Free Energy Reconstruction in Bidirectional Force Spectroscopy Experiments: The Effect of the Device Stiffness

2010 ◽  
Vol 114 (7) ◽  
pp. 2509-2516 ◽  
Author(s):  
Simone Marsili ◽  
Piero Procacci
Keyword(s):  
Free Energy ◽  
Force Spectroscopy ◽  
Energy Reconstruction

scholarly journals Single-molecule force spectroscopy reveals folding steps associated with hormone binding and activation of the glucocorticoid receptor

2018 ◽  
Vol 115 (46) ◽  
pp. 11688-11693 ◽  
Author(s):  
Thomas Suren ◽  
Daniel Rutz ◽  
Patrick Mößmer ◽  
Ulrich Merkel ◽  
Johannes Buchner ◽  
...  
Keyword(s):  
Free Energy ◽  
Glucocorticoid Receptor ◽  
Ligand Binding ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Mechanical Load ◽  
Force Spectroscopy ◽  
Folding Pathway ◽  
Hormone Binding ◽  
Single Molecule Force Spectroscopy

The glucocorticoid receptor (GR) is a prominent nuclear receptor linked to a variety of diseases and an important drug target. Binding of hormone to its ligand binding domain (GR-LBD) is the key activation step to induce signaling. This process is tightly regulated by the molecular chaperones Hsp70 and Hsp90 in vivo. Despite its importance, little is known about GR-LBD folding, the ligand binding pathway, or the requirement for chaperone regulation. In this study, we have used single-molecule force spectroscopy by optical tweezers to unravel the dynamics of the complete pathway of folding and hormone binding of GR-LBD. We identified a “lid” structure whose opening and closing is tightly coupled to hormone binding. This lid is located at the N terminus without direct contacts to the hormone. Under mechanical load, apo-GR-LBD folds stably and readily without the need of chaperones with a folding free energy of 41 kBT (24 kcal/mol). The folding pathway is largely independent of the presence of hormone. Hormone binds only in the last step and lid closure adds an additional 12 kBT of free energy, drastically increasing the affinity. However, mechanical double-jump experiments reveal that, at zero force, GR-LBD folding is severely hampered by misfolding, slowing it to less than 1·s−1. From the force dependence of the folding rates, we conclude that the misfolding occurs late in the folding pathway. These features are important cornerstones for understanding GR activation and its tight regulation by chaperones.

scholarly journals Thermal versus Mechanical Unfolding in a Model Protein

2019 ◽  
Author(s):  
Rafael Tapia-Rojo ◽  
Juan J. Mazo ◽  
Fernando Falo
Keyword(s):  
Free Energy ◽  
Force Spectroscopy ◽  
Reaction Coordinate ◽  
Force Extension ◽  
Thermal Dynamics ◽  
Zero Force ◽  
Protein Model ◽  
Model Protein ◽  
State Models ◽  
Competing Pathways

Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to that obtained using other denaturants, since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is unlikely meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is first unfolded mechanically through typical force spectroscopy-like protocols, and next thermally. When unfolded by non-equilibrium force extension and constant force protocols, we recover a simple two-barrier landscape, as the protein reaches the extended conformation through a metastable intermediate. Interestingly, folding-unfolding equilibrium simulations at low forces suggested a totally different scenario, where this metastable state plays little role in the unfolding mechanism, and the protein unfolds through two competing pathways27. Finally, we use Markov state models to describe the configurational space of the unperturbed protein close to the critical temperature. The thermal dynamics is well understood by a one-dimensional landscape along an appropriate reaction coordinate, however very different from the mechanical picture. In this sense, in our protein model the mechanical and thermal descriptions provide incompatible views of the folding/unfolding landscape of the system, and the estimated quantities to zero force result hard to interpret.

scholarly journals Free energy reconstruction from steered dynamics without post-processing

2010 ◽  
Vol 229 (19) ◽  
pp. 7129-7146 ◽  
Author(s):  
Manuel Athènes ◽  
Mihai-Cosmin Marinica
Keyword(s):  
Free Energy ◽  
Post Processing ◽  
Energy Reconstruction

Estimation of the free energy of adsorption of a polypeptide on amorphous SiO2 from molecular dynamics simulations and force spectroscopy experiments

Soft Matter ◽  
2015 ◽  
Vol 11 (31) ◽  
pp. 6254-6265 ◽  
Author(s):  
Robert Horst Meißner ◽  
Gang Wei ◽  
Lucio Colombi Ciacchi
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Silica Surface ◽  
Force Spectroscopy ◽  
Free Energy Of Adsorption ◽  
Amorphous Sio2 ◽  
Dynamics Simulations ◽  
Smd Simulations

Combination of AFM-force spectroscopy and SMD simulations to assess the free energy of adsorption of a (poly)tetrapeptide on a silica surface.

scholarly journals Metashooting: a novel tool for free energy reconstruction from polymorphic phase transition mechanisms

2018 ◽  
Vol 211 ◽  
pp. 235-251
Author(s):  
Samuel Alexander Jobbins ◽  
Salah Eddine Boulfelfel ◽  
Stefano Leoni
Keyword(s):  
Phase Transition ◽  
Free Energy ◽  
Surface Reconstruction ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Polymorphic Phase Transition ◽  
Energy Reconstruction ◽  
Transformation Mechanisms ◽  
Simulation Scheme

Metashooting, a novel simulation scheme, combines free energy surface reconstruction and detailed elucidation of transformation mechanisms.

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