Protein interface redesign facilitates conversion of zero-dimensional protein nanomaterials to their one- and two-dimensional analogues

2021 ◽  
Author(s):  
Xiaorong Zhang ◽  
Yu Liu ◽  
Bowen Zheng ◽  
Jiachen Zang ◽  
Chenyan Lv ◽  
...  
Keyword(s):  
Thermotoga Maritima ◽  
Building Blocks ◽  
Protein Interface ◽  
Protein Assemblies ◽  
Viral Capsids ◽  
Different Dimensions ◽  
2D Nanomaterials ◽  
Dimeric Protein ◽  
External Stimuli ◽  
Artificial Protein

Abstract Although various artificial protein nanoarchitectures have been constructed, controlling conversion between protein assemblies with different dimensions has largely been unexplored. Here, we describe a simple, effective approach to regulate conversion between 0D protein nanomaterials and their 1D or 2D analogues by adjusting the geometric arrangement of dimeric protein building blocks. Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimeric protein, twelve of which interact with each other in a head-to-side manner to generate 0D 24-meric protein nanocage in the presence of Ca2+. By tuning two contiguous dimeric proteins to interact in a fully or partially side-by-side fashion through protein interface redesign, we can render the conversion of the inherent salt-mediated 0D protein nanocage into 1D or 2D nanomaterials in response to multiple external stimuli. Thus, one kind of dimeric protein building block can generate three protein materials with different dimensions in a manner that highly resembles natural pentamer building blocks from viral capsids that form different protein assemblies.

scholarly journals Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiaorong Zhang ◽  
Yu Liu ◽  
Bowen Zheng ◽  
Jiachen Zang ◽  
Chenyan Lv ◽  
...  
Keyword(s):  
Self Assembly ◽  
Thermotoga Maritima ◽  
Building Blocks ◽  
The Self ◽  
Protein Interface ◽  
Protein Assemblies ◽  
Viral Capsids ◽  
2D Nanomaterials ◽  
External Stimuli ◽  
Artificial Protein

AbstractAlthough various artificial protein nanoarchitectures have been constructed, controlling the transformation between different protein assemblies has largely been unexplored. Here, we describe an approach to realize the self-assembly transformation of dimeric building blocks by adjusting their geometric arrangement. Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer; twelve of these dimers interact with each other in a head-to-side manner to generate 24-meric hollow protein nanocage in the presence of Ca2+ or PEG. By tuning two contiguous dimeric proteins to interact in a fully or partially side-by-side fashion through protein interface redesign, we can render the self-assembly transformation of such dimeric building blocks from the protein nanocage to filament, nanorod and nanoribbon in response to multiple external stimuli. We show similar dimeric protein building blocks can generate three kinds of protein materials in a manner that highly resembles natural pentamer building blocks from viral capsids that form different protein assemblies.

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.

scholarly journals Recent Progress in the Synthesis and Characterization of Diarylethene-based MOFs

2014 ◽  
Vol 70 (a1) ◽  
pp. C1223-C1223
Author(s):  
Jason Benedict ◽  
Ian Walton ◽  
Dan Patel ◽  
Jordan Cox
Keyword(s):  
Chemical Properties ◽  
Building Blocks ◽  
Synthesis And Characterization ◽  
Next Generation ◽  
Design Synthesis ◽  
Thermally Induced ◽  
Potential Applications ◽  
External Stimuli ◽  
Physical And Chemical

Metal-organic Frameworks (MOFs) remain an extremely active area of research given the wide variety of potential applications and the enormous diversity of structures that can be created from their constituent building blocks. While MOFs are typically employed as passive materials, next-generation materials will exhibit structural and/or electronic changes in response to applied external stimuli including light, charge, and pH. Herein we present recent results in which advanced photochromic diarylethenes are combined with MOFs through covalent and non-covalent methods to create photo-responsive permanently porous crystalline materials. This presentation will describe the design, synthesis, and characterization of next-generation photo-switchable diarylethene based ligands which are subsequently used to photo-responsive MOFs. These UBMOF crystals are, by design, isostructural with previously reported non-photoresponsive frameworks which enables a systematic comparison of their physical and chemical properties. While the photoswitching of the isolated ligand in solution is fully reversible, the cycloreversion reaction is suppressed in the UBMOF single crystalline phase. Spectroscopic evidence for thermally induced cycloreversion will be presented, as well as a detailed analysis addressing the limits of X-ray diffraction techniques applied to these systems.

