Secondary structure prediction and folding of globular protein: Refolding of ferredoxin

摘要: The physicochemical mechanism of protein folding has been elucidated by the island model, describing a growth type folding. pathway is closely related with nucleation on polypeptide chain and thus formation small local structures or secondary at earliest stage essential to all following steps. model applicable any protein, but high precision structure prediction indispensable simulation. formed are supposed be standard form, they usually deformed during process, especially last stage, although degree deformation different for each protein. Ferredoxin an example having this property. According X-ray investigation (1FDX), ferredoxin not have structures. However, if we assumed that in residues coil state, could attain correct similar native one. Further, found some parts flexible, suggesting presence structures, agreement recent PDB data (1DUR). Assuming (α-helices β-strands) nonflexible early folding, deforming these final one was obtained. Another peculiarity absence disulfide bonds, spite its eight cysteines. reason cysteines do form bonds became clear applying lampshade criterion, more importantly, two groups ready make iron complexes, respectively, rather later poor accuracy conventional methods discussed.