Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity.
A method to reconstruct the energy landscape of small peptides is presented with reference to a two-dimensional off-lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly connected pairs (DCP). As the mutual distance of DCP is typically much smaller than that of generic pairs, a metric criterion can be established to identify the great majority of DCP. Advantages and limits of this approach are thoroughly analyzed for three different heteropolymeric chains. A funnel-like structure of the energy landscape is found in all of the three cases, but the escape rates clearly reveal that the native configuration is more easily accessible (and is significantly more stable) for the sequence that is expected to behave as a real protein.
Bongini
Lorenzo
L
Dipartimento di Fisica, Universitá di Firenze, via Sansone, 1-I-50019 Sesto Fiorentino, Italy. bongini@fi.infn.it
Livi
Roberto
R
Politi
Antonio
A
Torcini
Alessandro
A
D000595:Amino Acid Sequence; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013816:Thermodynamics
D011506:Proteins