Single-Molecule Measurements of the Impact of Lipid Phase Behavior on Anchor Strengths

2005 ◽  
Vol 109 (12) ◽  
pp. 5985-5993 ◽  
Author(s):  
Julie A. Wieland ◽  
Andrew A. Gewirth ◽  
Deborah E. Leckband
Keyword(s):  
Phase Behavior ◽  
Single Molecule ◽  
Lipid Phase ◽  
The Impact

Mechanically-Tunable Quantum Interference in Ferrocene-Based Single-Molecule Junctions

2020 ◽  
Author(s):  
María Camarasa-Gómez ◽  
Daniel Hernangómez-Pérez ◽  
Michael S. Inkpen ◽  
Giacomo Lovat ◽  
E-Dean Fung ◽  
...  
Keyword(s):  
Single Molecule ◽  
Quantum Interference ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Ferrocene Derivative ◽  
Single Molecule Junctions ◽  
Molecule Junction ◽  
Single Molecule Junction ◽  
The Impact ◽  
D Orbitals

Ferrocenes are ubiquitous organometallic building blocks that comprise a Fe atom sandwiched between two cyclopentadienyl (Cp) rings that rotate freely at room temperature. Of widespread interest in fundamental studies and real-world applications, they have also attracted<br>some interest as functional elements of molecular-scale devices. Here we investigate the impact of<br>the configurational degrees of freedom of a ferrocene derivative on its single-molecule junction<br>conductance. Measurements indicate that the conductance of the ferrocene derivative, which is<br>suppressed by two orders of magnitude as compared to a fully conjugated analog, can be modulated<br>by altering the junction configuration. Ab initio transport calculations show that the low conductance is a consequence of destructive quantum interference effects that arise from the hybridization of metal-based d-orbitals and the ligand-based π-system. By rotating the Cp rings, the hybridization, and thus the quantum interference, can be mechanically controlled, resulting in a conductance modulation that is seen experimentally.<br>

Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

2018 ◽  
Author(s):  
Alexander Carl DeHaven
Keyword(s):  
Energy Transfer ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Förster Resonance Energy Transfer ◽  
U2 Snrna ◽  
Folding Dynamics ◽  
The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

scholarly journals The Impact of Lipid Handling and Phase Distribution on the Acoustic Behavior of Microbubbles

Pharmaceutics ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 119
Author(s):  
Simone A.G. Langeveld ◽  
Inés Beekers ◽  
Gonzalo Collado-Lara ◽  
Antonius F. W. van der Steen ◽  
Nico de Jong ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Molecular Imaging ◽  
High Speed ◽  
Phase Distribution ◽  
Direct Method ◽  
Ultrasound Contrast Agents ◽  
Lipid Phase ◽  
Acoustic Behavior ◽  
Ultrasound Molecular Imaging ◽  
The Impact

Phospholipid-coated microbubbles are ultrasound contrast agents that can be employed for ultrasound molecular imaging and drug delivery. For safe and effective implementation, microbubbles must respond uniformly and predictably to ultrasound. Therefore, we investigated how lipid handling and phase distribution affected the variability in the acoustic behavior of microbubbles. Cholesterol was used to modify the lateral molecular packing of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)-based microbubbles. To assess the effect of lipid handling, microbubbles were produced by a direct method, i.e., lipids directly dispersed in an aqueous medium or indirect method, i.e., lipids first dissolved in an organic solvent. The lipid phase and ligand distribution in the microbubble coating were investigated using confocal microscopy, and the acoustic response was recorded with the Brandaris 128 ultra-high-speed camera. In microbubbles with 12 mol% cholesterol, the lipids were miscible and all in the same phase, which resulted in more buckle formation, lower shell elasticity and higher shell viscosity. Indirect DSPC microbubbles had a more uniform response to ultrasound than direct DSPC and indirect DSPC-cholesterol microbubbles. The difference in lipid handling between direct and indirect DSPC microbubbles significantly affected the acoustic behavior. Indirect DSPC microbubbles are the most promising candidate for ultrasound molecular imaging and drug delivery applications.

scholarly journals Next-Generation Sequencing: From Basic Research to Diagnostics

2009 ◽  
Vol 55 (4) ◽  
pp. 641-658 ◽  
Author(s):  
Karl V Voelkerding ◽  
Shale A Dames ◽  
Jacob D Durtschi
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Basic Research ◽  
Clinical Diagnostics ◽  
Massively Parallel ◽  
Next Generation ◽  
New Paradigm ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. Summary: In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.

