2004/11/30 by Patrícia F. N. Faísca, P. F. N. Faisca, M. M. Telo da Gama +2 · 1 citation
Biochemistry, Genetics and Molecular Biology · Chemistry · Mathematics · Physics and Astronomy · #Chemical physics #Chemistry #Classical mechanics #Contact order #Coupling (piping) #Crystallography #Downhill folding #Energy landscape #Folding (DSP implementation) #Force Microscopy Techniques and Applications #Kinetics #Lattice (music) #Lattice protein #Materials science #Mathematics #Molecular physics #Monte Carlo method #Native state #Phi value analysis #Physics #Protein Structure and Dynamics #Protein folding #Range (aeronautics) #Statistical physics #Theoretical and Computational Physics #Thermodynamics #q-bio.BM
paper · pdf · doi:10.1002/prot.20521
published as Proteins: Structure, Function and Bioinformatics 60, 712-722 (2005) · 12 pages, 26 figures, RevTex. Accepted in Proteins: Structure, Function and Bioinformatics
arxiv created 2005/03/09 · openalex publication_date 2005/07/14 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modeled by the Gō potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long-range interactions to the native state's energy is decreased from approximately 50% towards zero. However, the dispersion of the simulated folding times is strongly dependent on native geometry and Gō polymers folding to one of the target structures exhibits folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long-range contacts, which means that, when this coupling exists, the formation of long-range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling results in a kinetics that is more sensitive to the interaction energy parameters; in this case, the formation of local contacts is not capable of promoting the establishment of long-range ones when the latter are strongly penalized energetically and this results in longer folding times.