Literature DB >> 24336839

Shedding light on protein folding landscapes by single-molecule fluorescence.

Priya R Banerjee1, Ashok A Deniz.   

Abstract

Single-molecule (SM) fluorescence methods have been increasingly instrumental in our current understanding of a number of key aspects of protein folding and aggregation landscapes over the past decade. With the advantage of a model free approach and the power of probing multiple subpopulations and stochastic dynamics directly in a heterogeneous structural ensemble, SM methods have emerged as a principle technique for studying complex systems such as intrinsically disordered proteins (IDPs), globular proteins in the unfolded basin and during folding, and early steps of protein aggregation in amyloidogenesis. This review highlights the application of these methods in investigating the free energy landscapes, folding properties and dynamics of individual protein molecules and their complexes, with an emphasis on inherently flexible systems such as IDPs.

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Year:  2014        PMID: 24336839      PMCID: PMC3958939          DOI: 10.1039/c3cs60311c

Source DB:  PubMed          Journal:  Chem Soc Rev        ISSN: 0306-0012            Impact factor:   54.564


  146 in total

Review 1.  Ratiometric single-molecule studies of freely diffusing biomolecules.

Authors:  A A Deniz; T A Laurence; M Dahan; D S Chemla; P G Schultz; S Weiss
Journal:  Annu Rev Phys Chem       Date:  2001       Impact factor: 12.703

2.  Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2.

Authors:  A A Deniz; T A Laurence; G S Beligere; M Dahan; A B Martin; D S Chemla; P E Dawson; P G Schultz; S Weiss
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-09       Impact factor: 11.205

3.  The cooperativity of burst phase reactions explored.

Authors:  M J Parker; S Marqusee
Journal:  J Mol Biol       Date:  1999-11-12       Impact factor: 5.469

4.  Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy.

Authors:  D S Talaga; W L Lau; H Roder; J Tang; Y Jia; W F DeGrado; R M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2000-11-21       Impact factor: 11.205

5.  Impairment of the ubiquitin-proteasome system by protein aggregation.

Authors:  N F Bence; R M Sampat; R R Kopito
Journal:  Science       Date:  2001-05-25       Impact factor: 47.728

6.  Fluorescent stains, with special reference to amyloid and connective tissues.

Authors:  P S VASSAR; C F CULLING
Journal:  Arch Pathol       Date:  1959-11

Review 7.  Protein folding and the organization of the protein topology universe.

Authors:  Kresten Lindorff-Larsen; Peter Røgen; Emanuele Paci; Michele Vendruscolo; Christopher M Dobson
Journal:  Trends Biochem Sci       Date:  2005-01       Impact factor: 13.807

8.  Three-color single-molecule fluorescence resonance energy transfer.

Authors:  Jean-Pierre Clamme; Ashok A Deniz
Journal:  Chemphyschem       Date:  2005-01       Impact factor: 3.102

Review 9.  Intrinsically unstructured proteins and their functions.

Authors:  H Jane Dyson; Peter E Wright
Journal:  Nat Rev Mol Cell Biol       Date:  2005-03       Impact factor: 94.444

Review 10.  Going new places using an old MAP: tau, microtubules and human neurodegenerative disease.

Authors:  M L Garcia; D W Cleveland
Journal:  Curr Opin Cell Biol       Date:  2001-02       Impact factor: 8.382

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  29 in total

1.  Denaturant-specific effects on the structural energetics of a protein-denatured ensemble.

Authors:  Mahdi Muhammad Moosa; Asha Z Goodman; Josephine C Ferreon; Chul Won Lee; Allan Chris M Ferreon; Ashok A Deniz
Journal:  Eur Biophys J       Date:  2017-10-27       Impact factor: 1.733

2.  Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells.

Authors:  Iwo König; Arash Zarrine-Afsar; Mikayel Aznauryan; Andrea Soranno; Bengt Wunderlich; Fabian Dingfelder; Jakob C Stüber; Andreas Plückthun; Daniel Nettels; Benjamin Schuler
Journal:  Nat Methods       Date:  2015-07-06       Impact factor: 28.547

3.  Three-Color Single-Molecule FRET and Fluorescence Lifetime Analysis of Fast Protein Folding.

Authors:  Janghyun Yoo; John M Louis; Irina V Gopich; Hoi Sung Chung
Journal:  J Phys Chem B       Date:  2018-10-10       Impact factor: 2.991

4.  Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins.

Authors:  Jianhui Song; Gregory-Neal Gomes; Tongfei Shi; Claudiu C Gradinaru; Hue Sun Chan
Journal:  Biophys J       Date:  2017-09-05       Impact factor: 4.033

5.  Site-Specific Three-Color Labeling of α-Synuclein via Conjugation to Uniquely Reactive Cysteines during Assembly by Native Chemical Ligation.

Authors:  Taehyung C Lee; Crystal R Moran; Philip A Cistrone; Philip E Dawson; Ashok A Deniz
Journal:  Cell Chem Biol       Date:  2018-04-19       Impact factor: 8.116

Review 6.  Dynamics of IRES-mediated translation.

Authors:  Alex G Johnson; Rosslyn Grosely; Alexey N Petrov; Joseph D Puglisi
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-03-19       Impact factor: 6.237

7.  Effect of acidic pH on the stability of α-synuclein dimers.

Authors:  Zhengjian Lv; Alexey V Krasnoslobodtsev; Yuliang Zhang; Daniel Ysselstein; Jean Christophe Rochet; Scott C Blanchard; Yuri L Lyubchenko
Journal:  Biopolymers       Date:  2016-10       Impact factor: 2.505

Review 8.  Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation.

Authors:  Irem Nasir; Paulo L Onuchic; Sergio R Labra; Ashok A Deniz
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2019-05-02       Impact factor: 3.036

9.  Protein folding on biosensor tips: folding of maltodextrin glucosidase monitored by its interactions with GroEL.

Authors:  Ashutosh Pastor; Amit K Singh; Mark T Fisher; Tapan K Chaudhuri
Journal:  FEBS J       Date:  2016-08-01       Impact factor: 5.542

10.  Fast single-molecule FRET spectroscopy: theory and experiment.

Authors:  Hoi Sung Chung; Irina V Gopich
Journal:  Phys Chem Chem Phys       Date:  2014-09-21       Impact factor: 3.676

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