ArticleBiophysical journal2010
The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562.The Journal of chemical physics · 2015Article
- Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed.Journal of chemical theory and computation · 2014Article
- Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins.The journal of physical chemistry letters · 2013Article
- Quantification of excluded volume effects on the folding landscape of Pseudomonas aeruginosa apoazurin in vitro.Biophysical journal · 2013Article
- An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.Journal of chemical theory and computation · 2013Article
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
- Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation.Physical biology · 2013Article
- Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details.Biophysical reviews · 2013Article
- Influence of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling.FEBS letters · 2013Review
- Using simulations to provide the framework for experimental protein folding studies.Archives of biochemistry and biophysics · 2013Review
- A method for computing association rate constants of atomistically represented proteins under macromolecular crowding.Physical biology · 2012Article
- Effects of macromolecular crowding on protein conformational changes.PLoS computational biology · 2010Article
- Rate theories for biologists.Quarterly reviews of biophysics · 2010Review
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Authors and funding
2 authors.
Funding
Abstract
The four-helix bundle protein Rd-apocyt b(562), a redesigned stable variant of apocytochrome b(562), exhibits two-state folding kinetics. Its transition-state ensemble has been characterized by Phi-value analysis. To elucidate the molecular basis of the transition-state ensemble, we have carried out high-temperature molecular dynamics simulations of the unfolding process. In six parallel simulations, unfolding started with the melting of helix I and the C-terminal half of helix IV, and followed by helix III, the N-terminal half of helix IV and helix II. This ordered melting of the helices is consistent with the conclusion from native-state hydrogen exchange, and can be rationalized by differences in intrinsic helix propensity. Guided by experimental Phi-values, a putative transition-state ensemble was extracted from the simulations. The residue helical probabilities of this transition-state ensemble show good correlation with the Phi-values. To further validate the putative transition-state ensemble, the effect of macromolecular crowding on the relative stability between the unfolded ensemble and the transition-state ensemble was calculated. The resulting effect of crowding on the folding kinetics agrees well with experimental observations. This study shows that molecular dynamics simulations combined with calculation of crowding effects provide an avenue for characterize the transition-state ensemble in atomic details.
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