Solvent-Induced Tuning of Internal Structure in a Protein Amyloid Protofibril

Jha, Anjali; Narayan, Satya; Udgaonkar, Jayant B.; Krishnamoorthy, G.

doi:10.1016/j.bpj.2012.07.021

Cited by 12 publications

(6 citation statements)

References 49 publications

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“…This indicates that presence of TFE not only acts by modulating the formation of the initial nucleus but also induces structural diversity in URN1-FF fibrils. Our results are consistent with recent data obtained for barstar, in which the protofibrils formed in the presence and absence of trifluorethanol were shown to differ not only in the orientation and number of β-sheet motifs but also in the number of protein residues involved in the maintenance of the protofibrillar structure [33]. …”

Section: Resultssupporting

confidence: 93%

Trifluoroethanol Modulates Amyloid Formation by the All α-Helical URN1 FF Domain

Marinelli

Castillo

Ventura

2013

IJMS

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Amyloid fibril formation is implicated in different human diseases. The transition between native α-helices and nonnative intermolecular β-sheets has been suggested to be a trigger of fibrillation in different conformational diseases. The FF domain of the URN1 splicing factor (URN1-FF) is a small all-α protein that populates a molten globule (MG) at low pH. Despite the fact that this conformation maintains most of the domain native secondary structure, it progressively converts into β-sheet enriched and highly ordered amyloid fibrils. In this study, we investigated if 2,2,2-trifluoroethanol (TFE) induced conformational changes that affect URN1-FF amyloid formation. Despite TFE having been shown to induce or increase the aggregation of both globular and disordered proteins at moderate concentrations, we demonstrate here that in the case of URN1-FF it reinforces its intrinsic α-helical structure, which competes the formation of aggregated assemblies. In addition, we show that TFE induces conformational diversity in URN1-FF fibrils, in such a way that the fibrils formed in the presence and absence of the cosolvent represent different polymorphs. It is suggested that the effect of TFE on both the soluble and aggregated states of URN1-FF depends on its ability to facilitate hydrogen bonding.

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Section: Resultssupporting

confidence: 93%

Trifluoroethanol Modulates Amyloid Formation by the All α-Helical URN1 FF Domain

Marinelli

Castillo

Ventura

2013

IJMS

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“…Fluorinated hydrocarbons such as trifluoroethanol (TFE) have been widely used for years to accelerate the rate of amyloid formation ( 47 , 48 , 49 ) and control fibril morphology ( 50 ) during in vitro experiments. The chemical mechanisms of action of fluorinated co-solvents on protein structure, folding, and self-assembly are not clearly understood ( 51 , 52 ).…”

Section: Resultsmentioning

confidence: 99%

How Do Gyrating Beads Accelerate Amyloid Fibrillization?

Abdolvahabi

Shi

Rasouli

et al. 2017

Biophysical Journal

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The chemical and physical mechanisms by which gyrating beads accelerate amyloid fibrillization in microtiter plate assays are unclear. Identifying these mechanisms will help optimize high-throughput screening assays for molecules and mutations that modulate aggregation and might explain why different research groups report different rates of aggregation for identical proteins. This article investigates how the rate of superoxide dismutase-1 (SOD1) fibrillization is affected by 12 different beads with a wide range of hydrophobicity, mass, stiffness, and topology but identical diameter. All assays were performed on D90A apo-SOD1, which is a stable and wild-type-like variant of SOD1. The most significant and uniform correlation between any material property of each bead and that bead's effect on SOD1 fibrillization rate was with regard to bead mass. A linear correlation existed between bead mass and rate of fibril elongation (R = 0.7): heavier beads produced faster rates and shorter fibrils. Nucleation rates (lag time) also correlated with bead mass, but only for non-polymeric beads (i.e., glass, ceramic, metallic). The effect of bead mass on fibrillization correlated (R = 0.96) with variations in buoyant forces and contact forces (between bead and microplate well), and was not an artifact of residual momentum during intermittent gyration. Hydrophobic effects were observed, but only for polymeric beads: lag times correlated negatively with contact angle of water and degree of protein adhesion (surface adhesion and hydrophobic effects were negligible for non-polymeric beads). These results demonstrate that contact forces (alone) explain kinetic variation among non-polymeric beads, whereas surface hydrophobicity and contact forces explain kinetic variation among polymeric beads. This study also establishes conditions for high-throughput amyloid assays of SOD1 that enable the control over fibril morphologies and produce eightfold faster lag times and fourfold less stochasticity than in previous studies.

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“…[27,28] Ti-sapphire pulses at 732 nm frequency doubled to 366 nm using GWU frequency doubler by Spectra Physics, USA, were used for exciting CDs.…”

Section: Time-resolved Fluorescencementioning

confidence: 99%

Insight into the Excitation‐Dependent Fluorescence of Carbon Dots

et al. 2019

Self Cite

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High quantum yield, photoluminescence tunability, and sensitivity to the environment are a few distinct trademarks that make carbon nanodots (CDs) interesting for fundamental research, with potential to replace the prevalent inorganic semiconductor quantum dots. Currently, application and fundamental understanding of CDs are constrained because it is difficult to make a quantitative comparison among different types of CDs simply because their photoluminescence properties are directly linked to their size distribution, the surface functionalization, the carbon core structures (graphitic or amorphous) and the number of defects. Herein, we report a facile one-step synthesis of mono-dispersed and highly fluorescent nanometre size CDs from a 'family' of glucose-based sugars. These CDs are stable in aqueous solutions with photoluminescence in the visible range. Our results show several common features in the family of CDs synthesized in that the fluorescence, in the visible region, is due to a weak absorption in the 300-400 nm from a heterogeneous population of fluorophores. Fluorescence quenching experiments suggest the existence of not only surface-exposed fluorophores but more importantly solvent inaccessible fluorophores present within the core of CDs. Interestingly, time-resolved fluorescence anisotropy experiments directly suggest that a fast exchange of excitation energy occurs that results in a homo-FRET based depolarization within 150 ps of excitation.[a] Dr.

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Solvent-Induced Tuning of Internal Structure in a Protein Amyloid Protofibril

Cited by 12 publications

References 49 publications

Trifluoroethanol Modulates Amyloid Formation by the All α-Helical URN1 FF Domain

Trifluoroethanol Modulates Amyloid Formation by the All α-Helical URN1 FF Domain

How Do Gyrating Beads Accelerate Amyloid Fibrillization?

Insight into the Excitation‐Dependent Fluorescence of Carbon Dots

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