scholarly journals Self-assembly of toroidal proteins explored using native mass spectrometry

2018 ◽  
Vol 9 (28) ◽  
pp. 6099-6106 ◽  
Author(s):  
N. Amy Yewdall ◽  
Timothy M. Allison ◽  
F. Grant Pearce ◽  
Carol V. Robinson ◽  
Juliet A. Gerrard
Keyword(s):  
Mass Spectrometry ◽  
Self Assembly ◽  
Building Blocks ◽  
Native Mass Spectrometry ◽  
Quaternary Structures ◽  
Protein Nanotubes

The peroxiredoxins are a well characterised family of toroidal proteins which can self-assemble into a striking array of quaternary structures, including protein nanotubes, making them attractive as building blocks for nanotechnology.

scholarly journals Metallo-organic ensembles of tritopic subphthalocyanine ligands

2017 ◽  
Vol 21 (12) ◽  
pp. 782-789 ◽  
Author(s):  
M. Ángel Revuelta-Maza ◽  
Ettore Fazio ◽  
Gema de la Torre ◽  
Tomás Torres
Keyword(s):  
Mass Spectrometry ◽  
Self Assembly ◽  
Direct Injection ◽  
Building Blocks ◽  
The Self ◽  
Assembly Process ◽  
Text Structures ◽  
Assembly Method ◽  
Injection Techniques

Organic building blocks containing amines and aldehydes can be used for the preparation of complex metallo-organic structures, such as M[Formula: see text]L[Formula: see text] triple helicates or face-capped M[Formula: see text]L[Formula: see text] tetrahedral cages, through the formation of both dynamic covalent and coordinative linkages during the self-assembly process. Herein we describe how the subcomponent self-assembly method can be succesfully applied over a triamine-functionalized subphthalocyanine (SubPc) ligand to build metallo-supramolecular helicates. Two isomeric SubPcs (C[Formula: see text]-SubPc1 and C[Formula: see text]-SubPc1) have been prepared from the corresponding C[Formula: see text]-SubPcI[Formula: see text] and C[Formula: see text]-SubPcI[Formula: see text] precursors under optimized Suzuki conditions. We selected the tritopic C[Formula: see text]-SubPc1 derivative as ligand for the subcomponent self-assembly experiments, which involved the reaction with 2-formylpyridine and different Fe(II) salts. The self-assembly process was mainly studied by mass spectrometry (ESI direct injection techniques), and in all the conditions applied, we could observe the formation of helicate-type Fe[Formula: see text]SubPc[Formula: see text] structures and/or Fe[Formula: see text]SubPc[Formula: see text] species, which can be considered as open precursors of Fe[Formula: see text]SubPc[Formula: see text] tetrahedral cages.

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.

A Bottom-Up Approach to Solution-Processed, Atomically Precise Graphitic Cylinders on Surfaces

2018 ◽  
Author(s):  
Erik Leonhardt ◽  
Jeff M. Van Raden ◽  
David Miller ◽  
Lev N. Zakharov ◽  
Benjamin Aleman ◽  
...  
Keyword(s):  
Self Assembly ◽  
Carbon Nanostructures ◽  
Carbon Nanomaterials ◽  
Circle Packing ◽  
Pyrolytic Graphite ◽  
Building Blocks ◽  
Bottom Up ◽  
Casting Technique ◽  
New Class ◽  
Solution Casting Technique

Extended carbon nanostructures, such as carbon nanotubes (CNTs), exhibit remarkable properties but are difficult to synthesize uniformly. Herein, we present a new class of carbon nanomaterials constructed via the bottom-up self-assembly of cylindrical, atomically-precise small molecules. Guided by supramolecular design principles and circle packing theory, we have designed and synthesized a fluorinated nanohoop that, in the solid-state, self-assembles into nanotube-like arrays with channel diameters of precisely 1.63 nm. A mild solution-casting technique is then used to construct vertical “forests” of these arrays on a highly-ordered pyrolytic graphite (HOPG) surface through epitaxial growth. Furthermore, we show that a basic property of nanohoops, fluorescence, is readily transferred to the bulk phase, implying that the properties of these materials can be directly altered via precise functionalization of their nanohoop building blocks. The strategy presented is expected to have broader applications in the development of new graphitic nanomaterials with π-rich cavities reminiscent of CNTs.

