HYDROGEN-BONDING IN HELICAL POLYPEPTIDES FROM MOLECULAR-DYNAMICS SIMULATIONS AND AMIDE HYDROGEN-EXCHANGE ANALYSIS - ALAMETHICIN AND MELITTIN IN METHANOL

Molecular dynamics simulations of ion channel peptides alamethicin and melittin, solvated in methanol at 27 degrees C, were run with either regular alpha-helical starting structures (alamethicin, 1 ns; melittin 500 ps either with or without chloride counterions), or with the x-ra y crystal coordinates of alamethicin as a starting structure(1 ns). Th e hydrogen bond patterns and stabilities were characterized by analysi s of the dynamics trajectories with specified hydrogen bond angle and distance criteria, and were compared with hydrogen bond patterns and s tabilities previously determined from high-resolution NMR structural a nalysis and amide hydrogen exchange measurements in methanol. The two alamethicin simulations rapidly converged to a persistent hydrogen bon d pattern with a high level of 3(10) hydrogen bonding involving the am ide NH's of residues 3, 4, 9, 15, and 18. The 3(10) hydrogen bonds sta bilizing amide NH's of residues C-terminal to P2 and P14 were previous ly proposed to explain their high amide exchange stabilities. The abse nce, or low levels of 3(10) hydrogen bonds at the N-terminus or for Al 5 NH, respectively, in the melittin simulations, is also consistent w ith interpretations from amide exchange analysis. Perturbation of heli cal hydrogen bonding in the residues before P14(Aib10-P14, alamethicin ; T11-P14, melittin) was characterized in both peptides by variable hy drogen bond patterns that included pi and gamma hydrogen bonds. The ge neral agreement in hydrogen bond patterns determined in the simulation s and from spectroscopic analysis indicates that with suitable conditi ons (including solvent composition and counterions where required), lo cal hydrogen-bonded secondary structure in helical peptides may be pre dicted from dynamics simulations from alpha-helical starting structure s. Each peptide, particularly alamethicin, underwent some large amplit ude structural fluctuations in which several hydrogen bonds were coope ratively broken. The recovery of the persistent hydrogen bonding patte rns after these fluctuations demonstrates the stability of intramolecu lar hydrogen-bonded secondary structure in methanol (consistent with s pectroscopic observations), and is promising for simulations on extend ed timescales to characterize the nature of the backbone fluctuations that underlie amide exchange from isolated helical polypeptides.