Physiologic Adaptation by Means of Antagonistic Dynamics

2011 ◽  
pp. 3086-3092 ◽  
Author(s):  
Juergen Perl
Keyword(s):  
Response Model ◽  
Input Stimulus ◽  
Mental Work ◽  
Biochemical Adaptation ◽  
Behavioral Systems ◽  
Stimulus Response ◽  
Future Performance ◽  
Different Dimensions ◽  
External Stimuli ◽  
Gathering Data

In particular in technical contexts, information systems and analysing techniques help a lot for gathering data and making information available. Regarding dynamic behavioral systems like athletes or teams in sports, however, the situation is difficult: data from training and competition do not give much information about current and future performance without an appropriate model of interaction and adaptation. Physiologic adaptation is one major aspect of targetoriented behavior, in physical training as well as in mental learning. In a simplified way it can be described by a stimulus- response-model, where external stimuli change situation or status of an organism and so cause activities in order to adapt. This aspect can appear in quite different dimensions like individual biochemical adaptation that needs only milliseconds up to selection of the fittest of a species, which can last millions of years. Well-known examples can be taken from learning processes or other mental work as well as from sport and exercising. Most of those examples are characterized by a phenomenon that we call antagonism: The input stimulus causes two contradicting responses, which control each other and – by balancing out – finally enable to reach a given target. For example, the move of a limb is controlled by antagonistic groups of muscles, and the result of a game is controlled by the efforts of competing teams. In order to understand and eventually improve such adaptation, models are necessary that make the processes transparent and help for simulating dynamics like for example, the increase of heart rate as an reaction of speeding up in jogging. With such models it becomes possible not only to analyze past processes but also to predict and schedule indented future ones. In the Background section, main aspects of modeling antagonistic adaptation systems are briefly discussed, which is followed by a more detailed description of the developed PerPot-model and a number of examples of application in the Main Focus section.

scholarly journals The first ribonucleotide reductase without an activating radical cysteine

2014 ◽  
Vol 70 (a1) ◽  
pp. C1053-C1053
Author(s):  
Oskar Aurelius ◽  
Renzo Johansson ◽  
Viktoria Bågenholm ◽  
Daniel Lundin ◽  
Alexander Balhuizen ◽  
...  
Keyword(s):  
Thermotoga Maritima ◽  
Building Blocks ◽  
Time Frame ◽  
Wide Distribution ◽  
Reduction Reaction ◽  
Cysteine Residue ◽  
Substrate Reduction ◽  
Allosteric Effector ◽  
Metal Cofactor ◽  
The Many

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks for DNA synthesis, and are found in all but a few organisms. RNRs use radical chemistry to catalyze the reduction reaction. Despite RNR having evolved several different mechanisms for generation of different kinds of essential radicals across a large evolutionary time frame, for over 30 years the paradigm has been that this initial radical is always channeled to a strictly conserved cysteine residue directly adjacent to the substrate for initiation of substrate reduction. Such a cysteine residue has been present in the structure of each of the many RNRs determined to date. We present the crystal structure of an anaerobic RNR from the extreme thermophile Thermotoga maritima (tmNrdD), both alone and in complex with allosteric effector dATP and substrate CTP. Remarkably, tmNrdD lacks a cysteine for radical transfer to the substrate, and is the first structurally or biochemically characterized RNR to do so. However in many other respects tmNrdD appears to be a normal anaerobic RNR, including gene structure, expression levels, metal cofactor and binding of allosteric effectors and substrates in the expected conformations. Furthermore, it is possible to generate a glycyl radical as expected. We present evidence that the structure of tmNrdD is representative for the new RNR subclass IIIh, present in all Thermotoga species plus a wider group of bacteria from the distantly related phyla Firmicutes, Bacteroidetes and Proteobacteria, all lacking the canonical cysteine residue. The wide distribution provides further evidence that the subclass IIIh is a functional RNR. Taken together, the results imply that an alternative initiation route for the RNR reduction reaction must exist that do not require channeling through a cysteine side chain.

