ArticleProceedings of the National Academy of Sciences of the United States of America2013
A transformation for the mechanical fingerprints of complex biomolecular interactions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Stepwise DNA-unwinding gates TnpB genome-editing activity.Molecular cell · 2026Article
- Massively parallel bead-free force spectroscopy with fluorescence.Science advances · 2026Article
- Single Molecule Force Spectroscopy to Probe Intermediates and Energetics of Membrane Protein Folding.Chemical reviews · 2026Review
- Stepwise DNA unwinding gates TnpB genome-editing activity.bioRxiv : the preprint server for biology · 2026Article
- Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates.Nature communications · 2025Article
- Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Single-Molecule Studies of Protein Folding with Optical Tweezers.Annual review of biochemistry · 2020Review
- Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Membrane-Protein Unfolding Intermediates Detected with Enhanced Precision Using a Zigzag Force Ramp.Biophysical journal · 2020Article
- Watching helical membrane proteins fold reveals a common N-to-C-terminal folding pathway.Science (New York, N.Y.) · 2019Article
- Elasticity of individual protocadherin 15 molecules implicates tip links as the gating springs for hearing.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase.Biophysical journal · 2018Article
- Do Actomyosin Single-Molecule Mechanics Data Predict Mechanics of Contracting Muscle?International journal of molecular sciences · 2018Review
- Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.The Journal of chemical physics · 2018Article
- Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins.Science (New York, N.Y.) · 2017Article
- Distinguishing Signatures of Multipathway Conformational Transitions.Physical review letters · 2017Article
- Modular, Nondegenerate Polyprotein Scaffolds for Atomic Force Spectroscopy.Biomacromolecules · 2016Article
- Targeted binding of nucleocapsid protein transforms the folding landscape of HIV-1 TAR RNA.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Probing the structural dynamics of proteins and nucleic acids with optical tweezers.Current opinion in structural biology · 2015Review
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2 authors.
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Abstract
Biological processes are carried out through molecular conformational transitions, ranging from the structural changes within biomolecules to the formation of macromolecular complexes and the associations between the complexes themselves. These transitions cover a vast range of timescales and are governed by a tangled network of molecular interactions. The resulting hierarchy of interactions, in turn, becomes encoded in the experimentally measurable "mechanical fingerprints" of the biomolecules, their force-extension curves. However, how can we decode these fingerprints so that they reveal the kinetic barriers and the associated timescales of a biological process? Here, we show that this can be accomplished with a simple, model-free transformation that is general enough to be applicable to molecular interactions involving an arbitrarily large number of kinetic barriers. Specifically, the transformation converts the mechanical fingerprints of the system directly into a map of force-dependent rate constants. This map reveals the kinetics of the multitude of rate processes in the system beyond what is typically accessible to direct measurements. With the contributions from individual barriers to the interaction network now "untangled", the map is straightforward to analyze in terms of the prominent barriers and timescales. Practical implementation of the transformation is illustrated with simulated biomolecular interactions that comprise different patterns of complexity--from a cascade of activation barriers to competing dissociation pathways.
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