Uncoupling the Folding and Binding of an Intrinsically Disordered Protein

Poosapati, Anusha; Gregory, Emily L.; Borcherds, Wade M.; Chemes, Lucía B.; Daughdrill, Gary W.

doi:10.1016/j.jmb.2018.05.045

Cited by 20 publications

(23 citation statements)

References 39 publications

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“…Even in the fuzzy encounter complex ensemble, seg1 of ArkA is largely folded into a PPII helix, exhibiting a binding strategy also employed by other IDPs, where one segment with pre-formed structure can dock into place first, followed by the coupled folding and binding of more flexible segments [ 5 , 7 , 11 , 25 , 26 , 48 ]. Polyproline sequences are especially well adapted to this strategy as PPII helices are rigid, allowing them to project from folded parts of a larger full length protein, and hydrophobic yet also highly soluble in water [ 5 ].…”

Section: Resultsmentioning

confidence: 99%

“…Seg2 of ArkA is more flexible and therefore less likely to form the first tight interactions with the AbpSH3 binding surface. Modulating the amount of intrinsic 3 10 helix structure in seg2 would be unlikely to affect the peptide binding affinity [25], since this segment also remains quite flexible in the fully engaged complex.…”

Section: Arka Intrinsic Structure Affects the Binding Pathwaymentioning

confidence: 99%

“…Additionally, if one segment of the IDP possesses more intrinsic pre-folded structure, binding may proceed starting with this segment and then extending to the rest of the sequence which folds upon interaction with the partner protein [ 11 , 24 ]. Thus, pre-formed secondary structure can improve affinity and influence the binding pathway, including the nature of intermediate states [ 25 , 26 ], but too much structure can slow binding without improving affinity [ 11 , 27 ]. Additionally, the ability of IDPs to form nonnative contacts during binding, and the presence of significant disorder even after binding can also be important for IDP function [ 20 , 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

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A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

et al. 2020

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Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 3 10 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.

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Section: Resultsmentioning

confidence: 99%

Section: Arka Intrinsic Structure Affects the Binding Pathwaymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

et al. 2020

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“…Even in the fuzzy encounter complex ensemble, seg1 of ArkA is largely folded into a PPII helix, exhibiting a binding strategy also employed by other IDPs, where one segment with pre-formed structure can dock into place first, followed by the coupled folding and binding of more flexible segments [5,7,11,25,26,48]. Polyproline sequences are especially well adapted to this strategy as PPII helices are rigid, allowing them to project from folded parts of a larger full length protein, and hydrophobic yet also highly soluble in water [5].…”

Section: Resultsmentioning

confidence: 99%

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

Gerlach

Carrock

Stix

et al. 2020

Preprint

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Protein-protein interactions are involved in a wide range of cell processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains.However, the details of IDP binding pathways are hard to characterize using experimental approaches that cannot always capture low populations of intermediate states. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function.Molecular dynamics simulations were used to characterize the binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA, to capture all steps along the pathway. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 3 10 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations revealed that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex 3 intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs more generally. Author SummaryComplex cellular processes are mediated by interactions between proteins, and to determine how these physical interactions affect cellular function we need to understand the protein binding pathway. Many protein interaction domains, such as the SH3 domain, bind to intrinsically disordered proteins in a coupled folding and binding process. Using molecular dynamics simulations, we find that the binding of the disordered ArkA peptide to the yeast Abp1p SH3 domain proceeds through a flexible, disordered encounter complex before reaching a more stable fully bound state. This encounter complex is stabilized by nonspecific long-range electrostatic interactions and nonspecific hydrophobic interactions between the peptide and domain. Our simulations highlight the important role of hydrophobic interactions in the entire SH3 binding process, both nonspecific hydrophobic contacts in the encounter complex and specific hydrophobic contacts in the fully bound complex. The enc...

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“…For example, the extent of disorder within certain IDRs is finely tuned to modulate affinity for functional partners [20]. In new studies, Poosapati et al [12] examine how the residual structure of an IDP affects its interaction using the c-Myb transactivation domain as a model system. The review article by Berlow et al [1] illustrates mechanisms through which intrinsic disorder enables allosteric regulation.…”

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confidence: 99%

Intrinsically Disordered Proteins: Structure, Function and Therapeutics

Chen

Kriwacki

2018

Journal of Molecular Biology

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Over the past two decades, the prevalence of intrinsically disordered proteins (IDPs) in biology has become broadly appreciated, which has been paralleled with understanding of the mechanisms that mediate their diverse functions. IDPs often exist as heterogeneous ensembles of fluctuating structures under physiological conditions, which offer advantages for many cellular functions. In particular, the inherent thermodynamic instability of IDPs could allow for their conformational properties to respond to numerous stimuli including binding to ligands or membrane surfaces, changes in the cellular environment, and posttranslational modifications (PTMs). Multiple stimuli can readily be integrated through cooperative effects on their dynamic structural ensembles. These properties enable IDPs to fulfill the complex signaling and regulatory needs of higher organisms. As a consequence of their vital biological roles, IDPs are frequently associated with human diseases, including neurodegenerative diseases, numerous cancer types, and diabetes. This Special Issue contains five review articles [1

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Uncoupling the Folding and Binding of an Intrinsically Disordered Protein

Cited by 20 publications

References 39 publications

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

Intrinsically Disordered Proteins: Structure, Function and Therapeutics

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