scholarly journals Biochemical Frequency Control by Synchronisation of Coupled Repressilators: AnIn SilicoStudy of Modules for Circadian Clock Systems

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Thomas Hinze ◽  
Mathias Schumann ◽  
Christian Bodenstein ◽  
Ines Heiland ◽  
Stefan Schuster
Keyword(s):  
Frequency Control ◽  
Building Blocks ◽  
Research Field ◽  
Phase Locked Loops ◽  
Diffusion Parameters ◽  
Interesting Candidate ◽  
Unified View ◽  
External Stimuli ◽  
And Diffusion ◽  
Reaction And Diffusion

Exploration of chronobiological systems emerges as a growing research field within bioinformatics focusing on various applications in medicine, agriculture, and material sciences. From a systems biological perspective, the question arises whether biological control systems for regulation of oscillatory signals and their technical counterparts utilise similar mechanisms. If so, modelling approaches and parameterisation adopted from building blocks can help to identify general components for frequency control in circadian clocks along with gaining insight into mechanisms of clock synchronisation to external stimuli like the daily rhythm of sunlight and darkness. Phase-locked loops could be an interesting candidate in this context. Both, biology and engineering, can benefit from a unified view resulting from systems modularisation. In a first experimental study, we analyse a model of coupled repressilators. We demonstrate its ability to synchronise clock signals in a monofrequential manner. Several oscillators initially deviate in phase difference and frequency with respect to explicit reaction and diffusion rates. Accordingly, the duration of the synchronisation process depends on dedicated reaction and diffusion parameters whose settings still lack to be sufficiently captured analytically.

A light-remote-controllable Core-Shell-Brush nanosystem prepared through a sequential one-pot strategy

2019 ◽  
Author(s):  
Maria Jazmín Penelas ◽  
Cintia Belén Contreras ◽  
Paula C. Angelomé ◽  
Alejandro Wolosiuk ◽  
Omar Azzaroni ◽  
...  
Keyword(s):  
Mechanical Response ◽  
Building Blocks ◽  
Core Shell ◽  
Silica Layer ◽  
Sequential Method ◽  
One Pot ◽  
Direct Light ◽  
Or Gene ◽  
Mechanical Transduction ◽  
External Stimuli

<p>The development of smart nanosystems that transduce external stimuli to physical changes is an inspiring challenge in current materials chemistry. In this framework, hybrid organic-inorganic nanosystems attract great attention due to the combination of building blocks that respond to specific external stimuli. Poly(<i>N</i>-isopropylacrylamide) –PNIPAm- has been explored in temperature-responsive actuators with applications in drug or gene delivery, biocatalysis, or separation. However, little work has been dedicated to produce nanosystems that couple thermal actuation with other external stimuli that can remote-control the mechanical response. In this work, we present a sequential method for obtaining core-shell-brush nanosystems that can transduce light irradiation into a mechanical response through a thermoplasmonic effect. We synthetize hybrid monodisperse silica colloids covered with controllable PNIPAm brushes, produced through a simple and reproducible radical photopolymerization. This methodology can be applied successfully to Au@SiO<sub>2</sub> nanoparticles, leading to a core-shell-brush architecture. When these systems are irradiated with green LED light, direct light-to-heat conversion leads to shrinkage of the polymer layer. Our results demonstrate that modular hybrid nanosystems composed of a plasmonic heating module, a buffer silica layer, and an external thermo-responsive brush can be designed and produced with photo-thermo-mechanical transduction, which can be applied in smart carriers or soft robotics.</p>

