Threonine mutations in proline helix II of bacteriorhodopsin: a molecular dynamics study

Abstract

Proline-containing helices are a part of many integral membrane proteins. In addition, several such helices contain polar residues such as serine and threonine in their helical segments. Such helices are known to play an important structural and functional role in membrane proteins such as channels and receptors. Although it is known that proline introduces a kink in the helix, the role of serine and threonine is not clear. In helices of globular proteins, these residues are often found to be involved in side chain to main chain hydrogen bonds. In the present work, the role of these polar residues on the conformation and stability of proline-containing helices was investigated using molecular dynamics simulation studies. A native amino acid sequence of helix II of the membrane protein bacteriorhodopsin was chosen for study. The 25-residue sequence has a proline residue at position 13, threonine residues at positions 9, 10 and 18 and a serine residue at position 22. Three sequences in the helical conformation were generated by mutation, all the Thr(3)/Ser(1), Thr/Ser on the N-terminal and C-terminal side of the proline by the non-polar residues of appropriate size. The four helical sequences thus obtained were subjected to molecular dynamics simulation for 500 ps and the results obtained were analysed for structural features and to investigate the flexibility involved in these oligopeptides. The results are interpreted in terms of the effect of the Ser/Thr position with respect to proline.