Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties.

@article{Veitshans1997ProteinFK,
  title={Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties.},
  author={T Veitshans and Dmitri K. Klimov and D. Thirumalai},
  journal={Folding \& design},
  year={1997},
  volume={2 1},
  pages={
          1-22
        }
}

Cell dynamics of folding in two-dimensional model proteins.

Can Theory Predict Two-State Protein Folding Rates? An Experimental Perspective

TLDR
Reviewing theoretical models of protein folding kinetics in terms of their ability to qualitatively rationalize this most basic of experimental observations finds that the properties known to account for variations in the folding rates of simple on- and off-lattice computational models do not account for the vast range of two-state folding rates observed in the laboratory.

Molecular dynamics of folding of secondary structures in Go-type models of proteins

TLDR
This work considers six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without, which are found to be better folders and to be more stable.

Toward a quantitative description of microscopic pathway heterogeneity in protein folding.

TLDR
Predictive methodology reveals the presence of rich ensembles of folding mechanisms that are generally invisible in experiments, reconciles the contradictory observations from experiments and simulations and provides an experimentally consistent avenue to quantify folding heterogeneity.

Ultrafast folding kinetics of WW domains reveal how the amino acid sequence determines the speed limit to protein folding

TLDR
The special properties of fast-folding proteins are exploited to experimentally resolve the folding rate prefactor and investigate how much it varies among structural homologs, and the results confirm long-standing theoretical predictions and bring into focus the ratePrefactor as an essential element for understanding the mechanisms of folding.

Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters.

TLDR
A method is introduced to construct a better approximation for the reaction coordinate for protein folding from known order parameters by introducing a rotation in the phase space of the order parameters Q and Qn that leads to a fivefold improvement in the estimate of the folding rate.

Fast‐folding protein kinetics, hidden intermediates, and the sequential stabilization model

TLDR
This study finds that the present microscopic model is indeed consistent with HIs and transition states, but such states occur in parallel, rather than along the single pathway predicted by the sequential stabilization model.

The folding pathways and thermodynamics of semiflexible polymers.

TLDR
A rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states, and knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium.

LINKING RATES OF FOLDING IN LATTICE MODELS OF PROTEINS WITH UNDERLYING THERMODYNAMIC CHARACTERISTICS

TLDR
It is shown that, under the simulation conditions when the native basin of attraction (NBA) is the most stable, there is an excellent correlation between folding times τF and the dimensionless parameter σT=(Tθ−TF)/T δ, where Tθ is the collapse temperature and TF is the folding transition temperature.

Intermediates and transition states in protein folding.

TLDR
There appears to be a relationship between the diversity of structures in the denatured state ensemble and the extent to which the TSE is plastic, and the consequences of multiple routes and intermediates on the transition state ensemble (TSE) in folding.
...

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