Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein

Abstract

Integrated-tempering-sampling molecular dynamics simulation is utilized to investigate the folding of a 67-residue three-α-helix bundle, α₃W. Reversible folding and unfolding can be observed in individual trajectories and a total of 28 folding events are achieved within 7 μs simulation, giving sufficient sampling on the configuration space of protein folding. The native-like state with a left-handed topology constitutes the largest fraction of the conformational ensemble sampled by the simulation. In addition, a misfolded state with mirror-image (right-handed) topology is observed with smaller population. The free energy landscape analysis demonstrates that the folding of α₃W is initiated by the formation of α-helical secondary structures and is followed by the assembling of folded α-helices to construct tertiary structure. The “correct” α-helix assembling which leads to the native structure is mainly dominated by inter-helical hydrophobic interactions whereas the “incorrect” assembling which leads to a misfolded mirror-image structure is highly affected by not only hydrophobic but also charge interactions. It is speculated on the basis of the present study on α₃W and other studies on the B domain of protein A and α₃D that the misfolding probability of α-helix bundle proteins is dependent on the strength of intra-protein hydrophobic and charge interactions: proteins containing stronger hydrophobic interactions but weaker charge interactions should have smaller misfolding probability. The importance of intra-protein hydrophobic interactions in preventing protein misfolding has been also seen in our previous studies on β-hairpins. Therefore, the present study along with our previous studies provide comprehensive, atomic-level picture of the folding/misfolding of α-helix bundle and β-hairpin proteins.