ArticleProtein science : a publication of the Protein Society2004
Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Caseins: Versatility of Their Micellar Organization in Relation to the Functional and Nutritional Properties of Milk.Molecules (Basel, Switzerland) · 2023Review
- Probing protein aggregation using discrete molecular dynamics.Frontiers in bioscience : a journal and virtual library · 2008Review
- Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations.Journal of the American Chemical Society · 2006Article
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3 authors.
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Abstract
Amino acid residue-solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction-energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid-solvent interactions by introducing a contrast parameter for the hydrophobicity, C(s), and a mean attraction parameter for the amino acids, omega. Changes in the interaction energies strongly affect many protein properties. We present an optimized energy parameter set for best representing realistic behavior typical for many proteins (fast folding and high cooperativity for single chains). Our optimal parameters feature a much weaker hydrophobicity contrast and mean attraction than does the original interaction scale. The proposed interaction scale is designed for calculating the behavior of proteins in bulk and at interfaces as a function of solvent characteristics, as well as protein size and sequence.
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