scholarly journals Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape

2018 ◽  
Vol 122 (49) ◽  
pp. 11126-11136 ◽  
Author(s):  
William M. Jacobs ◽  
Eugene I. Shakhnovich
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Transition Path

High-resolution free energy landscape analysis of protein folding

2015 ◽  
Vol 43 (2) ◽  
pp. 157-161 ◽  
Author(s):  
Polina V. Banushkina ◽  
Sergei V. Krivov
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
High Resolution ◽  
Energy Landscape ◽  
Quantitative Description ◽  
Free Energy Landscape ◽  
Transition Path ◽  
Exponential Factor ◽  
Basic Properties ◽  
Folding Dynamics

The free energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. The profile together with the optimal coordinate allows one to directly determine such basic properties of folding dynamics as the configurations of the minima and transition states, the heights of the barriers, the value of the pre-exponential factor and its relation to the transition path times. In the present study, we review the framework, in particular, the approach to determine such an optimal coordinate, and its application to the analysis of simulated protein folding dynamics.

scholarly journals Accurate protein-folding transition-path statistics from a simple free-energy landscape

2018 ◽  
Author(s):  
William M. Jacobs ◽  
Eugene I. Shakhnovich
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Coarse Grained ◽  
Free Energy Landscape ◽  
Configuration Model ◽  
Trajectory Data ◽  
Transition Path ◽  
One Dimensional ◽  
Transition Paths

A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths — the rare trajectories that transit between the folded and unfolded ensembles — using only thermodynamic information, such as a low-dimensional equilibrium free-energy landscape. However, commonly used one-dimensional landscapes typically fall short of this aim, because an empirical coordinate-dependent diffusion coefficient has to be fit to transition-path trajectory data in order to reproduce the transition-path dynamics. We show that an alternative, first-principles free-energy landscape predicts transition-path statistics that agree well with simulations and single-molecule experiments without requiring dynamical data as an input. This ‘topological configuration’ model assumes that distinct, native-like substructures assemble on a timescale that is slower than native-contact formation but faster than the folding of the entire protein. Using only equilibrium simulation data to determine the free energies of these coarse-grained intermediate states, we predict a broad distribution of transition-path transit times that agrees well with the transition-path durations observed in simulations. We further show that both the distribution of finite-time displacements on a one-dimensional order parameter and the ensemble of transition-path trajectories generated by the model are consistent with the simulated transition paths. These results indicate that a landscape based on transient folding intermediates, which are often hidden by one-dimensional projections, can form the basis of a predictive model of protein-folding transition-path dynamics.

Quantifying the Roughness on the Free Energy Landscape:  Entropic Bottlenecks and Protein Folding Rates

2004 ◽  
Vol 126 (27) ◽  
pp. 8426-8432 ◽  
Author(s):  
Leslie L. Chavez ◽  
José N. Onuchic ◽  
Cecilia Clementi
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Folding Rates

scholarly journals High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape

2016 ◽  
Vol 111 (11) ◽  
pp. 2368-2376 ◽  
Author(s):  
Martin J. Fossat ◽  
Thuy P. Dao ◽  
Kelly Jenkins ◽  
Mariano Dellarole ◽  
Yinshan Yang ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
High Resolution ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Repeat Protein ◽  
High Resolution Mapping ◽  
Resolution Mapping ◽  
Folding Free Energy

Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding

Biochemistry ◽  
2017 ◽  
Vol 56 (31) ◽  
pp. 4053-4063 ◽  
Author(s):  
Pooja Malhotra ◽  
Prashant N. Jethva ◽  
Jayant B. Udgaonkar
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Free Energy Landscape

scholarly journals Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape

2016 ◽  
Vol 111 (2) ◽  
pp. 287-293 ◽  
Author(s):  
Paulo Ricardo Mouro ◽  
Vinícius de Godoi Contessoto ◽  
Jorge Chahine ◽  
Ronaldo Junio de Oliveira ◽  
Vitor Barbanti Pereira Leite
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Folding Free Energy
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