Experimental methods to study intrinsically disordered proteins

Nag, Niharika; Chetri, Purna B; Uversky, Vladimir N.; Giri, Rajanish; Tripathi, Timir

doi:10.1016/b978-0-323-90264-9.00031-3

Cited by 7 publications

(5 citation statements)

References 94 publications

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“…Both isoforms have a significant amount of antiparallel β-sheets and a few α-helices, consistent with the folds of the C 2 H 2 and PHD domains, each consisting of one α-helix and a pair of two antiparallel β-strands. Although the CD spectra revealed distinct fingerprints for the two isoforms, characterising IDPs containing folded domains interspersed with IDRs remains challenging by far-UV CD spectroscopy [ 85 ]. Nevertheless, the C-TER regions seem to adopt collapsed structures where β-sheets and α-helices in ZnFs are separated by disordered segments.…”

Section: Discussionmentioning

confidence: 99%

Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a

Leyder

Mignon

Mottet

et al. 2022

IJMS

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Double-PHD fingers 3 (DPF3) is a BAF-associated human epigenetic regulator, which is increasingly recognised as a major contributor to various pathological contexts, such as cardiac defects, cancer, and neurodegenerative diseases. Recently, we unveiled that its two isoforms (DPF3b and DPF3a) are amyloidogenic intrinsically disordered proteins. DPF3 isoforms differ from their C-terminal region (C-TERb and C-TERa), containing zinc fingers and disordered domains. Herein, we investigated the disorder aggregation properties of C-TER isoforms. In agreement with the predictions, spectroscopy highlighted a lack of a highly ordered structure, especially for C-TERa. Over a few days, both C-TERs were shown to spontaneously assemble into similar antiparallel and parallel β-sheet-rich fibrils. Altered metal homeostasis being a neurodegeneration hallmark, we also assessed the influence of divalent metal cations, namely Cu2+, Mg2+, Ni2+, and Zn2+, on the C-TER aggregation pathway. Circular dichroism revealed that metal binding does not impair the formation of β-sheets, though metal-specific tertiary structure modifications were observed. Through intrinsic and extrinsic fluorescence, we found that metal cations differently affect C-TERb and C-TERa. Cu2+ and Ni2+ have a strong inhibitory effect on the aggregation of both isoforms, whereas Mg2+ impedes C-TERb fibrillation and, on the contrary, enhances that of C-TERa. Upon Zn2+ binding, C-TERb aggregation is also hindered, and the amyloid autofluorescence of C-TERa is remarkably red-shifted. Using electron microscopy, we confirmed that the metal-induced spectral changes are related to the morphological diversity of the aggregates. While metal-treated C-TERb formed breakable and fragmented filaments, C-TERa fibrils retained their flexibility and packing properties in the presence of Mg2+ and Zn2+ cations.

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Section: Discussionmentioning

confidence: 99%

Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a

Leyder

Mignon

Mottet

et al. 2022

IJMS

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“…Critically, given the absence of experimental atomic-resolution structural biology methods directly capable of studying such systems, investigators will need to rely on indirect and/or low resolution experimental methods to corroborate observables from the simulation results as a means of validation. Indeed, a similar approach combining such experimental methods with simulations has been evolving to study intrinsically disordered proteins [ 208 , 209 , 210 , 211 ].…”

Section: Discussionmentioning

confidence: 99%

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

Guvench

2022

Molecules

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This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan’s flexibility and capacity for intra- and intermolecular non-covalent interactions.

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“…The use of complementary datasets from techniques such as CD, NMR, and cryo-EM has the potential to alleviate this bias ( 141 , 142 ). Unlike X-ray crystallography, these techniques allow one to directly discern the unique signatures of IDPs and IDRs ( 144 ). Rapid advances in artificial intelligence and machine learning promise to provide highly accurate structure prediction for proteins, including disordered ensembles ( 145 , 146 , 147 ).…”

Section: Structural Disorder and Flanking Regions Of Amyloid Coresmentioning

confidence: 99%

Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity

Bhopatkar

Kayed

2023

Journal of Biological Chemistry

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Experimental methods to study intrinsically disordered proteins

Cited by 7 publications

References 94 publications

Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a

Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity

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