ArticleBiophysical journal2006
Testing simplified proteins models of the hPin1 WW domain.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Tuning the binding behaviors of a protein YAP65WW domain on graphenic nano-sheets with boron or nitrogen atom doping.Nanoscale advances · 2020Article
- The Role of Data in Model Building and Prediction: A Survey Through Examples.Entropy (Basel, Switzerland) · 2018Article
- High-Resolution Mapping of the Folding Transition State of a WW Domain.Journal of molecular biology · 2016Article
- Challenges in protein folding simulations: Timescale, representation, and analysis.Nature physics · 2010Article
- Force field bias in protein folding simulations.Biophysical journal · 2009Article
- Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.The Journal of chemical physics · 2008Article
- Stability and kinetic properties of C5-domain from myosin binding protein C and its mutants.Biophysical journal · 2008Article
- Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.Biophysical journal · 2007Article
- Influence of hPin1 WW N-terminal domain boundaries on function, protein stability, and folding.Protein science : a publication of the Protein Society · 2007Article
- Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.Journal of the American Chemical Society · 2007Article
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Authors and funding
3 authors.
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Abstract
The WW domain of the human Pin1 protein for its simple topology and large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of this work is to compare the reliability of the chemically based Sorenson/Head-Gordon (SHG) model and a standard native centric model in reproducing, through molecular dynamics simulations, some of the well known features of the folding transition of this small domain. Our results show that the Gō model correctly reproduces the cooperative, two-state, folding mechanism of the WW-domain, while the SHG model predicts a transition occurring in two stages: a collapse, followed by a structural rearrangement. The lack of a cooperative folding in the SHG simulations appears to be related to the nonfunnel shape of the energy landscape featuring a partitioning of the native valley in subbasins corresponding to different chain chiralities. However, the SHG approach remains more reliable in estimating the phi-values with respect to Gō-like description. This may suggest that the WW-domain folding process is stirred by energetic and topological factors as well, and it highlights the better suitability of chemically based models in simulating mutations.
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