ArticleProceedings of the National Academy of Sciences of the United States of America2007
Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model.Science advances · 2024Article
- Spectroscopic characterization of rare events in colloidal particle stochastic thermodynamics.Frontiers in chemistry · 2022Article
- Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study.PloS one · 2016Article
- Collapse of a long axis: single-molecule Förster resonance energy transfer and serpin equilibrium unfolding.Biochemistry · 2014Article
- Probing DNA clamps with single-molecule force spectroscopy.Nucleic acids research · 2013Article
- The molecular mechanism underlying mechanical anisotropy of the protein GB1.Biophysical journal · 2012Article
- Single-molecule experiments reveal the flexibility of a Per-ARNT-Sim domain and the kinetic partitioning in the unfolding pathway under force.Biophysical journal · 2012Article
- BSDB: the biomolecule stretching database.Nucleic acids research · 2011Article
- Free energy profiles from single-molecule pulling experiments.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress.Biophysical journal · 2010Article
- Molecular basis for the structural stability of an enclosed β-barrel loop.Journal of molecular biology · 2010Article
- Differential binding of bispyridinium oxime drugs with acetylcholinesterase.Acta pharmacologica Sinica · 2010Article
- Temperature and chemical denaturant dependence of forced unfolding of titin I27.The journal of physical chemistry. B · 2009Article
- ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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4 authors.
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Abstract
We present a comprehensive study that integrates experimental and theoretical nonequilibrium techniques to map energy landscapes along well defined pull-axis specific coordinates to elucidate mechanisms of protein unfolding. Single-molecule force-extension experiments along two different axes of photoactive yellow protein combined with nonequilibrium statistical mechanical analysis and atomistic simulation reveal energetic and mechanistic anisotropy. Steered molecular dynamics simulations and free-energy curves constructed from the experimental results reveal that unfolding along one axis exhibits a transition-state-like feature where six hydrogen bonds break simultaneously with weak interactions observed during further unfolding. The other axis exhibits a constant (unpeaked) force profile indicative of a noncooperative transition, with enthalpic (e.g., H-bond) interactions being broken throughout the unfolding process. Striking qualitative agreement was found between the force-extension curves derived from steered molecular dynamics calculations and the equilibrium free-energy curves obtained by Jarzynski-Hummer-Szabo analysis of the nonequilibrium work data. The anisotropy persists beyond pulling distances of more than twice the initial dimensions of the folded protein, indicating a rich energy landscape to the mechanically fully unfolded state. Our findings challenge the notion that cooperative unfolding is a universal feature in protein stability.
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