2008/04/22 by L.N. Mazzoni, Lorenzo N. Mazzoni, Lapo Casetti
Biochemistry, Genetics and Molecular Biology · Chemistry · Engineering · Materials Science · Mathematics · Physics and Astronomy · #Biological system #Biology #Chemical physics #Chemistry #Computer science #Energy (signal processing) #Energy landscape #Engineering #Enzyme Structure and Function #Folding (DSP implementation) #Geometry #Material Dynamics and Properties #Mathematics #Mechanical engineering #Nuclear magnetic resonance #Physics #Protein Structure and Dynamics #Protein folding #Quantum mechanics #Simple (philosophy) #Statistical physics #Thermodynamics #Transition (genetics) #cond-mat.soft #cond-mat.stat-mech #q-bio.BM
paper · pdf · doi:10.1103/physreve.77.051917
to appear in Physical Review E
arxiv created 2008/04/22 · openalex publication_date 2008/05/29 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is completely determined by the potential energy. We consider different sequences, some with a definite proteinlike behavior, a unique native state and a folding transition, and others undergoing a hydrophobic collapse with no tendency to a unique native state. The global geometry of the energy landscape appears to contain relevant information on the behavior of the various sequences: in particular, the fluctuations of the curvature of the energy landscape, measured by means of numerical simulations, clearly mark the folding transition and allow the proteinlike sequences to be distinguished from the others.