Reversible microscale assembly of nanoparticles driven by the phase transition of a thermotropic liquid crystal

2017 ◽  
Author(s):  
Niamh Mac Fhionnlaoich ◽  
Stephen Schrettl ◽  
Nicholas B. Tito ◽  
Ye Yang ◽  
Malavika Nair ◽  
...  
Keyword(s):  
Phase Transition ◽  
Liquid Crystal ◽  
Self Assembly ◽  
Nematic Phase ◽  
Hierarchical Control ◽  
Building Blocks ◽  
Model System ◽  
Microscopic Level ◽  
Reversible Process ◽  
Thermotropic Liquid Crystal

The arrangement of nanoscale building blocks into patterns with microscale periodicity is challenging to achieve via self-assembly processes. Here, we report on the phase transition-driven collective assembly of gold nanoparticles in a thermotropic liquid crystal. A temperature-induced transition from the isotropic to the nematic phase leads to the assembly of individual nanometre-sized particles into arrays of micrometre-sized aggregates, whose size and characteristic spacing can be tuned by varying the cooling rate. This fully reversible process offers hierarchical control over structural order on the molecular, nanoscopic, and microscopic level and is an interesting model system for the programmable patterning of nanocomposites with access to micrometre-sized periodicities.

Rapid Online Buffer Exchange: A Method for Screening of Proteins, Protein Complexes, and Cell Lysates by Native Mass Spectrometry

2019 ◽  
Author(s):  
Zachary VanAernum ◽  
Florian Busch ◽  
Benjamin J. Jones ◽  
Mengxuan Jia ◽  
Zibo Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Speed ◽  
Structural Information ◽  
Protein Complexes ◽  
High Sensitivity ◽  
Native Mass Spectrometry ◽  
Structural Features ◽  
Consumer Products ◽  
Cell Lysates ◽  
Protein Expression And Purification

It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes, and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is timeconsuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes, or clarified cell lysates. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization.

Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single Particle Cryo-EM

2020 ◽  
Author(s):  
Paul Dominic B. Olinares ◽  
Jin Young Kang ◽  
Eliza Llewellyn ◽  
Courtney Chiu ◽  
James Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Single Particle ◽  
Native Mass Spectrometry ◽  
Optimal Sample

scholarly journals Synthesis and Self-assembly of Amphiphilic Precision Glycomacromolecules

2021 ◽  
Author(s):  
Alexander Banger ◽  
Julian Sindram ◽  
Marius Otten ◽  
Jessica Kania ◽  
Alexander Strzelczyk ◽  
...  
Keyword(s):  
Self Assembly ◽  
Solid Phase ◽  
Building Blocks ◽  
Polymer Synthesis

We present the synthesis of so called amphiphilic glycomacromolecules (APGs) by using solid-phase polymer synthesis. Based on tailor made building blocks, monosdisperse APGs with varying compositions are synthesized, introducing carbohydrate...

scholarly journals DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions

2021 ◽  
Author(s):  
Anirban Ghosh ◽  
Eric Largy ◽  
Valérie Gabelica
Keyword(s):  
Mass Spectrometry ◽  
Drug Targets ◽  
Native Mass Spectrometry ◽  
Drug Binding ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
Nmr Structures ◽  
G Quadruplex ◽  
Screening Assays

Abstract G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).

scholarly journals Development of a target identification approach using native mass spectrometry

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miaomiao Liu ◽  
Wesley C. Van Voorhis ◽  
Ronald J. Quinn
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Target Identification ◽  
Native Mass Spectrometry ◽  
Pharmaceutical Drugs ◽  
Ligand Complex ◽  
Experimental Conditions ◽  
Protein Mixture ◽  
Native Ms ◽  
Drug Target Identification

AbstractA key step in the development of new pharmaceutical drugs is the identification of the molecular target and distinguishing this from all other gene products that respond indirectly to the drug. Target identification remains a crucial process and a current bottleneck for advancing hits through the discovery pipeline. Here we report a method, that takes advantage of the specific detection of protein–ligand complexes by native mass spectrometry (MS) to probe the protein partner of a ligand in an untargeted method. The key advantage is that it uses unmodified small molecules for binding and, thereby, it does not require labelled ligands and is not limited by the chemistry required to tag the molecule. We demonstrate the use of native MS to identify known ligand–protein interactions in a protein mixture under various experimental conditions. A protein–ligand complex was successfully detected between parthenolide and thioredoxin (PfTrx) in a five-protein mixture, as well as when parthenolide was mixed in a bacterial cell lysate spiked with PfTrx. We provide preliminary data that native MS could be used to identify binding targets for any small molecule.

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