ArticleProtein science : a publication of the Protein Society2006
Sequence of events in folding mechanism: beyond the Gō model.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Multi-Journal of chemical theory and computation · 2024Article
- Thermodynamics of strongly allosteric inhibition: a model study of HIV-1 protease.European biophysics journal : EBJ · 2012Article
- Non-native interactions play an effective role in protein folding dynamics.Protein science : a publication of the Protein Society · 2010Article
- Identification of the folding inhibitors of hen-egg lysozyme: gathering the right tools.European biophysics journal : EBJ · 2010Article
- Analysis of the free-energy surface of proteins from reversible folding simulations.PLoS computational biology · 2009Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Subdomain competition, cooperativity, and topological frustration in the folding of CheY.Journal of molecular biology · 2008Article
- Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis.The Journal of chemical physics · 2008Article
- Early events in protein folding: Is there something more than hydrophobic burst?Protein science : a publication of the Protein Society · 2008Article
- Analyzing pathogenic mutations of C5 domain from cardiac myosin binding protein C through MD simulations.European biophysics journal : EBJ · 2008Article
- Stability and kinetic properties of C5-domain from myosin binding protein C and its mutants.Biophysical journal · 2008Article
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3 authors.
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Abstract
Simplified Gō models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a Calpha-based Gō model where different residues interact with different energies. The model is used to calculate the thermodynamics of three small proteins (Protein G, Src-SH3, and CI2) and the effect of mutations (DeltaDeltaGU-N, DeltaDeltaGdouble dagger-N, DeltaDeltaGdouble dagger-U, and phi-values) on the wild-type sequence. The model allows us to investigate some of the most controversial areas in protein folding, such as its earliest stages and the nature of the unfolded state, subjects that have lately received particular attention.
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