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Literature DB >> 26182121

Testing Landscape Theory for Biomolecular Processes with Single Molecule Fluorescence Spectroscopy.

Katherine Truex¹, Hoi Sung Chung¹, John M Louis¹, William A Eaton¹.

Abstract

Although Kramers' theory for diffusive barrier crossing on a 1D free energy profile plays a central role in landscape theory for complex biomolecular processes, it has not yet been rigorously tested by experiment. Here we test this 1D diffusion scenario with single molecule fluorescence measurements of DNA hairpin folding. We find an upper bound of 2.5 μs for the average transition path time, consistent with the predictions by theory with parameters determined from optical tweezer measurements.

Entities: Chemical Disease Mutation Species

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Year: 2015 PMID： 26182121 PMCID： PMC6252093 DOI： 10.1103/PhysRevLett.115.018101

Source DB: PubMed Journal: Phys Rev Lett ISSN： 0031-9007 Impact factor: 9.161

30 in total

Review 1. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors: Eugene Shakhnovich
Journal: Chem Rev Date: 2006-05 Impact factor: 60.622

Review 2. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models.

Authors: Hue Sun Chan; Zhuqing Zhang; Stefan Wallin; Zhirong Liu
Journal: Annu Rev Phys Chem Date: 2011 Impact factor: 12.703

3. Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform.

Authors: Megan C Engel; Dustin B Ritchie; Daniel A N Foster; Kevin S D Beach; Michael T Woodside
Journal: Phys Rev Lett Date: 2014-12-03 Impact factor: 9.161

4. Single-molecule fluorescence experiments determine protein folding transition path times.

Authors: Hoi Sung Chung; Kevin McHale; John M Louis; William A Eaton
Journal: Science Date: 2012-02-24 Impact factor: 47.728

5. Exploring the energy landscape of nucleic acid hairpins using laser temperature-jump and microfluidic mixing.

Authors: Ranjani Narayanan; Li Zhu; Yogambigai Velmurugu; Jorjethe Roca; Serguei V Kuznetsov; Gerd Prehna; Lisa J Lapidus; Anjum Ansari
Journal: J Am Chem Soc Date: 2012-11-07 Impact factor: 15.419

6. Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories.

Authors: Krishna Neupane; Dustin B Ritchie; Hao Yu; Daniel A N Foster; Feng Wang; Michael T Woodside
Journal: Phys Rev Lett Date: 2012-08-06 Impact factor: 9.161

7. Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements.

Authors: Michael T Woodside; John Lambert; Kevin S D Beach
Journal: Biophys J Date: 2014-10-07 Impact factor: 4.033

8. Anomalous dynamics of DNA hairpin folding.

Authors: R Frederickx; T In't Veld; E Carlon
Journal: Phys Rev Lett Date: 2014-05-15 Impact factor: 9.161

9. Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories.

Authors: Hoi Sung Chung; Troy Cellmer; John M Louis; William A Eaton
Journal: Chem Phys Date: 2013-08-30 Impact factor: 2.348

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

16 in total

Review 1. Protein folding transition path times from single molecule FRET.

Authors: Hoi Sung Chung; William A Eaton
Journal: Curr Opin Struct Biol Date: 2017-11-05 Impact factor: 6.809

2. Exact Solutions for Distributions of First-Passage, Direct-Transit, and Looping Times in Symmetric Cusp Potential Barriers and Wells.

Authors: Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal: J Phys Chem B Date: 2019-04-23 Impact factor: 2.991

Testing Landscape Theory for Biomolecular Processes with Single Molecule Fluorescence Spectroscopy.

Review 1. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Review 2. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models.

3. Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform.

4. Single-molecule fluorescence experiments determine protein folding transition path times.

5. Exploring the energy landscape of nucleic acid hairpins using laser temperature-jump and microfluidic mixing.

6. Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories.

7. Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements.

8. Anomalous dynamics of DNA hairpin folding.

9. Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories.

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

Review 1. Protein folding transition path times from single molecule FRET.

2. Exact Solutions for Distributions of First-Passage, Direct-Transit, and Looping Times in Symmetric Cusp Potential Barriers and Wells.

3. Measuring the average shape of transition paths during the folding of a single biological molecule.

4. Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.

5. Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics.

6. Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.

7. Oligomerization of the tetramerization domain of p53 probed by two- and three-color single-molecule FRET.

8. Mean Direct-Transit and Looping Times as Functions of the Potential Shape.

9. A new insight into diffusional escape from a biased cylindrical trap.

10. First passage, looping, and direct transition in expanding and narrowing tubes: Effects of the entropy potential.