ArticleBiophysical journal2010
A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.
Article in Biophysical journal, 2010. 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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Who cites it
12 citing papers in PubMed.
- 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
- Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein.Biophysical journal · 2019Article
- Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.Journal of chemical theory and computation · 2014Article
- Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.The journal of physical chemistry. B · 2013Article
- Multimolecule test-tube simulations of protein unfolding and aggregation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.PloS one · 2012Article
- Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: computational approaches.PloS one · 2012Article
- GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate.Biophysical journal · 2011Article
- Malleability of folding intermediates in the homeodomain superfamily.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Protein folds and protein folding.Protein engineering, design & selection : PEDS · 2011Review
- Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate.Biophysical journal · 2010Article
- Dynameomics: a comprehensive database of protein dynamics.Structure (London, England : 1993) · 2010Article
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Authors and funding
3 authors.
Funding
Abstract
The goal of the Dynameomics project is to perform, store, and analyze molecular dynamics simulations of representative proteins, of all known globular folds, in their native state and along their unfolding pathways. To analyze unfolding simulations, the location of the protein along the unfolding reaction coordinate (RXN) must be determined. Properties such as the fraction of native contacts and radius of gyration are often used; however, there is an issue regarding degeneracy with these properties, as native and nonnative species can overlap. Here, we used 15 physical properties of the protein to construct a multidimensional-embedded, one-dimensional RXN coordinate that faithfully captures the complex nature of unfolding. The unfolding RXN coordinates for 188 proteins (1534 simulations and 22.9 mus in explicit water) were calculated. Native, transition, intermediate, and denatured states were readily identified with the use of this RXN coordinate. A global native ensemble based on the native-state properties of the 188 proteins was created. This ensemble was shown to be effective for calculating RXN coordinates for folds outside the initial 188 targets. These RXN coordinates enable, high-throughput assignment of conformational states, which represents an important step in comparing protein properties across fold space as well as characterizing the unfolding of individual proteins.
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