ArticleBiophysical journal2001
Understanding beta-hairpin formation by molecular dynamics simulations of unfolding.
Article in Biophysical journal, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Effects of Externally Applied Electric Fields on the Manipulation of Solvated-Chignolin Folding: Static- versus Alternating-Field Dichotomy at Play.The journal of physical chemistry. B · 2022Article
- Modeling the mechanism of CLN025 beta-hairpin formation.The Journal of chemical physics · 2017Article
- Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways.International journal of molecular sciences · 2009Review
- Role of hydrophobic interactions and salt-bridges in beta-hairpin folding.Journal of molecular modeling · 2006Article
- Configurational temperature density of states simulations of proteins.Biophysical journal · 2003Article
- Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences.Protein science : a publication of the Protein Society · 2003Article
- Hydrophobicity of transmembrane proteins: spatially profiling the distribution.Protein science : a publication of the Protein Society · 2003Article
- Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs.Biophysical journal · 2002Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have studied the mechanism of formation of a 16-residue beta-hairpin from the protein GB1 using molecular dynamics simulations in an aqueous environment. The analysis of unfolding trajectories at high temperatures suggests a refolding pathway consisting of several transient intermediates. The changes in the interaction energies of residues are related with the structural changes during the unfolding of the hairpin. The electrostatic energies of the residues in the turn region are found to be responsible for the transition between the folded state and the hydrophobic core state. The van der Waals interaction energies of the residues in the hydrophobic core reflect the behavior of the radius of gyration of the core region. We have examined the opposing influences of the protein-protein (PP) energy, which favors the native state, and the protein-solvent (PS) energy, which favors unfolding, in the formation of the beta-hairpin structure. It is found that the behavior of the electrostatic components of PP and PS energies reflects the structural changes associated with the loss of backbone hydrogen bonding. Relative changes in the PP and PS van der Waals interactions are related with the disruption of the hydrophobic core of a protein. The results of the simulations support the hydrophobic collapse mechanism of beta-hairpin folding.
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