Coupled folding-binding versus docking: A lattice model study

Abstract

Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is unstructured. We obtain significant differences in their binding behavior. The stable sequence has rigid docking as its preferred binding mode, while the unstructured chain tends to first attach to the target and then fold. The free-energy profiles associated with these two binding modes are compared.

17 pages, 7 figures (to appear in J. Chem. Phys.)

References in corpus (4)

• Evidence for Non-Random Hydrophobicity Structures in Protein Chains
• Primary Sequences of Protein-Like Copolymers: Levy Flight Type Long Range Correlations
• Folding and Aggregation of Designed Proteins
• On Hydrophobicity Correlations in Protein Chains

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• Substrate Adhesion of a Nongrafted Flexible Polymer in a Cavity
• Conformational Mechanics of Polymer Adsorption Transitions at Attractive Substrates
• Adsorption and Pattern Recognition of Polymers at Complex Surfaces with Attractive Stripe-like Motifs
• Polymer Adsorption on Curved Surfaces