Applications of Bioinformatics and Experimental Methods to Intrinsic Disorder-Based Protein-Protein Interactions

Sun, Xiao; Jones, William T.; Uversky, Vladimir N.

doi:10.5772/29246

Cited by 4 publications

(3 citation statements)

References 98 publications

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“…Charge and hydropathy plot (CH-plot) of a protein can be used as a linear protein disorder classifier that differentiates proteins with substantial amounts of disorder from proteins with globular conformations [18,19]. Another binary disorder classifier, cumulative distribution function (CDF) analysis, differentiates all proteins containing any IDRs from those that contain mainly folded domains [20].…”

Section: Multiple Analyses Show That the Trds Domain Of Erf Proteins mentioning

confidence: 99%

Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions

Sun

Malhis

Zhao

et al. 2019

IJMS

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APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERFs) play crucial roles in adaptation to stresses such as those caused by pathogens, wounding and cold. Although their name suggests a specific role in ethylene signalling, some ERF members also co-ordinate signals regulated by other key plant stress hormones such as jasmonate, abscisic acid and salicylate. We analysed a set of ERF proteins from three divergent plant species for intrinsically disorder regions containing conserved segments involved in protein–protein interaction known as Molecular Recognition Features (MoRFs). Then we correlated the MoRFs identified with a number of known functional features where these could be identified. Our analyses suggest that MoRFs, with plasticity in their disordered surroundings, are highly functional and may have been shuffled between related protein families driven by selection. A particularly important role may be played by the alpha helical component of the structured DNA binding domain to permit specificity. We also present examples of computationally identified MoRFs that have no known function and provide a valuable conceptual framework to link both disordered and ordered structural features within this family to diverse function.

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Section: Multiple Analyses Show That the Trds Domain Of Erf Proteins mentioning

confidence: 99%

Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions

Sun

Malhis

Zhao

et al. 2019

IJMS

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“…IDPs possess both binding promiscuity (ability to interact with multiple partners) and binding plasticity (ability to undergo binding-induced folding to accommodate diverse binding sites for different partners), two key factors conferring IDPs functional advantages in stress responses, signaling, and regulation Sun et al, 2012b). Hub proteins play a central role in cellular biological processes by interacting with multiple (B) Premolten globule, which is more compact than random coil but still mostly disordered with some local residual secondary structures.…”

Section: Order From Disorder: Binding Promiscuity and Plasticitymentioning

confidence: 99%

Multifarious Roles of Intrinsic Disorder in Proteins Illustrate Its Broad Impact on Plant Biology

et al. 2013

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Intrinsically disordered proteins (IDPs) are highly abundant in eukaryotic proteomes. Plant IDPs play critical roles in plant biology and often act as integrators of signals from multiple plant regulatory and environmental inputs. Binding promiscuity and plasticity allow IDPs to interact with multiple partners in protein interaction networks and provide important functional advantages in molecular recognition through transient protein-protein interactions. Short interaction-prone segments within IDPs, termed molecular recognition features, represent potential binding sites that can undergo disorder-to-order transition upon binding to their partners. In this review, we summarize the evidence for the importance of IDPs in plant biology and evaluate the functions associated with intrinsic disorder in five different types of plant protein families experimentally confirmed as IDPs. Functional studies of these proteins illustrate the broad impact of disorder on many areas of plant biology, including abiotic stress, transcriptional regulation, light perception, and development. Based on the roles of disorder in the protein-protein interactions, we propose various modes of action for plant IDPs that may provide insight for future experimental approaches aimed at understanding the molecular basis of protein function within important plant pathways.

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“…A protein’s amino acid sequence can reveal its intrinsic unstructured content [ 40 , 41 ]. To derive insights about the degree of structural disorder in uN2A from its sequences, in silico analyses were applied that showed varying outcomes [ 32 , 34 ].…”

Section: Structural Conformations Of Titin’s N2a Domainmentioning

confidence: 99%

Titin N2A Domain and Its Interactions at the Sarcomere

Adewale

Ahn

2021

IJMS

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Titin is a giant protein in the sarcomere that plays an essential role in muscle contraction with actin and myosin filaments. However, its utility goes beyond mechanical functions, extending to versatile and complex roles in sarcomere organization and maintenance, passive force, mechanosensing, and signaling. Titin’s multiple functions are in part attributed to its large size and modular structures that interact with a myriad of protein partners. Among titin’s domains, the N2A element is one of titin’s unique segments that contributes to titin’s functions in compliance, contraction, structural stability, and signaling via protein–protein interactions with actin filament, chaperones, stress-sensing proteins, and proteases. Considering the significance of N2A, this review highlights structural conformations of N2A, its predisposition for protein–protein interactions, and its multiple interacting protein partners that allow the modulation of titin’s biological effects. Lastly, the nature of N2A for interactions with chaperones and proteases is included, presenting it as an important node that impacts titin’s structural and functional integrity.

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Applications of Bioinformatics and Experimental Methods to Intrinsic Disorder-Based Protein-Protein Interactions

Cited by 4 publications

References 98 publications

Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions

Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions

Multifarious Roles of Intrinsic Disorder in Proteins Illustrate Its Broad Impact on Plant Biology

Titin N2A Domain and Its Interactions at the Sarcomere

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