Single-Molecule Studies of Intrinsically Disordered Proteins

Brucale, Marco; Schuler, Benjamin; Samorı̀, Bruno

doi:10.1021/cr400297g

Cited by 132 publications

(148 citation statements)

References 417 publications

Supporting

Mentioning

144

Contrasting

Order By: Relevance

“…A value of R 0 in the absence of urea of 5.4 nm was used (41). Fluorescence anisotropies (determined for all urea concentrations based on the polarization-sensitive detection in the single-molecule instrument) were between 0.06 and 0.16 for the donor and between 0.04 and 0.13 for the acceptor, indicating rapid orientational averaging of the fluorophores (i.e., κ 2 ≈ 2/3), as usually observed for unfolded proteins (13,55).…”

Section: Methodsmentioning

confidence: 98%

“…Due to the very large number of conformational degrees of freedom of the unfolded polypeptide ensemble, it is of utmost importance to obtain as many independent experimental parameters as possible for a quantitative description of its behavior. Three experimental methods have been particularly informative in this respect: NMR spectroscopy (2,5,(7)(8)(9), small angle X-ray scattering (SAXS) (10,11), and single-molecule Förster resonance energy transfer spectroscopy (single-molecule FRET) (12,13).…”

mentioning

confidence: 99%

“…Single-molecule FRET has recently emerged as an additional method to study unfolded proteins (12,13). Single-molecule FRET provides intramolecular distance information in the range of tens of angstroms by measuring the Förster transfer between fluorescence donor and acceptor dyes attached to the polypeptide.…”

mentioning

confidence: 99%

See 2 more Smart Citations

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

Aznauryan

Delgado

Soranno

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

145

167

View full text Add to dashboard Cite

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), smallangle 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. FRETbased 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.protein folding | unfolded protein ensemble | Förster resonance energy transfer | nuclear magnetic resonance | small-angle X-ray scattering P roteins exist as ensembles of interconverting conformations.Obviously, unfolded polypeptide chains, such as chemically or physically denatured proteins and intrinsically disordered proteins (IDPs), can access extremely large numbers of conformations (1). A comprehensive description of their structural and dynamical behavior is a prerequisite for understanding protein folding (2-4) and the function of IDPs in health and disease (5, 6). Due to the very large number of conformational degrees of freedom of the unfolded polypeptide ensemble, it is of utmost importance to obtain as many independent experimental parameters as possible for a quantitative description of its behavior. Three experimental methods have been particularly informative in this respect: NMR spectroscopy (2, 5, 7-9), small angle X-ray scattering (SAXS) (10, 11), and single-molecule Förster resonance energy transfer spectroscopy (single-molecule FRET) (12, 13).NMR in solution provides very rich local structural and dynamical information at virtually any atom site with the exception of oxygen. Distance and angular information can be obtained from nuclear Overhauser enhancements (14), three-bond scalar couplings (15), paramagnetic relaxation enhancements (PREs) (16), pseudo contact shifts (17), residual dipolar couplings (RDCs) (8, 18), chemical shifts (19), and hydrogen bond scalar ...

show abstract

Section: Methodsmentioning

confidence: 98%

mentioning

confidence: 99%

See 1 more Smart Citation

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

Aznauryan

Delgado

Soranno

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

145

167

View full text Add to dashboard Cite

show abstract

“…More interesting is the research related to real applications or models. Examples are; spectroscopic characterization of vibrational modes in artificially designed DNA [5], nonlinear optical spectroscopy for biomolecular structure at solid-liquid interfaces [6], modeling and spectroscopic evidence of antimony adsorption on iron-oxide-rich red earth soils [7], single-molecule studies of intrinsically disordered proteins [8], spectroscopic study of model amyloid β-peptide oligomers [9] and other directions [10][11][12][13].The editors will always be pleased to receive the following types of inputs or submissions, among others: 1) Research Highlight articles-generally substantial, current review articles that can be expected to be of interest to the spectroscopy community, 2) Research Notes-research announcements, 3) News and Views, and "In Brief" items-announcements and news items, and 4) Meeting announcements, meeting reports and book reviews.On the side of education, as a community, we need to assess our strategy for teaching and maintaining interest in the field of spectroscopy. Spectroscopic research is rapidly changing and evolving, and it presents many opportunities.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Spectroscopy: Between Modeling, Simulation and Practical Investigation

Saleh¹

2014

SAR

View full text Add to dashboard Cite

Spectral Analysis Review is an international journal dedicated to the latest advancement of all areas of spectroscopy. The primary goal of this journal is to provide a plat-form for scientists and academicians all over the world to provide, share and discuss various new issues and developments in different aspects of spectroscopy. It aims to determine the state-of-the art and advances progress in the field of spectroscopy and get through its developments.I have reviewed the literature regarding spectroscopy. Most of the scientific reports recommend that more spectroscopic investigation should be on modeling and simulation, in addition to the spectroscopic properties of nanomaterials [1][2][3][4]. I would like to stress that modeling and simulation related work would not only promote understanding the spectroscopic properties of materials and nanomaterials but also enhance more bringing their applications to life. In the same way, coupling modeling and computational studies with nanotechnology will help to develop the designing of nanomaterials with required spectroscopic properties. More interesting is the research related to real applications or models. Examples are; spectroscopic characterization of vibrational modes in artificially designed DNA [5], nonlinear optical spectroscopy for biomolecular structure at solid-liquid interfaces [6], modeling and spectroscopic evidence of antimony adsorption on iron-oxide-rich red earth soils [7], single-molecule studies of intrinsically disordered proteins [8], spectroscopic study of model amyloid β-peptide oligomers [9] and other directions [10][11][12][13].The editors will always be pleased to receive the following types of inputs or submissions, among others: 1) Research Highlight articles-generally substantial, current review articles that can be expected to be of interest to the spectroscopy community, 2) Research Notes-research announcements, 3) News and Views, and "In Brief" items-announcements and news items, and 4) Meeting announcements, meeting reports and book reviews.On the side of education, as a community, we need to assess our strategy for teaching and maintaining interest in the field of spectroscopy. Spectroscopic research is rapidly changing and evolving, and it presents many opportunities. Many education innovators may embrace the advancements and examine the rebooting of the academy through a collection of essays. These may explore how to implement new approaches to teaching and research with the use of digital tools; ensure access to lessons and lectures; and take the class time to the high level of interactivity.Happy Reading. REFERENCES[1] S.

show abstract

Advances in Application of Azobenzene as a Trigger in Biomedicine: Molecular Design and Spontaneous Assembly

et al. 2021

View full text Add to dashboard Cite

Azobenzene is a well‐known derivative of stimulus‐responsive molecular switches and has shown superior performance as a functional material in biomedical applications. The results of multiple studies have led to the development of light/hypoxia‐responsive azobenzene for biomedical use. In recent years, long‐wavelength‐responsive azobenzene has been developed. Matching the longer wavelength absorption and hypoxia‐response characteristics of the azobenzene switch unit to the bio‐optical window results in a large and effective stimulus response. In addition, azobenzene has been used as a hypoxia‐sensitive connector via biological cleavage under appropriate stimulus conditions. This has resulted in on/off state switching of properties such as pharmacology and fluorescence activity. Herein, recent advances in the design and fabrication of azobenzene as a trigger in biomedicine are summarized.

show abstract

Single-Molecule Studies of Intrinsically Disordered Proteins

Cited by 132 publications

References 417 publications

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

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

Spectroscopy: Between Modeling, Simulation and Practical Investigation

Advances in Application of Azobenzene as a Trigger in Biomedicine: Molecular Design and Spontaneous Assembly

Contact Info

Product

Resources

About