ArticleBiophysical journal2010
Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate.
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 13 papers.
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Who cites it
13 citing papers in PubMed, 24 citations in OpenAlex.
- Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges.European biophysics journal : EBJ · 2016Article
- Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series.Biophysical journal · 2016Article
- REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain.Journal of molecular modeling · 2014Article
- Using simulations to provide the framework for experimental protein folding studies.Archives of biochemistry and biophysics · 2013Review
- Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.Protein engineering, design & selection : PEDS · 2013Article
- A study of the mechanism of the chaperone-like function of an scFv of human creatine kinase by computer simulation.PloS one · 2013Article
- Multimolecule test-tube simulations of protein unfolding and aggregation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study.Journal of the American Chemical Society · 2011Article
- Malleability of folding intermediates in the homeodomain superfamily.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- The folding of single domain proteins--have we reached a consensus?Current opinion in structural biology · 2011Review
- Folding of the Pit1 homeodomain near the speed limit.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
- Kinetics of chain motions within a protein-folding intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The ultrafast folding pathway of the engrailed homeodomain has been exceptionally well characterized by experiment and simulation. Helices II and III of the three-helix bundle protein form the native helix-turn-helix motif as an on-pathway intermediate within a few microseconds. The slow step is then the proper docking of the helices in approximately 15 mus. However, there is still the unexplained puzzle of why helix docking is relatively slow, which is part of the more general question as to why rearrangements of intermediates occur slowly. To address this problem, we performed 46 all-atom molecular dynamics refolding simulations in explicit water, for a total of 15 micros of simulation time. The simulations started from an intermediate state structure that was generated in an unfolding simulation at 498 K and was then quenched to folding-permissive temperatures. The protein refolded successfully in only one of the 46 simulations, and in that case the refolding pathway mirrored the unfolding pathway at high temperature. In the 45 simulations in which the protein did not fully fold, nonnative salt bridges trapped the protein, which explains why the protein folds relatively slowly from the intermediate state.
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Registered trials
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