Corrigendum to “Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding–Binding Process: A Critical Assessment of the “Fly-Casting” Mechanism” [J. Mol. Biol. 393 (2009) 1143–1159]

Intrinsically disordered proteins (IDPs) are abundant in all species. Their discovery challenges the traditional “sequence−structure−function” paradigm of protein science, because IDPs play important roles in various biological processes without preformed...

Download Full-text

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein

10.1101/2020.03.23.004283 ◽

2020 ◽

Author(s):

Paul Robustelli ◽

Stefano Piana ◽

David E. Shaw

Keyword(s):

Measles Virus ◽

Intrinsically Disordered Proteins ◽

Tertiary Structure ◽

Disordered Proteins ◽

Binding Process ◽

Intrinsically Disordered ◽

Disordered Protein ◽

Induced Folding ◽

Helical Content ◽

Intermolecular Contacts

AbstractIntrinsically disordered proteins (IDPs), which in isolation do not adopt a well-defined tertiary structure but instead populate a structurally heterogeneous ensemble of interconverting states, play important roles in many biological pathways. IDPs often fold into ordered states upon binding to their physiological interaction partners (a so-called “folding-upon-binding” process), but it has proven difficult to obtain an atomic-level description of the structural mechanisms by which they do so. Here, we describe in atomic detail the folding-upon-binding mechanism of an IDP segment to its binding partner, as observed in unbiased molecular dynamics simulations. In our simulations, we observed over 70 binding and unbinding events between the α-helical molecular recognition element (α-MoRE) of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the measles virus phosphoprotein complex. We found that folding-upon-binding primarily occurred through induced-folding pathways (in which intermolecular contacts form before or concurrently with the secondary structure of the disordered protein)—an observation supported by previous experiments—and that the transition state ensemble was characterized by the formation of just a few key intermolecular contacts, and was otherwise highly structurally heterogeneous. We found that when a large amount of helical content was present early in a transition path, NTAIL typically unfolded, then refolded after additional intermolecular contacts formed. We also found that, among conformations with similar numbers of intermolecular contacts, those with less helical content had a higher probability of ultimately forming the native complex than conformations with more helical content, which were more likely to unbind. These observations suggest that even after intermolecular contacts have formed, disordered regions can have a kinetic advantage over folded regions in the folding-upon-binding process.

Download Full-text

Critical Assessment of Protein Intrinsic Disorder Prediction

10.1101/2020.08.11.245852 ◽

2020 ◽

Author(s):

Marco Necci ◽

Damiano Piovesan ◽

Silvio C.E. Tosatto ◽

◽

Keyword(s):

Intrinsically Disordered Proteins ◽

Intrinsic Disorder ◽

Critical Assessment ◽

Disordered Proteins ◽

Blind Test ◽

Disorder Prediction ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Binding Regions ◽

Protein Intrinsic Disorder

AbstractIntrinsically disordered proteins defying the traditional protein structure-function paradigm represent a challenge to study experimentally. As a large part of our knowledge rests on computational predictions, it is crucial for their accuracy to be high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in predicting intrinsically disordered regions in proteins and the subset of disordered residues involved in binding other molecules. A total of 43 methods, 32 for disorder and 11 for binding regions, were evaluated on a dataset of 646 novel manually curated proteins from DisProt. The best methods use deep learning techniques and significantly outperform widely used earlier physicochemical methods across different types of targets. Disordered binding regions remain hard to predict correctly. Depending on the definition used, the top disorder predictor has an FMax of 0.483 (DisProt) or 0.792 (DisProt-PDB). As the top binding predictor only attains an FMax of 0.231, this suggests significant potential for improvement. Intriguingly, computing times among the top performing methods vary by up to four orders of magnitude.

Download Full-text

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

10.1101/2020.03.23.003269 ◽

2020 ◽

Author(s):

Gabriella J. Gerlach ◽

Rachel Carrock ◽

Robyn Stix ◽

Elliott J. Stollar ◽

K. Aurelia Ball

Keyword(s):

Intrinsically Disordered Proteins ◽

Hydrophobic Interactions ◽

Sh3 Domain ◽

Bound State ◽

Disordered Proteins ◽

Binding Process ◽

Intrinsically Disordered ◽

Encounter Complex ◽

Complex Forms ◽

Dynamics Simulations

AbstractProtein-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 310 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.Author SummaryComplex cellular processes are mediated by interactions between proteins, and to determine how these interactions affect cellular function and binding kinetics we often must 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 stable fully bound state. The 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 encounter complex could be key to understanding the functional behavior of SH3 domain interactions because the encounter complex forms very quickly and the transition to the fully bound state is slower. In cells, an SH3 domain may form an encounter complex quickly and nonspecifically with many potential binding partners, allowing it to search for the correct recognition sequence before completing the binding process.

Download Full-text

Critical assessment of protein intrinsic disorder prediction

Nature Methods ◽

10.1038/s41592-021-01117-3 ◽

2021 ◽

Cited By ~ 2

Author(s):

Marco Necci ◽

◽

Damiano Piovesan ◽

Silvio C. E. Tosatto ◽

Keyword(s):

Intrinsically Disordered Proteins ◽

Intrinsic Disorder ◽

Critical Assessment ◽

Disordered Proteins ◽

Blind Test ◽

Disorder Prediction ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Full Dataset ◽

Protein Intrinsic Disorder

AbstractIntrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude.

Download Full-text

Interplay between folding and binding modulates protein sequences, structures, functions and regulation

10.1101/211524 ◽

2017 ◽

Cited By ~ 1

Author(s):

Bálint Mészáros ◽

László Dobson ◽

Erzsébet Fichó ◽

Gábor E. Tusnády ◽

Zsuzsanna Dosztányi ◽

...

Keyword(s):

Structural Properties ◽

Regulatory Networks ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Binding Modes ◽

Sequence Structure ◽

Binding Partner ◽

Binding Process ◽

Intrinsically Disordered ◽

Protein Interactome

SummaryIntrinsically Disordered Proteins (IDPs) fulfill critical biological roles without having the potential to fold on their own. While lacking inherent structure, the majority of IDPs do reach a folded state via interaction with a protein partner, presenting a deep entanglement of the folding and binding process. Protein disorder has been recognized as a major determinant in several properties of proteins; yet the way the binding process is reflected in these features in general lacks this detail of description. Recent advances in database development enabled us to identify three basic scenarios of the interplay between folding and binding in unprecedented detail. These scenarios have fundamentally different properties in terms of protein sequence, structure, function and regulation, depending on the structural properties of the interacting partners. Strikingly, the existence of a binding partner and its structural properties influence all analyzed properties of proteins to the same extent as the divide between inherent order or disorder. The appreciation of this interplay between folding and binding is the basis for the successful charting of unknown territories in the protein interactome, the understanding of how different binding modes assemble regulatory networks, and the development of future pharmaceutical applications.

Download Full-text