Search results for "molecular machine"

Quantitative characterization of translational riboregulators using an in vitro transcription–translation system

2018

Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX-TL) system provides valuable information about the performances of in silico designed riboregulators. We first propose a …

Fracture Mechanics of Collagen Fibrils: Influence of Natural Cross-Links

2013

AbstractTendons are important load-bearing structures, which are frequently injured in both sports and work. Type I collagen fibrils are the primary components of tendons and carry most of the mechanical loads experienced by the tissue, however, knowledge of how load is transmitted between and within fibrils is limited. The presence of covalent enzymatic cross-links between collagen molecules is an important factor that has been shown to influence mechanical behavior of the tendons. To improve our understanding of how molecular bonds translate into tendon mechanics, we used an atomic force microscopy technique to measure the mechanical behavior of individual collagen fibrils loaded to failu…

Autonomous artificial nanomotor powered by sunlight

2006

Light excitation powers the reversible shuttling movement of the ring component of a rotaxane between two stations located at a 1.3-nm distance on its dumbbell-shaped component. The photoinduced shuttling movement, which occurs in solution, is based on a “four-stroke” synchronized sequence of electronic and nuclear processes. At room temperature the deactivation time of the high-energy charge-transfer state obtained by light excitation is ≈10 μs, and the time period required for the ring-displacement process is on the order of 100 μs. The rotaxane behaves as an autonomous linear motor and operates with a quantum efficiency up to ≈12%. The investigated system is a unique example of an artif…

Molecular Rearrangement of an Aza-Scorpiand Macrocycle Induced by pH: A Computational Study †

2016

Rearrangements and their control are a hot topic in supramolecular chemistry due to the possibilities that these phenomena open in the design of synthetic receptors and molecular machines. Macrocycle aza-scorpiands constitute an interesting system that can reorganize their spatial structure depending on pH variations or the presence of metal cations. In this study, the relative stabilities of these conformations were predicted computationally by semi-empirical and density functional theory approximations, and the reorganization from closed to open conformations was simulated by using the Monte Carlo multiple minimum method Financial support by the Spanish Ministerio de Economía y Competitiv…

Tips and turns of bacteriophytochrome photoactivation

2020

Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module,…

ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space.

2015

Molecular machines or macromolecular complexes are supramolecular assemblies of biomolecules that ensure cellular homeostasis. Structure determination of those complexes in a purified state is often a tedious undertaking due to the compositional complexity and the related relative structural instability. To improve the stability of macromolecular complexes in vitro, we present here a generic method that optimizes the stability, homogeneity and solubility of macromolecular complexes by sparse-matrix screening of their thermal unfolding behaviour in the presence of various buffers and small molecules. The method includes the automated analysis of thermal unfolding curves based on a newly deve…

Towards Organization of Molecular Machines at Interfaces. Langmuir Films and Langmuir-Blodgett Multilayers of an Acid-Base Switchable Rotaxane

2006

In this context we investigated, for the first time, the organi-zation of a non-amphiphilic tricationic switchable rotaxaneand its dumbbell-shaped component into Langmuir films andLangmuir–Blodgett (LB) multilayers by using a cospreadingstrategy. The Langmuir films have been characterized by sur-face pressure–area (

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

2020

Crown ethers are common building blocks in supramolecular chemistry and are frequently applied as cation sensors or as subunits in synthetic molecular machines. Developing switchable and specifically designed crown ethers enables the implementation of function into molecular assemblies. Seven tailor-made redox-active crown ethers incorporating tetrathiafulvalene (TTF) or naphthalene diimide (NDI) as redox-switchable building blocks are described with regard to their potential to form redox-switchable rotaxanes. A combination of isothermal titration calorimetry and voltammetric techniques reveals correlations between the binding energies and redox-switching properties of the corresponding ps…

Directional Shuttling of a Stimuli-Responsive Cone-Like Macrocycle on a Single-State Symmetric Dumbbell Axle

2018

Rotaxane-based molecular shuttles are often operated using low-symmetry axles and changing the states of the binding stations. A molecular shuttle capable of directional shuttling of an acid-responsive cone-like macrocycle on a single-state symmetric dumbbell axle is now presented. The axle contains three binding stations: one symmetric di(quaternary ammonium) station and two nonsymmetric phenyl triazole stations arranged in opposite orientations. Upon addition of an acid, the protonated macrocycle shuttles from the di(quaternary ammonium) station to the phenyl triazole binding station closer to its butyl groups. This directional shuttling presumably originates from charge repulsion and an …

Preface

2012