostructures. Experimental realization remains challenging because of the requirement of a layered polar crystal. Here, we demonstrate a rational design approach to engineering 2D ferroelectrics from a non-ferroelectric parent compound via employing van der Waals assembly. Parallel-stacked bilayer boron nitride exhibits out-of-plane electric polarization that reverses depending on the stacking order. The polarization switching is probed via the resistance of an adjacently stacked graphene sheet. Twisting the boron nitride sheets by a small angle changes the dynamics of switching thanks to the formation of moiré ferroelectricity with staggered polarization. The ferroelectricity persists to room temperature while keeping the high mobility of graphene, paving the way for potential ultrathin nonvolatile memory applications.

scholarly journals Engineering a Minimal Cloning Vector from a pUC18 Plasmid Backbone with an Extended Multiple Cloning Site

2018 ◽  
Author(s):  
Jens Staal ◽  
Wouter De Schamphelaire ◽  
Rudi Beyaert
Keyword(s):  
Synthetic Biology ◽  
Molecular Biology ◽  
Restriction Enzyme ◽  
Essential Role ◽  
Building Blocks ◽  
Cloning Vector ◽  
Multiple Cloning Site ◽  
Unique Restriction ◽  
Plasmid Backbone

Minimal plasmids play an essential role in many intermediate steps in molecular biology. They can for example be used to assemble building blocks in synthetic biology or be used as intermediate cloning plasmids that are ideal for PCR-based mutagenesis methods. A small backbone also opens up for additional unique restriction enzyme cloning sites. Here we describe the generation of pICOz, a 1185 bp fully functional high-copy cloning plasmid with an extended multiple cloning site (MCS). To our knowledge, this is the smallest high-copy cloning vector ever described.

Synthesis of Nitrile-Functionalized Polydentate N-Heterocycles as Building Blocks for Covalent Triazine Frameworks

Synthesis ◽  
2021 ◽  
Author(s):  
Christian V. Stevens ◽  
Jonas Everaert ◽  
Maarten Debruyne ◽  
Flore Vanden Bussche ◽  
Kristof Van Hecke ◽  
...  
Keyword(s):  
Rational Design ◽  
Building Blocks ◽  
Heterocyclic Ligands ◽  
Support Materials ◽  
Polydentate Ligands ◽  
Catalytic Metal ◽  
Composition Structure ◽  
And Function ◽  
Application Access ◽  
Modular Nature

AbstractCovalent triazine frameworks (CTFs) based on polydentate ligands are highly promising supports to anchor catalytic metal complexes. The modular nature of CTFs allows to tailor the composition, structure, and function to its specific application. Access to a broad range of chelating building blocks is therefore essential. In this respect, we extended the current available set of CTF building blocks with new nitrile-functionalized N-heterocyclic ligands. This paper presents the synthesis of the six ligands which vary in the extent of the aromatic system and the denticity. The new building blocks may help in a rational design of enhanced support materials in catalysis.

scholarly journals Collective excitation of plasmon-coupled Au-nanochain boosts photocatalytic hydrogen evolution of semiconductor

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Guiyang Yu ◽  
Jun Qian ◽  
Peng Zhang ◽  
Bo Zhang ◽  
Wenxiang Zhang ◽  
...  
Keyword(s):  
Electromagnetic Field ◽  
Metal Nanoparticles ◽  
Hydrogen Evolution ◽  
Rational Design ◽  
Collective Excitation ◽  
Formation Rate ◽  
Building Blocks ◽  
Localized Surface Plasmon ◽  
Plasmonic Enhancement ◽  
Photocatalytic Hydrogen Evolution

Abstract Localized surface plasmon resonance (LSPR) offers a valuable opportunity to improve the efficiency of photocatalysts. However, plasmonic enhancement of photoconversion is still limited, as most of metal-semiconductor building blocks depend on LSPR contribution of isolated metal nanoparticles. In this contribution, the concept of collective excitation of embedded metal nanoparticles is demonstrated as an effective strategy to enhance the utilization of plasmonic energy. The contribution of Au-nanochain to the enhancement of photoconversion is 3.5 times increase in comparison with that of conventional isolated Au nanoparticles. Experimental characterization and theoretical simulation show that strongly coupled plasmonic nanostructure of Au-nanochain give rise to highly intensive electromagnetic field. The enhanced strength of electromagnetic field essentially boosts the formation rate of electron-hole pair in semiconductor, and ultimately improves photocatalytic hydrogen evolution activity of semiconductor photocatalysts. The concept of embedded coupled-metal nanostructure represents a promising strategy for the rational design of high-performance photocatalysts.

scholarly journals A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI

2020 ◽  
Vol 13 (11) ◽  
pp. 338
Author(s):  
Joanna Bojarska ◽  
Milan Remko ◽  
Martin Breza ◽  
Izabela Madura ◽  
Andrzej Fruziński ◽  
...  
Keyword(s):  
Drug Design ◽  
In Silico ◽  
Rational Design ◽  
Enzyme Inhibitors ◽  
Building Blocks ◽  
Angiotensin Converting Enzyme Inhibitors ◽  
Converting Enzyme Inhibitors ◽  
Supramolecular Synthons ◽  
Comprehensive Classification ◽  
Proline Derivatives

Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO−), -N+ and -COOH(-COO−), -NH and -COOH(-COO−), -NH+ and -COOH(-COO−), and -NH2+ and -COOH(-COO−). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.

scholarly journals Predicting the bulk modulus of single-layer covalent organic frameworks with square-lattice topology from molecular building-block properties

Nanoscale ◽  
2021 ◽  
Author(s):  
Antonios Raptakis ◽  
Arezoo Dianat ◽  
Alexander Croy ◽  
Gianaurelio Cuniberti
Keyword(s):  
Bulk Modulus ◽  
Elastic Properties ◽  
Building Block ◽  
Rational Design ◽  
Computational Study ◽  
Single Layer ◽  
Building Blocks ◽  
Square Lattice ◽  
New Materials ◽  
Molecular Building Block

This computational study establishes a correlation between the elastic properties of COFs and their building-blocks towards the rational design of new materials with tailored properties.

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