Novel Heat-Promoted Folding Dynamics of the yybP-ykoY Manganese Riboswitch: Kinetic and Thermodynamic Studies at the Single-Molecule Level

2019 ◽  
Vol 123 (26) ◽  
pp. 5412-5422 ◽  
Author(s):  
Hsuan-Lei Sung ◽  
David J. Nesbitt
Keyword(s):  
Single Molecule ◽  
Thermodynamic Studies ◽  
Single Molecule Level ◽  
Folding Dynamics ◽  
Kinetic And Thermodynamic Studies

scholarly journals Identical Sequences, Different Behaviors: Protein Diversity Captured at the Single-Molecule Level

2021 ◽  
Author(s):  
Rafael Tapia-Rojo ◽  
Alvaro Alonso-Caballero ◽  
Carmen L. Badilla ◽  
Julio M. Fernandez
Keyword(s):  
Single Molecule ◽  
Magnetic Tweezers ◽  
Complete Characterization ◽  
Force Response ◽  
Folding Kinetics ◽  
Single Molecule Level ◽  
Biochemical Assays ◽  
Folding Dynamics ◽  
Instrumental Development

AbstractThe classical “one sequence, one structure, one function” paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype. While the emergence of single-molecule techniques opened the gates to interrogating individual molecules, technical shortcomings typically limit the duration of these measurements to a few minutes, which prevents to completely characterize a protein individual and, hence, to capture the heterogeneity among molecular populations. Here, we introduce a magnetic tweezers design, which showcases enhanced stability and resolution that allows us to measure the folding dynamics of a single protein during several uninterrupted days with a high temporal and spatial resolution. Thanks to this instrumental development, we do a complete characterization of two proteins with a very different force-response: the talin R3IVVI domain and protein L. Days-long recordings on the same single molecule accumulate several thousands of folding transitions sampled with sub-ms resolution, which allows us to reconstruct their free energy landscapes and describe how they evolve with force. By mapping the nanomechanical identity of many different protein individuals, we directly capture their molecular diversity as a quantifiable dispersion on their force response and folding kinetics. Our instrumental development offers a new tool for profiling individual molecules, opening the gates to the characterization of biomolecular heterogeneity.

Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

2018 ◽  
Author(s):  
Alexander Carl DeHaven
Keyword(s):  
Energy Transfer ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Förster Resonance Energy Transfer ◽  
U2 Snrna ◽  
Folding Dynamics ◽  
The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

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