2004/01/11 by Marek Cieplak · 15 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Materials Science · Mathematics · Physics and Astronomy · #Binding site #Biochemistry #Chemical physics #Chemistry #Condensed matter physics #Contact order #Cooperative binding #Cooperativity #Crystallography #Folding (DSP implementation) #Material Dynamics and Properties #Mathematical analysis #Mathematics #Monotonic function #Native state #Physics #Protein Structure and Dynamics #Protein folding #Spectroscopy and Quantum Chemical Studies #Statistical physics #Universality (dynamical systems) #cond-mat.soft #q-bio.BM
paper · pdf · doi:10.1103/physreve.69.031907
published in Physical Review E 69(3), 031907 (American Physical Society) · 18 pages 6 figures. Phys. Rev. E in press
arxiv created 2004/01/11 · openalex publication_date 2004/03/23 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as in the absence of cooperativity. For a fixed native geometry, small changes in the effective contact map may affect the folding times in a chance way, and, to an extent that is comparable to the shift in the folding times due to cooperativity. The contact order controls folding scenarios: the average times necessary to bring pairs of amino acids into their near native separations depend on the sequential distances within the pairs. This dependence is largely monotonic, regardless of the cooperativity, and the dominant trend could be described by a single parameter like the average contact order. However, it is the deviations from the trend which are usually found to set the net folding times.