Sequence characteristics responsible for protein‐protein interactions in the intrinsically disordered regions of caseins, amelogenins, and small heat‐shock proteins

Small heat shock proteins (sHsps) are adenosine triphosphate–independent chaperones that protect cells from misfolded proteins. In this issue, Grousl et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201708116) show that the yeast sHsp Hsp42 uses a prion-like intrinsically disordered domain to bind and sequester misfolded proteins in protein deposition sites.

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Glutamate promotes SSB protein–protein Interactions via intrinsically disordered regions

Journal of Molecular Biology ◽

10.1016/j.jmb.2017.07.021 ◽

2017 ◽

Vol 429 (18) ◽

pp. 2790-2801 ◽

Cited By ~ 23

Author(s):

Alexander G. Kozlov ◽

Min Kyung Shinn ◽

Elizabeth A. Weiland ◽

Timothy M. Lohman

Keyword(s):

Protein Interactions ◽

Protein Protein Interactions ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

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Affinity versus specificity in coupled binding and folding reactions

Protein Engineering Design and Selection ◽

10.1093/protein/gzz020 ◽

2019 ◽

Author(s):

Stefano Gianni ◽

Per Jemth

Keyword(s):

Protein Interactions ◽

Intrinsically Disordered Proteins ◽

Intrinsically Disordered Protein ◽

High Specificity ◽

Disordered Proteins ◽

Protein Protein Interactions ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Interaction Interface ◽

Disordered Regions

Abstract Intrinsically disordered protein regions may fold upon binding to an interaction partner. It is often argued that such coupled binding and folding enables the combination of high specificity with low affinity. The basic tenet is that an unfavorable folding equilibrium will make the overall binding weaker while maintaining the interaction interface. While theoretically solid, we argue that this concept may be misleading for intrinsically disordered proteins. In fact, experimental evidence suggests that interactions of disordered regions usually involve extended conformations. In such cases, the disordered region is exceptionally unlikely to fold into a bound conformation in the absence of its binding partner. Instead, these disordered regions can bind to their partners in multiple different conformations and then fold into the native bound complex, thus, if anything, increasing the affinity through folding. We concede that (de)stabilization of native structural elements such as helices will modulate affinity, but this could work both ways, decreasing or increasing the stability of the complex. Moreover, experimental data show that intrinsically disordered binding regions display a range of affinities and specificities dictated by the particular side chains and length of the disordered region and not necessarily by the fact that they are disordered. We find it more likely that intrinsically disordered regions are common in protein–protein interactions because they increase the repertoire of binding partners, providing an accessible route to evolve interactions rather than providing a stability–affinity trade-off.

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Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome

10.1101/2021.04.13.439572 ◽

2021 ◽

Author(s):

Caroline Benz ◽

Muhammad Ali ◽

Izabella Krystkowiak ◽

Leandro Simonetti ◽

Ahmed Sayadi ◽

...

Keyword(s):

Amino Acid ◽

Protein Interactions ◽

Human Proteome ◽

Cell Physiology ◽

Protein Protein Interactions ◽

Linear Motif ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Wide Range ◽

Disordered Regions

Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies using a wide range of experimental approaches have identified tens of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional and cell type-specific interactions are likely to be disproportionately under-represented. Moreover, for most known protein-protein interactions the binding regions remain uncharacterized. We previously developed proteomic peptide phage display (ProP-PD), a method for simultaneous proteome-scale identification of short linear motif (SLiM)-mediated interactions and footprinting of the binding region with amino acid resolution. Here, we describe the second-generation human disorderome (HD2), an optimized ProP-PD library that tiles all disordered regions of the human proteome and allows the screening of ~1,000,000 overlapping peptides in a single binding assay. We define guidelines for how to process, filter and rank the results and provide PepTools, a toolkit for annotation and analysis of identified hits. We uncovered 2,161 interaction pairs for 35 known SLiM-binding domains and confirmed a subset of 38 interactions by biophysical or cell-based assays. Finally, we show how the amino acid resolution binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the human proteome. The HD2 ProP-PD library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.

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Functioning of Mycobacterial Heat Shock Repressors Requires the Master Virulence Regulator PhoP

Journal of Bacteriology ◽

10.1128/jb.00013-19 ◽

2019 ◽

Vol 201 (12) ◽

Cited By ~ 5

Author(s):

Ritesh Rajesh Sevalkar ◽

Divya Arora ◽

Prabhat Ranjan Singh ◽

Ranjeet Singh ◽

Vinay K. Nandicoori ◽

...

Keyword(s):

Heat Shock ◽

Heat Shock Proteins ◽

Protein Interactions ◽

Regulatory Pathway ◽

Protein Protein Interactions ◽

Specific Expression ◽

Content Type ◽

Shock Proteins ◽

Pathogenic Determinant ◽

Virulence Regulator

ABSTRACT A hallmark feature of Mycobacterium tuberculosis pathogenesis lies in the ability of the pathogen to survive within macrophages under a stressful environment. Thus, coordinated regulation of stress proteins is critically important for an effective adaptive response of M. tuberculosis, the failure of which results in elevated immune recognition of the tubercle bacilli with reduced survival during chronic infections. Here, we show that virulence regulator PhoP impacts the global regulation of heat shock proteins, which protect M. tuberculosis against stress generated by macrophages during infection. Our results identify that in addition to classical DNA-protein interactions, newly discovered protein-protein interactions control complex mechanisms of expression of heat shock proteins, an essential pathogenic determinant of M. tuberculosis. While the C-terminal domain of PhoP binds to its target promoters, the N-terminal domain of the regulator interacts with the C-terminal end of the heat shock repressors. Remarkably, our findings delineate a regulatory pathway which involves three major transcription factors, PhoP, HspR, and HrcA, that control in vivo recruitment of the regulators within the target genes and regulate stress-specific expression of heat shock proteins via protein-protein interactions. The results have implications on the mechanism of regulation of PhoP-dependent stress response in M. tuberculosis. IMPORTANCE The regulation of heat shock proteins which protect M. tuberculosis against stress generated by macrophages during infection is poorly understood. In this study, we show that PhoP, a virulence regulator of the tubercle bacilli, controls heat shock-responsive genes, an essential pathogenic determinant of M. tuberculosis. Our results unravel that in addition to classical DNA-protein interactions, complex mechanisms of regulation of heat shock-responsive genes occur through multiple protein-protein interactions. Together, these findings delineate a fundamental regulatory pathway where transcription factors PhoP, HspR, and HrcA interact with each other to control stress-specific expression of heat shock proteins.

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