ArticleJournal of molecular biology2005
Folding cooperativity in a three-stranded beta-sheet model.
Article in Journal of molecular biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation.The journal of physical chemistry. B · 2016Article
- Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization.Biopolymers · 2016Article
- Improved Generalized Born Solvent Model Parameters for Protein Simulations.Journal of chemical theory and computation · 2013Article
- Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation.Journal of molecular graphics & modelling · 2010Article
- Modeling of peptides connecting the ligand-binding and transmembrane domains in the GluR2 glutamate receptor.Proteins · 2009Article
- Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation.International journal of molecular sciences · 2009Article
- Structural insights for designed alanine-rich helices: comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation.Biopolymers · 2008Article
- Recent advances in implicit solvent-based methods for biomolecular simulations.Current opinion in structural biology · 2008Review
- Protein folding by zipping and assembly.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Two-stage folding of HP-35 from ab initio simulations.Journal of molecular biology · 2007Article
- Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein.Journal of the American Chemical Society · 2007Article
- Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.The journal of physical chemistry. B · 2007Article
- The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure.Journal of molecular biology · 2006Article
- Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.Biophysical journal · 2006Article
- A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.Journal of chemical theory and computation · 2006Article
- Chemical shifts provide fold populations and register of beta hairpins and beta sheets.Journal of biomolecular NMR · 2005Article
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3 authors.
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Abstract
The thermodynamic behavior of a previously designed three-stranded beta-sheet was studied via several microseconds of standard and replica exchange molecular dynamics simulations. The system is shown to populate at least four thermodynamic minima, including two partially folded states in which only a single hairpin is formed. Simulated melting curves show different profiles for the C and N-terminal hairpins, consistent with differences in secondary structure content in published NMR and CD/FTIR measurements, which probed different regions of the chain. Individual beta-hairpins that comprise the three-stranded beta-sheet are observed to form cooperatively. Partial folding cooperativity between the component hairpins is observed, and good agreement between calculated and experimental values quantifying this cooperativity is obtained when similar analysis techniques are used. However, the structural detail in the ensemble of conformations sampled in the simulations permits a more direct analysis of this cooperativity than has been performed on the basis of experimental data. The results indicate the actual folding cooperativity perpendicular to strand direction is significantly larger than the lower bound obtained previously.
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