Three-body correlations in protein folding: the origin of cooperativity

Ariel Fernández, Andrés Colubri and R. Stephen Berry

Physica A: Statistical Mechanics and its Applications, 2002, vol. 307, issue 1, 235-259

Abstract: The success of the protein folding process requires that the peptide chain find a structure that ensures the survival of its intramolecular H-bonds. In this work, we identify and model how water is hindered from invading and destroying the intramolecular H-bonds: a three-body protective association establishes itself when a hydrophobic residue approaches a pair of residues held by an amide–carbonyl H-bond. This proximity disrupts the water structure surrounding the backbone H-bond, driving water molecules away so they cannot solvate the backbone. These three-body contributions often compensate thermodynamically for concurrent two-body hydrophobic–polar mismatches. A previously-developed theoretical method to generate folding pathways is extended to reveal the role of three-residue correlations in stabilizing the collapse-inducing folding nucleus; successful computer runs exhibit their formation and how they protect and scaffold incipient secondary structure.

Keywords: Protein folding; Collapse-inducing nucleus; Ubiquitin; Folding topology (search for similar items in EconPapers)
Date: 2002
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:307:y:2002:i:1:p:235-259

DOI: 10.1016/S0378-4371(01)00586-6

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