Supramolecular Systems Prepared by Terpyridine-containing Pillararenes

2021 ◽  
Author(s):  
Chang Liu ◽  
Le Zhou ◽  
Shuai Cao ◽  
Huacheng Zhang ◽  
Jie Han ◽  
...  
Keyword(s):  
Building Blocks ◽  
Stimuli Responsive ◽  
Supramolecular Systems ◽  
External Stimuli

The recent progresses in the preparation of terpyridine-containing pillararene, as well as the utilization of such building blocks for fabricating external stimuli-responsive supramolecular systems were summarized in this review. Different...

scholarly journals Applications of DNA-Functionalized Proteins

2021 ◽  
Vol 22 (23) ◽  
pp. 12911
Author(s):  
Zhaoqiu Gong ◽  
Yuanyuan Tang ◽  
Ningning Ma ◽  
Wenhong Cao ◽  
Yong Wang ◽  
...  
Keyword(s):  
Rapid Development ◽  
Dna Nanotechnology ◽  
Protein Detection ◽  
Protein Assemblies ◽  
Application Process ◽  
Body Protein ◽  
Recognition Ability ◽  
Biological Catalysis ◽  
Structural Dna Nanotechnology ◽  
Artificial Protein

As an important component that constitutes all the cells and tissues of the human body, protein is involved in most of the biological processes. Inspired by natural protein systems, considerable efforts covering many discipline fields were made to design artificial protein assemblies and put them into application in recent decades. The rapid development of structural DNA nanotechnology offers significant means for protein assemblies and promotes their application. Owing to the programmability, addressability and accurate recognition ability of DNA, many protein assemblies with unprecedented structures and improved functions have been successfully fabricated, consequently creating many brand-new researching fields. In this review, we briefly introduced the DNA-based protein assemblies, and highlighted the limitations in application process and corresponding strategies in four aspects, including biological catalysis, protein detection, biomedicine treatment and other applications.

scholarly journals Increasing the Functional Group Diversity in Helical β-Peptoids: Achievement of Solvent- and pH-Dependent Folding

2020 ◽  
Author(s):  
Isabelle Wellhöfer ◽  
Janina Beck ◽  
Karla Frydenvang ◽  
Stefan Bräse ◽  
Christian Adam Olsen
Keyword(s):  
Metal Ion ◽  
Building Blocks ◽  
Cd Spectroscopy ◽  
Metal Ion Binding ◽  
Helical Content ◽  
Acid And Base ◽  
Coupling Strategy ◽  
Group Diversity ◽  
External Stimuli ◽  
Hydroxy Groups

We report the synthesis of a series of bis-functionalized <i>b</i>-peptoid oligomers of the hexamer length. This was achieved by synthesizing and incorporating protected amino- or azido-functionalized chiral building blocks into precursor oligomers by a trimer segment coupling strategy. The resulting hexamers were readily elaborated to provide target compounds displaying amino groups, carboxy groups, hydroxy groups, or triazolo-pyridines, which should enable metal ion binding. Analysis of the novel hexamers by CD spectroscopy and HSQC NMR spectroscopy revealed robust helical folding propensity in acetonitrile. CD analysis showed solvent-dependent degree of helical content in the structural ensembles when adding different ratios of protic solvents including aqueous buffer. These studies were enabled by the substantial increase in solubility compared to previously analyzed <i>b</i>-peptoid oligomers. This also allowed for investigation of the effect of pH on folding propensity of the amino- and carboxy-functionalized oligomers, respectively. Interestingly, we could demonstrate a reversible effect of sequentially adding acid and base, resulting in a switching between compositions of folded ensembles with varying helical content. We envision that the present discoveries can form the basis for the development of functional peptidomimetic materials responsive to external stimuli.

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