DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server

Barik, Amita; Katuwawala, Akila; Hanson, Jack; Paliwal, Kuldip K.; Zhou, Yaoqi; Kurgan, Lukasz

doi:10.1016/j.jmb.2019.12.030

Cited by 50 publications

(37 citation statements)

References 66 publications

(86 reference statements)

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“…In its C-terminal part, both PrDOS and Disopred3 predicted disordered and highly disordered regions (orange and blue colors, respectively, on Figure 5 A). The tendencies are similar with IUPred2A, ANCHOR2 [ 56 ], and the approaches proposed in DECIPHER [ 70 ]), while N eq was around 2 at these positions (red color on Figure 5 A), i.e., a quite rigid region. Indeed, the visualization of the protein ensemble ( Figure 5 B) does not show any ordered regions, while PB distribution showed ( Figure 5 C, Figures S4 and S5 ) a large proportion of PB d around this region, i.e., a curved region ( Figure 5 D).…”

Section: Discussionsupporting

confidence: 83%

“…Intrinsically-disordered proteins and regions are complicated, as they do not have unique and simple characteristics. Hence, IDPs represent complete disordered proteins that stay disordered, but they can also adopt one conformation when they bind to their ligands or partners [ 66 , 67 ] or participate in multiple systems [ 68 ], they are essential to functions [ 69 , 70 ], drug design [ 71 ], and protein design [ 72 ].…”

Section: Discussionmentioning

confidence: 99%

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Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Brevern

2020

Biomolecules

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Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function theory. Moreover, IDPs are over-represented in major disease pathways and are now often targeted using small molecules for therapeutic purposes. This has had created a complex continuum from order-that encompasses rigid and flexible regions-to disorder regions; the latter being not accessible through classical crystallographic methodologies. In X-ray structures, the notion of order is dictated by access to resolved atom positions, providing rigidity and flexibility information with low and high experimental B-factors, while disorder is associated with the missing (non-resolved) residues. Nonetheless, some rigid regions can be found in disorder regions. Using ensembles of IDPs, their local conformations were analyzed in the light of a structural alphabet. An entropy index derived from this structural alphabet allowed us to propose a continuum of states from rigidity to flexibility and finally disorder. In this study, the analysis was extended to comparing these results to disorder predictions, underlying a limited correlation, and so opening new ideas to characterize and predict disorder.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Brevern

2020

Biomolecules

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“…Several databases gathering information about protein disorder have been developed in the last decade, including DisProt (the largest repository of manually curated intrinsically disordered regions-IDRs, for which disorder has been assessed experimentally) [9,45], MobiDB [46], DisBind [47], FuzDB [48], and Protein Ensemble Database [35,39]. Besides, the information on disorder content has been shown to facilitate the functional annotations of proteins [49,50].…”

Section: Introduction To Intrinsically Disordered Proteins (Idps)mentioning

confidence: 99%

Liquid–Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus–Host Interactions

Brocca

Grandori

Longhi

et al. 2020

IJMS

125

122

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Intrinsically disordered proteins (IDPs) are unable to adopt a unique 3D structure under physiological conditions and thus exist as highly dynamic conformational ensembles. IDPs are ubiquitous and widely spread in the protein realm. In the last decade, compelling experimental evidence has been gathered, pointing to the ability of IDPs and intrinsically disordered regions (IDRs) to undergo liquid–liquid phase separation (LLPS), a phenomenon driving the formation of membrane-less organelles (MLOs). These biological condensates play a critical role in the spatio-temporal organization of the cell, where they exert a multitude of key biological functions, ranging from transcriptional regulation and silencing to control of signal transduction networks. After introducing IDPs and LLPS, we herein survey available data on LLPS by IDPs/IDRs of viral origin and discuss their functional implications. We distinguish LLPS associated with viral replication and trafficking of viral components, from the LLPS-mediated interference of viruses with host cell functions. We discuss emerging evidence on the ability of plant virus proteins to interfere with the regulation of MLOs of the host and propose that bacteriophages can interfere with bacterial LLPS, as well. We conclude by discussing how LLPS could be targeted to treat phase separation-associated diseases, including viral infections.

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“…Secondary structures were predicted using PHYRE2, QUARK and PEP-FOLD3 (29)(30)(31). Intrinsically disordered regions (IDRs) were predicted using DEPICTER, DISOPRED3 and VSL2B (32)(33)(34) Table S2). VSL2B is the baseline predictor of VSL2 that is using only the amino-acid composition-based features that can be calculated directly from the protein sequence (34).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

Mermet

Voisin

Mordier

et al. 2021

Preprint

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The nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear morphology and gene expression. To understand how the Arabidopsis nucleoskeleton physically connects to the nuclear periphery, we investigated the nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. Computational predictions identified three evolutionary conserved peptide motifs within the N-terminal region of KAKU4. Functional analysis revealed that these motifs are required for homomerization of KAKU4, interaction with the nucleoskeleton proteins CROWDED NUCLEI (CRWN) and localization at the nuclear periphery. We find that similar protein motifs are present in NUP82 and NUP136, two plant specific nucleoporins from the Nuclear Pore Complex (NPC) basket. These conserved motifs allow the two nucleoporins to bind CRWN proteins, thus revealing a physical link between the nucleoskeleton and nuclear pores in plants. Finally, whilst NUP82, NUP136 and KAKU4 have a common evolutionary history predating non-vascular land plants, KAKU4 mainly localizes outside the NPC suggesting neofunctionalization of an ancient nucleoporin into a new nucleoskeleton component.

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DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server

Cited by 50 publications

References 66 publications

Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet

Liquid–Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus–Host Interactions

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

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