2007/08/02 by Rui D. M. Travasso, M. M. Telo da Gama, Patrícia F. N. Faísca +1 · 12 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Engineering · Materials Science · Mathematics · Physics and Astronomy · #Biology #Biophysics #Chemical physics #Chemistry #Cluster (spacecraft) #Computer science #Contact order #Crystallography #Downhill folding #Engineering #Enzyme Structure and Function #Folding (DSP implementation) #Folding funnel #Geometry #Lattice (music) #Mathematics #Monte Carlo method #Native state #Nucleation #Phi value analysis #Physics #Protein Structure and Dynamics #Protein folding #Statistical physics #Structural engineering #Theoretical and Computational Physics #Thermodynamics #q-bio.BM
paper · pdf · doi:10.1063/1.2777150
published in The Journal of Chemical Physics 127(14), 145106 (American Institute of Physics) · Accepted in J. Chem. Phys
arxiv created 2007/08/02 · openalex publication_date 2007/10/12 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
We perform extensive Monte Carlo simulations of a lattice model and the Gō potential [N. Gō and H. Taketomi, Proc. Natl. Acad. Sci. U.S.A. 75, 559563 (1978)] to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e., that with more nonlocal contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.