The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy

Cubuk, Jasmine; Stuchell‐Brereton, Melissa D.; Soranno, Andrea

doi:10.1042/ebc20220065

Cited by 10 publications

(5 citation statements)

References 146 publications

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“…Single‐molecule fluorescent techniques, such as fluorescence resonance energy transfer (FRET) and FCS, are two commonly used approaches to study IDPs. These techniques offer several advantages over classical ensemble methods, including the ability to distinguish distinct conformational ensembles, examine protein dynamics in a context‐specific manner and operate at low concentrations (picomolar range) to enable access to the monomeric form of the proteins 44 . FCS enables the determination of the diffusion time and hydrodynamic radius R H .…”

Section: The Dynamic Structures Of Idpsmentioning

confidence: 99%

“…These techniques offer several advantages over classical ensemble methods, including the ability to distinguish distinct conformational ensembles, examine protein dynamics in a context-specific manner and operate at low concentrations (picomolar range) to enable access to the monomeric form of the proteins. 44 FCS enables the determination of the diffusion time and hydrodynamic radius R H . FRET functions as a "spectroscopic ruler," enabling nanometer-scale distance measurements.…”

Section: Single-molecule Fluorescencementioning

confidence: 99%

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Rational drug design targeting intrinsically disordered proteins

Wang,

Xiong,

Lai

2023

WIREs Comput Mol Sci

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Intrinsically disordered proteins (IDPs) are proteins that perform important biological functions without well‐defined structures under physiological conditions. IDPs can form fuzzy complexes with other molecules, participate in the formation of membraneless organelles, and function as hubs in protein–protein interaction networks. The malfunction of IDPs causes major human diseases. However, drug design targeting IDPs remains challenging due to their highly dynamic structures and fuzzy interactions. Turning IDPs into druggable targets provides a great opportunity to extend the druggable target‐space for novel drug discovery. Integrative structural biology approaches that combine information derived from computational simulations, artificial intelligence/data‐driven analysis and experimental studies have been used to uncover the dynamic structures and interactions of IDPs. An increasing number of ligands that directly bind IDPs have been found either by target‐based experimental and computational screening or phenotypic screening. Along with the understanding of IDP binding with its partners, structure‐based drug design strategies, especially conformational ensemble‐based computational ligand screening and computer‐aided ligand optimization algorithms, have greatly accelerated the development of IDP ligands. It is inspiring that several IDP‐targeting small‐molecule and peptide drugs have advanced into clinical trials. However, new computational methods need to be further developed for efficiently discovering and optimizing specific and potent ligands for the vast number of IDPs. Along with the understanding of their dynamic structures and interactions, IDPs are expected to become valuable treasure of drug targets.This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics

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Section: The Dynamic Structures Of Idpsmentioning

confidence: 99%

Section: Single-molecule Fluorescencementioning

confidence: 99%

Rational drug design targeting intrinsically disordered proteins

Wang,

Xiong,

Lai

2023

WIREs Comput Mol Sci

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“…Although powerful techniques such as X-ray crystallography, (nuclear magnetic resonance) NMR spectroscopy, circular dichroism (CD) spectroscopy, protease digestion, and radius determination have been used to characterize IDP/IDR structure in the past, the various limitations associated with each technique have long been known (14). More recently, other techniques such as single-molecule fluorescence spectroscopy (15), atomic force microscopy (AFM) (16), small angle X-ray scattering (SAXS) (17), and small angle neutron scattering (SANS) (18) have been demonstrated as tools in the characterization of IDP/IDR structure and dynamics.…”

Section: Introductionmentioning

confidence: 99%

Structure Characterization of a Disordered Peptide Using In-Droplet Hydrogen Deuterium Exchange Mass Spectrometry and Molecular Dynamics

Rahman,

Sultana,

Sharif

et al. 2024

Preprint

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The highly dynamic nature of intrinsically disordered proteins (IDPs), those containing intrinsically disordered regions (IDRs), makes their structural characterization very difficult using traditional measurement approaches. Especially challenging is the determination of the propensity to form specific types of structure upon interacting with binding partners. Here, the reactivities of select peptides ranging from highly-structured to unstructured species have been examined with in-droplet hydrogen-deuterium exchange (HDX) techniques. Overall, the consideration of intrinsic rates (kint) of exchange for different backbone sites is shown to be a poor predictor of peptide reactivity. Here, we develop a new model for HDX prediction that combines the use of protection factors (PF) from molecular dynamics (MD) simulations with kint to obtain high-accuracy HDX predictability for peptides having various structural types. The relationship of peptide structural flexibility and HDX reactivity for different peptides is elucidated. Additionally, the model is used to characterize the degree of structural bias for the disease-relevant Nt17; although highly flexible, being primed for facile conversion to α-helical conformation upon binding with molecular partners imparts HDX protection. In the future a scale may be developed whereby HDX reactivity is associated with the degree of IDR structural flexibility and bias. Such structural resolution may ultimately be used for high-throughput screening of IDR structural transformation (including structural flexibility and bias) upon binding of drug candidates.

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“…As such, there is a need for high-resolution, quantitative descriptions of IDR ensembles and how phosphorylation may bias the conformations accessed by the protein. Solution-state experimental methods, such as nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), and Förster Resonance Energy Transfer (FRET) can collectively provide ensemble-level and atomistic details of IDR conformations (19)(20)(21)(22)(23)(24). Molecular simulations of IDRs are a powerful complement to experiments; simulations enable the atomistic study of the sequence-ensemble relationship of IDRs (25)(26)(27)(28)(29)(30).…”

Section: Introductionmentioning

confidence: 99%

Phosphorylation of disordered proteins tunes local and global intramolecular interactions

Usher,

Fossat,

Holehouse

2024

Preprint

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Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.SIGNIFICANCESpatially and temporally controlled phosphorylation in disordered protein regions is critical to many facets of protein function and broader cellular health. Intrinsically disordered protein regions (IDRs) are overrepresented as targets of phosphorylation, but the structural and functional consequences of such modifications remain elusive for many systems. Toward rigorous modeling of phosphorylated IDRs using all-atom simulations, we present new parameters for phosphoserine and phosphothreonine for the ABSINTH implicit solvent paradigm. Through the study of four example phospho-IDRs, we demonstrate excellent agreement between our phospho-IDR simulations and published datasets.

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The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy

Cited by 10 publications

References 146 publications

Rational drug design targeting intrinsically disordered proteins

Rational drug design targeting intrinsically disordered proteins

Structure Characterization of a Disordered Peptide Using In-Droplet Hydrogen Deuterium Exchange Mass Spectrometry and Molecular Dynamics

Phosphorylation of disordered proteins tunes local and global intramolecular interactions

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