Molecular dynamics simulations of apocytochrome b(562) - The highly ordered limit of molten globules

Background: Cytochrome b(562) is a heme-containing, four-helix bundle. It has been proposed that the apo form of the protein is a molten globule. We present a molecular dynamics study of apocytochrome b(562) to investigate its structural and dynamic properties. Results: Our simulations suggest that all four helices are essentially intact and confirm that the experimental difficulties of assigning helical NOEs in the C-terminal helix are not due to structural disorder. The increased 'moltenness' of the apoprotein is due to an increased mobility of the sidechains. The small observed increase in compressibility for the apoprotein is proposed to be the result of an increase in the intrinsic protein compressibility, which is opposed by the increase in the size of the protein hydration shell. Conclusions: Apocytochrome b(562) is postulated to be near the highly ordered limit of the molten globule state, a structure whose molten character is due primarily to increased sidechain mobility with concurrent loss in tertiary contacts between the helices, rather than changes in the folding topology or substantially increased disorder of the secondary structure. (C) Current Biology Ltd