Protein Folding Transition Path Times from Single Molecule FRET

Overview

Journal Curr Opin Struct Biol

Date 2017 Oct 29

PMID 29080467

Citations 47

Authors

Hoi Sung Chung

William A Eaton

Affiliations

Soon will be listed here.

Abstract

The transition path is the tiny segment of a single molecule trajectory when the free energy barrier between states is crossed and for protein folding contains all of the information about the self-assembly mechanism. As a first step toward obtaining structural information during the transition path from experiments, single molecule FRET spectroscopy has been used to determine average transition path times from a photon-by-photon analysis of fluorescence trajectories. These results, obtained for several different proteins, have already provided new and demanding tests that support both the accuracy of all-atom molecular dynamics simulations and the basic postulates of energy landscape theory of protein folding.

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References

Eaton W, Munoz V, Hagen S, Jas G, Lapidus L, Henry E . Fast kinetics and mechanisms in protein folding. Annu Rev Biophys Biomol Struct. 2000; 29:327-59. PMC: 4782274. DOI: 10.1146/annurev.biophys.29.1.327. View

Englander S, Mayne L . The case for defined protein folding pathways. Proc Natl Acad Sci U S A. 2017; 114(31):8253-8258. PMC: 5547639. DOI: 10.1073/pnas.1706196114. View

Orte A, D Craggs T, White S, Jackson S, Klenerman D . Evidence of an intermediate and parallel pathways in protein unfolding from single-molecule fluorescence. J Am Chem Soc. 2008; 130(25):7898-907. DOI: 10.1021/ja709973m. View

Baldwin R . Clash between energy landscape theory and foldon-dependent protein folding. Proc Natl Acad Sci U S A. 2017; 114(32):8442-8443. PMC: 5559053. DOI: 10.1073/pnas.1709133114. View

Campos L, Liu J, Wang X, Ramanathan R, English D, Munoz V . A photoprotection strategy for microsecond-resolution single-molecule fluorescence spectroscopy. Nat Methods. 2011; 8(2):143-6. DOI: 10.1038/nmeth.1553. View

Best R, Merchant K, Gopich I, Schuler B, Bax A, Eaton W . Effect of flexibility and cis residues in single-molecule FRET studies of polyproline. Proc Natl Acad Sci U S A. 2007; 104(48):18964-9. PMC: 2141891. DOI: 10.1073/pnas.0709567104. View

Kubelka J, Henry E, Cellmer T, Hofrichter J, Eaton W . Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci U S A. 2008; 105(48):18655-62. PMC: 2596247. DOI: 10.1073/pnas.0808600105. View

Kim P, Baldwin R . Intermediates in the folding reactions of small proteins. Annu Rev Biochem. 1990; 59:631-60. DOI: 10.1146/annurev.bi.59.070190.003215. View

Shakhnovich E . Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev. 2006; 106(5):1559-88. PMC: 2735084. DOI: 10.1021/cr040425u. View

10.

Hazan N, Tomov T, Tsukanov R, Liber M, Berger Y, Masoud R . Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence. Biophys J. 2015; 109(8):1676-85. PMC: 4623893. DOI: 10.1016/j.bpj.2015.07.004. View

11.

Eaton W . Searching for "downhill scenarios" in protein folding. Proc Natl Acad Sci U S A. 1999; 96(11):5897-9. PMC: 34202. DOI: 10.1073/pnas.96.11.5897. View

12.

Mallam A, Jackson S . Use of protein engineering techniques to elucidate protein folding pathways. Prog Mol Biol Transl Sci. 2009; 84:57-113. DOI: 10.1016/S0079-6603(08)00403-0. View

13.

Chung H, Gopich I . Fast single-molecule FRET spectroscopy: theory and experiment. Phys Chem Chem Phys. 2014; 16(35):18644-57. PMC: 4154966. DOI: 10.1039/c4cp02489c. View

14.

Zheng Q, Juette M, Jockusch S, Wasserman M, Zhou Z, Altman R . Ultra-stable organic fluorophores for single-molecule research. Chem Soc Rev. 2013; 43(4):1044-56. PMC: 3946787. DOI: 10.1039/c3cs60237k. View

15.

Chung H, Cellmer T, Louis J, Eaton W . Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories. Chem Phys. 2014; 422:229-237. PMC: 3892999. DOI: 10.1016/j.chemphys.2012.08.005. View

16.

Chung H, McHale K, Louis J, Eaton W . Single-molecule fluorescence experiments determine protein folding transition path times. Science. 2012; 335(6071):981-4. PMC: 3878298. DOI: 10.1126/science.1215768. View

17.

Neupane K, Foster D, Dee D, Yu H, Wang F, Woodside M . Direct observation of transition paths during the folding of proteins and nucleic acids. Science. 2016; 352(6282):239-42. DOI: 10.1126/science.aad0637. View

18.

Jackson S, Fersht A . Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry. 1991; 30(43):10428-35. DOI: 10.1021/bi00107a010. View

19.

Lindorff-Larsen K, Piana S, Dror R, Shaw D . How fast-folding proteins fold. Science. 2011; 334(6055):517-20. DOI: 10.1126/science.1208351. View

20.

Chung H, Piana-Agostinetti S, Shaw D, Eaton W . Structural origin of slow diffusion in protein folding. Science. 2015; 349(6255):1504-10. PMC: 6260792. DOI: 10.1126/science.aab1369. View