Topology to geometry in protein folding: beta-lactoglobulin.
Evolution of protein structure from random coil to native is first represented topologically by its time-dependent sequences of discretized Ramachandran basins occupied by successive backbone residues. Introducing energetic and entropic criteria at each instant of observation transforms the description from a structurally ambiguous topological representation to an unambiguous geometric picture of the folding process. The method is applied with success to folding of beta-lactoglobulin, traditionally perplexing because of its reputed nonhierarchical folding pattern. This molecule passes through a stage, ca. 0.1 microseconds duration, of transient, "flickering" alpha-helical structure, until a bit of tertiary structure forms that stabilizes the system long enough to allow it to pass to its native beta-sheet.
Fernández
A
A
James Franck Institute and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
Colubri
A
A
Berry
R S
RS
D003198:Computer Simulation; D007782:Lactoglobulins / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary
D007782:Lactoglobulins