ArticleBiophysical journal2007
A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 24 citations in OpenAlex.
- Molecular Dynamics Methods for Antibody Design.Methods in molecular biology (Clifton, N.J.) · 2023Article
- High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants.Biomolecules · 2022Article
- Insights from molecular dynamics simulations for computational protein design.Molecular systems design & engineering · 2017Article
- Multimolecule test-tube simulations of protein unfolding and aggregation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate.Biophysical journal · 2010Article
- A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.Biophysical journal · 2010Article
- The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.Biophysical journal · 2010Article
- Dynameomics: a comprehensive database of protein dynamics.Structure (London, England : 1993) · 2010Article
- Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease.PLoS computational biology · 2010Article
- Extracting Kinetic and Stationary Distribution Information from Short MD Trajectories via a Collection of Surrogate Diffusion Models.Journal of chemical theory and computation · 2009Article
- Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain.Biochemistry · 2008Article
- Combining experiment and simulation in protein folding: closing the gap for small model systems.Current opinion in structural biology · 2008Review
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2 authors at 1 institution in 1 country.
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Abstract
A properly identified transition state ensemble (TSE) in a molecular dynamics (MD) simulation can reveal a tremendous amount about how a protein folds and offer a point of comparison to experimentally derived Phi(F) values, which reflect the degree of structure in these transient states. In one such method of TSE identification, dubbed P(fold), MD simulations of individual protein structures taken from an unfolding trajectory are used to directly assess an input structure's probability of folding before unfolding, and P(fold) is, by definition, 0.5 for the TSE. Other, less computationally intensive methods, such as multidimensional scaling (MDS) of the pairwise root mean-squared deviation (RMSD) matrix of the conformations sampled in a thermal unfolding trajectory, have also been used to identify the TSE. Identification of the TSE is made from the original MD simulation without the need to run further simulations. Here we present a P(fold)-like study and describe methods for identification of the TSE through the derivation of a high fidelity, bounded, one-dimensional reaction coordinate for protein folding. These methods are applied to the engrailed homeodomain. The TSE identified by this approach is essentially identical to the TSE identified previously by MDS of the pairwise RMSD matrix. However, the cost of performing P(fold), or even our reduced P(fold)-like calculations, is at least 36,000 times greater than the MDS method.
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