A model for transmembrane helix with a cis-Proline in the middle

Abstract

The presence of a higher percentage of Proline in the transmembrane helices of transport proteins indicates that they are involved in the function of these integral membrane proteins (IMPs). In many cases, the possible involvement of cis-trans isomerization in function/folding of IMPs has been suggested. The introduction of cis-Pro in an ideal a-helix results in a heli-turn-helix motif. A molecular dynamics (MD) simulation is carried out on the sequence ACE-(ALA)₁₀-cis-Pro-(ALA)₁₀-NME with ideal α -helical structure to investigate if and how a straight helix can accommodate a cis-Pro. The analysis of the conformations accessed during MD simulation showed that the residues near cis-Pro can adopt alternate conformations other than the right-handed helical conformation such that an almost straight helix is obtained. This may have implications in the involvement of cis-trans isomerization in folding and/or function of IMPs.