ArticleProceedings of the National Academy of Sciences of the United States of America1996
The folding mechanism of larger model proteins: role of native structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1996. 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.
- Hydrophobic Homopolymer's Coil-Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions.The journal of physical chemistry. B · 2023Article
- Coarse-grained (hybrid) integrative modeling of biomolecular interactions.Computational and structural biotechnology journal · 2020Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.PloS one · 2014Article
- Hydrophobic forces and the length limit of foldable protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Protein-folding landscapes in multichain systems.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.Protein science : a publication of the Protein Society · 2004Article
- Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics.Protein science : a publication of the Protein Society · 2004Article
- A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state.Biophysical journal · 2003Article
- Protein folding: matching theory and experiment.Biophysical journal · 1998Article
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3 authors.
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Abstract
The folding mechanism of a 125-bead heteropolymer model for proteins is investigated with Monte Carlo simulations on a cubic lattice. Sequences that do and do not fold in a reasonable time are compared. The overall folding behavior is found to be more complex than that of models for smaller proteins. Folding begins with a rapid collapse followed by a slow search through the semi-compact globule for a sequence-dependent stable core with about 30 out of 176 native contacts which serves as the transition state for folding to a near-native structure. Efficient search for the core is dependent on structural features of the native state. Sequences that fold have large amounts of stable, cooperative structure that is accessible through short-range initiation sites, such as those in anti-parallel sheets connected by turns. Before folding is completed, the system can encounter a second bottleneck, involving the condensation and rearrangement of surface residues. Overly stable local structure of the surface residues slows this stage of the folding process. The relation of the results from the 125-mer model studies to the folding of real proteins is discussed.
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