@article{oai:nagoya.repo.nii.ac.jp:00012279,
 author = {Mori, Takaharu and Okamoto, Yuko},
 issue = {16},
 journal = {THE JOURNAL OF CHEMICAL PHYSICS},
 month = {Oct},
 note = {Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β^6.3-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β^4.4-helix as the lowest-potential-energy structure, and left-handed β^4.4-helix, right-handed and left-handed β^6.3-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β^6.3-helix and β^4.4-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β^6.3-helix is more stable than β^4.4-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the β^6.3-helix conformation.},
 pages = {165103--165103},
 title = {Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study},
 volume = {131},
 year = {2009}
}