Intrinsically disordered proteins in biology: One for all, all for one

Yruela, Inmaculada; Neira, José L.

doi:10.1016/j.abb.2020.108328

Cited by 6 publications

(4 citation statements)

References 33 publications

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“…It is important to note that the functions of IDPs are diverse and context-dependent, and their roles can vary across different biological systems and processes [28,29]. For example, some IDPs are involved in cellular signaling pathways and regulatory networks, acting as molecular switches that undergo disorder-to-order transitions upon binding to specific partners or post-translational modifications [30]. In the case of Oxa1-CTD, although it did not exhibit stable secondary structures, it could form transient secondary structure elements, which could be further stabilized through binding to other partners.…”

Section: Discussionmentioning

confidence: 99%

NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes

Liu,

Yang,

Ruan

et al. 2023

IJMS

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In mitochondria, the major subunits of oxidative phosphorylation complexes are translated by the mitochondrial ribosome (mito-ribosome). The correct insertion and assembly of these subunits into the inner mitochondrial membrane (IMM) are facilitated by mitochondrial oxidase assembly protein 1 (Oxa1) during the translation process. This co-translational insertion process involves an association between the mito-ribosome and the C-terminus of Oxa1 (Oxa1-CTD) Nuclear magnetic resonance (NMR) methods were mainly used to investigate the structural characterization of yeast Oxa1-CTD and its mode of interaction with the E. coli 70S ribosome. Oxa1-CTD forms a transient α-helical structure within the residues P342–Q385, which were reported to form an α-helix when combining with the ribosome. Two conserved contact sites that could interact with the ribosome were further identified. The first site was located on the very end of the N-terminus (V321–I327), and the second one encompassed a stretch of amino acid residues I348–Q370. Based on our discoveries and previous reports, a model has been proposed in which Oxa1-CTD interacts with ribosomes, accompanied by transient-to-stable transitions at the second contact site. These observations may enhance our understanding of the potential role of Oxa1-CTD in facilitating the assembly of oxidative phosphorylation complexes and provide insight into the structural characteristics of Oxa1-CTD.

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Section: Discussionmentioning

confidence: 99%

NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes

Liu,

Yang,

Ruan

et al. 2023

IJMS

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“…The main point of many works is the recognition of the mechanism of amyloid transformation [ 17 , 18 , 19 , 20 ]. One of the proposed approaches links amyloid transformation with intrinsically disordered proteins [ 21 , 22 , 23 , 24 , 25 , 26 ]. Experiments identify external factors favoring the amyloid transformation [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

Roterman

Stąpor

Fabian

et al. 2021

IJMS

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The role of the environment in amyloid formation based on the fuzzy oil drop model (FOD) is discussed here. This model assumes that the hydrophobicity distribution within a globular protein is consistent with a 3D Gaussian (3DG) distribution. Such a distribution is interpreted as the idealized effect of the presence of a polar solvent—water. A chain with a sequence of amino acids (which are bipolar molecules) determined by evolution recreates a micelle-like structure with varying accuracy. The membrane, which is a specific environment with opposite characteristics to the polar aquatic environment, directs the hydrophobic residues towards the surface. The modification of the FOD model to the FOD-M form takes into account the specificity of the cell membrane. It consists in “inverting” the 3DG distribution (complementing the Gaussian distribution), which expresses the exposure of hydrophobic residues on the surface. It turns out that the influence of the environment for any protein (soluble or membrane-anchored) is the result of a consensus factor expressing the participation of the polar environment and the “inverted” environment. The ratio between the proportion of the aqueous and the “reversed” environment turns out to be a characteristic property of a given protein, including amyloid protein in particular. The structure of amyloid proteins has been characterized in the context of prion, intrinsically disordered, and other non-complexing proteins to cover a wider spectrum of molecules with the given characteristics based on the FOD-M model.

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“…The unstructured segments are the so-called intrinsically disordered regions (IDRs). [17][18][19] IDRs were present in at least 2.0% of archaeal, 4.2% of eubacterial and 33.0% of eukaryotic proteins. 20 IDPs/IDRs are generally found in nature.…”

Section: Introductionmentioning

confidence: 99%

“…Ab[16][17][18][19][20][21][22] Dimer normalized distributions of the radius of gyration (R g ), the end-to-end distance (d ee ), the order parameter (P 2 ), the intermolecular backbone H-bonds (N hbond C ), the intermolecular side chainÀside chain contacts (N sc C ), and the solvent accessible surface area (SASA). Reprinted with permission from Man et al148 Copyright 2019 American Chemical Society.…”

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confidence: 99%

Folding and self-assembly of short intrinsically disordered peptides and protein regions

Argudo

Giner‐Casares

2021

Nanoscale Adv.

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Intrinsically disordered proteins in biology: One for all, all for one

Cited by 6 publications

References 33 publications

NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes

NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes

In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

Folding and self-assembly of short intrinsically disordered peptides and protein regions

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