The Effects of Protein Charge Patterning on Complex Coacervation

2021 ◽  
Author(s):  
Nicholas Zervoudis ◽  
Allie Obermeyer
Keyword(s):  
Phase Boundary ◽  
Phase Behavior ◽  
Predictive Models ◽  
Phase Portraits ◽  
Complex Coacervation ◽  
Protein Encapsulation ◽  
Protein Charge ◽  
Polypeptide Sequence ◽  
The Impact ◽  
Coacervate Phase

The complex coacervation of proteins with other macromolecules has applications in protein encapsulation and delivery and for determining the function of cellular coacervates. Theoretical or empirical predictions for protein coacervates would enable the design of these coacervates with tunable and predictable structure-function relationships; unfortunately, no such theories exist. To help establish predictive models, the impact of protein-specific parameters on complex coacervation were probed in this study. The complex coacervation of sequence-specific, polypeptide-tagged, GFP variants and a strong synthetic polyelectrolyte was used to evaluate the effects of protein charge patterning on phase behavior. Phase portraits for the protein coacervates demonstrated that charge patterning dictates the protein’s binodal phase boundary. Protein concentrations over 100 mg mL<sup>-1</sup> were achieved in the coacervate phase, with concentrations dependent on the polypeptide sequence. In addition to shifting the binodal phase boundary, polypeptide charge patterning provided entropic advantages over isotropically patterned proteins. Together, these results show that modest changes of only a few amino acids alter the coacervation thermodynamics and can be used to tune the phase behavior of polypeptides or proteins of interest.

scholarly journals Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis

2018 ◽  
Vol 115 (45) ◽  
pp. 11525-11530 ◽  
Author(s):  
Marcelo E. Guerin ◽  
Guillaume Stirnemann ◽  
David Giganti
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Conformational Sampling ◽  
Enzymatic Reactions ◽  
Sequence Specificity ◽  
Proteomics Data ◽  
Conformational Entropy ◽  
Substrate Peptide ◽  
The Impact

An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.

Strictly linear trinuclear Dy–Ca/Mg–Dy single-molecule magnets: the impact of long-range f–f ferromagnetic interactions on suppressing quantum tunnelling of magnetization leading to slow magnetic relaxation

2017 ◽  
Vol 46 (25) ◽  
pp. 8259-8268 ◽  
Author(s):  
Wan-Ying Zhang ◽  
Yong-Mei Tian ◽  
Hong-Feng Li ◽  
Peng Chen ◽  
Yi-Quan Zhang ◽  
...  
Keyword(s):  
Long Range ◽  
Single Molecule ◽  
Magnetic Relaxation ◽  
Single Molecule Magnets ◽  
Quantum Tunnelling ◽  
Trinuclear Complexes ◽  
Slow Magnetic Relaxation ◽  
Ferromagnetic Interactions ◽  
The Impact

A series of linear trinuclear complexes Ln2M(OQ)8 [Ln(iii) = Dy and Er, M(ii) = Ca and Mg] were structurally and magnetically investigated.

scholarly journals Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88

2018 ◽  
Author(s):  
Ailís O’Carroll ◽  
Brieuc Chauvin ◽  
James Brown ◽  
Ava Meagher ◽  
Joanne Coyle ◽  
...  
Keyword(s):  
Single Molecule ◽  
Self Assembly ◽  
Point Mutations ◽  
Adaptor Protein ◽  
Full Length ◽  
Binary Response ◽  
Death Domain ◽  
Tir Domain ◽  
The Impact

AbstractA novel concept has emerged whereby the higher-order self-assembly of proteins provides a simple and robust mechanism for signal amplification. This appears to be a universal signalling mechanism within the innate immune system, where the recognition of pathogens or danger-associated molecular patterns need to trigger a strong, binary response within cells. Previously, multiple structural studies have been limited to single domains, expressed and assembled at high protein concentrations. We therefore set out to develop new in vitro strategies to characterise the behaviour of full-length proteins at physiological levels. In this study we focus on the adaptor protein MyD88, which contains two domains with different self-assembly properties: a TIR domain that can polymerise similarly to the TIR domain of Mal, and a Death Domain that has been shown to oligomerise with helical symmetry in the Myddosome complex. To visualize the behaviour of full-length MyD88 without purification steps, we use single-molecule fluorescence coupled to eukaryotic cell-free protein expression. These experiments demonstrate that at low protein concentration, only full-length MyD88 forms prion-like polymers. We also demonstrate that the metastability of MyD88 polymerisation creates the perfect binary response required in innate signalling: the system is silenced at normal concentrations but upstream signalling creates a “seed” that triggers polymerisation and amplification of the response. These findings pushed us to re-interpret the role of polymerisation in MyD88-related diseases and we studied the impact of disease-associated point mutations L93P, R196C and L252P/L265P at the molecular level. We discovered that all mutations completely block the ability of MyD88 to polymerise. We also confirm that L252P, a gain-of-function mutation, allows the MyD88 mutant to form extremely stable oligomers, even when expressed at low nanomolar concentrations. Thus, our results are consistent with and greatly add to the findings on the Myddosomes digital ‘all-or-none’ responses and the behaviour of the oncogenic mutation of MyD88.

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