Abstract
Immunoglobulin-binding B1 domain of streptococcal protein G (PGB1) is a small (56 residues) protein with an α-helix (from Ala23 to Asp 36) lying on top of two pairs of anti-parallel β-sheets, β-hairpin 1 (from Met1 to Ala20) and β-hairpin 2 (from Glu42 to Glu56), covering the hydrophobic core. PGB1 contains no disulfide bonds in its structure and makes it an excellent model protein for folding study. Our simulation results showed that the α-helix and β-hairpin 2 had interacted prior than β-hairpin 1 in early folding stage. Similar experimental results can be observed by monitoring the folding intermediates of PGB1, which are performed by an over-critical refolding process, by using fluorescence resonance energy transfer (FRET) technique, the technique is a precisely optical technique which can reveal the distance difference within angstrom scale. The FRET analysis of PGB1 also indicated that the distance between α-helix and β-hairpin 2 remained approximately unchanged in all folding intermediates. However, the distance between β-hairpin1 and β-hairpin 2 decreased during the folding process. Therefore both simulation and FRET analysis were in consistence. The molecular dynamics of PGB1 during its folding process can be demonstrated.