scholarly journals Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET

2018 ◽  
Vol 149 (1) ◽  
pp. 010901 ◽  
Author(s):  
Benjamin Schuler
Keyword(s):  
Single Molecule ◽  
Fluorescence Correlation Spectroscopy ◽  
Intrinsically Disordered Proteins ◽  
Correlation Spectroscopy ◽  
Disordered Proteins ◽  
Chain Dynamics ◽  
Fluorescence Correlation ◽  
Intrinsically Disordered ◽  
Single Molecule Fret

scholarly journals Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins

Biomolecules ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 140 ◽  
Author(s):  
Sharonda LeBlanc ◽  
Prakash Kulkarni ◽  
Keith Weninger
Keyword(s):  
Single Molecule ◽  
Biological Networks ◽  
Intrinsically Disordered Proteins ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Polymer Physics ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Single Molecule Fret ◽  
Random Fluctuations

Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.

Single-Molecule FRET of Intrinsically Disordered Proteins

2020 ◽  
Vol 71 (1) ◽  
pp. 391-414 ◽  
Author(s):  
Lauren Ann Metskas ◽  
Elizabeth Rhoades
Keyword(s):  
Single Molecule ◽  
Protein Interactions ◽  
Intrinsically Disordered Proteins ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Disordered Proteins ◽  
Protein Protein Interactions ◽  
Cellular Functions ◽  
Intrinsically Disordered ◽  
Single Molecule Fret

Intrinsically disordered proteins (IDPs) are now widely recognized as playing critical roles in a broad range of cellular functions as well as being implicated in diverse diseases. Their lack of stable secondary structure and tertiary interactions, coupled with their sensitivity to measurement conditions, stymies many traditional structural biology approaches. Single-molecule Förster resonance energy transfer (smFRET) is now widely used to characterize the physicochemical properties of these proteins in isolation and is being increasingly applied to more complex assemblies and experimental environments. This review provides an overview of confocal diffusion-based smFRET as an experimental tool, including descriptions of instrumentation, data analysis, and protein labeling. Recent papers are discussed that illustrate the unique capability of smFRET to provide insight into aggregation-prone IDPs, protein–protein interactions involving IDPs, and IDPs in complex experimental milieus.

scholarly journals Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS

2016 ◽  
Vol 113 (37) ◽  
pp. E5389-E5398 ◽  
Author(s):  
Mikayel Aznauryan ◽  
Leonildo Delgado ◽  
Andrea Soranno ◽  
Daniel Nettels ◽  
Jie-rong Huang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Intrinsically Disordered Proteins ◽  
Local Level ◽  
Resonance Energy ◽  
Correlation Spectroscopy ◽  
Disordered Proteins ◽  
Time Range ◽  
Unfolded Proteins ◽  
Intrinsically Disordered ◽  
Unfolded State

The properties of unfolded proteins are essential both for the mechanisms of protein folding and for the function of the large group of intrinsically disordered proteins. However, the detailed structural and dynamical characterization of these highly dynamic and conformationally heterogeneous ensembles has remained challenging. Here we combine and compare three of the leading techniques for the investigation of unfolded proteins, NMR spectroscopy (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET), with the goal of quantitatively testing their consistency and complementarity and for obtaining a comprehensive view of the unfolded-state ensemble. Using unfolded ubiquitin as a test case, we find that its average dimensions derived from FRET and from structural ensembles calculated using the program X-PLOR-NIH based on NMR and SAXS restraints agree remarkably well; even the shapes of the underlying intramolecular distance distributions are in good agreement, attesting to the reliability of the approaches. The NMR-based results provide a highly sensitive way of quantifying residual structure in the unfolded state. FRET-based nanosecond fluorescence correlation spectroscopy allows long-range distances and chain dynamics to be probed in a time range inaccessible by NMR. The combined techniques thus provide a way of optimally using the complementarity of the available methods for a quantitative structural and dynamical description of unfolded proteins both at the global and the local level.

scholarly journals Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics

2021 ◽  
Author(s):  
James Losey ◽  
Michael Jauch ◽  
David S. Matteson ◽  
Mahmoud Moradi
Keyword(s):  
Single Molecule ◽  
Intrinsically Disordered Proteins ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Disordered Proteins ◽  
Analysis Techniques ◽  
Intrinsically Disordered ◽  
Single Molecule Fret ◽  
Great Progress

AbstractSingle molecule Förster resonance energy transfer experiments have added a great deal to the under-standing of conformational states of biologically important molecules. While great progress has been made, much is still unknown in systems that are highly flexible such as intrinsically disordered proteins because of the high degeneracy of distance states, particularly when freely diffusing smFRET experiments are used. Simulated smFRET data allows for the control of underlying process that generates the data to examine if analytic techniques can detect these underlying differences. We have extended the PyBroMo software that simulates the freely diffusing smFRET data to include a distribution of inter-dye distances generated using Langevin dynamics in order to model proteins with greater flexibility or disorder in structure. Standard analysis techniques for smFRET data compared highlighted the differences observed between data generated with the base software and data that included the distribution of inter-dye distance.

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