Funnel sculpting for in silico assembly of secondary structure elements of proteins.
We present a method for designing a funnel-shaped free-energy surface that reproducibly assembles secondary structure elements of proteins into their native conformations from a random extended configuration. Assuming a priori knowledge of secondary structure, our method can design a funnel-shaped surface for folding of alpha, beta, and alphabeta structures individually. We design energy surfaces that fold up to five unrelated sequences with the same energy parameters. We develop a measure of the foldability of an energy landscape in silico and present an alternative way to view energy landscapes.
Fain
Boris
B
Department of Structural Biology, Stanford University, Stanford, CA 94305, USA. bfain@stanford.edu
Levitt
Michael
M
D000465:Algorithms; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D011506:Proteins