EXTENSIVE MOLECULAR-DYNAMICS SIMULATIONS OF A BETA-HAIRPIN-FORMING PEPTIDE

Molecular dynamics simulations of the water-solvated, beta-hairpin-for ming linear peptide Y-Q-N-P-D-G-S-Q-A (one-letter amino acid code) [F. J. Blanco et al. (1993) J. Am. Chem. Sec. 115, 5887-5888] were perfor med at simulation temperatures of 278 K and 270 K. At 278 K, the overa ll beta-hairpin state remained stable for approximately 2.06 ns, after which it underwent an unfolding transition to a more disordered, rand om coil-like state that was maintained for the remainder of the 3.50-n s simulation. A comparison of experimental H-alpha-C-alpha order param eters determined at 278 K with order parameters derived from the simul ation revealed that the beta-hairpin state is consistent with the expe rimental results, whereas the random coil-like state yields order para meters that are all much lower than the experimental values. This indi cates that the random coil-like state is not highly populated in the e xperimental system. An examination of the dynamic behavior of the simu lated peptide/solvent system indicated that a lower temperature may yi eld a more stable trajectory. At 270 K, the beta-hairpin conformation remained stable for approximately 2.32 ns, after which the peptide aga in unfolded and maintained a less-ordered state for the remainder of t he 3.50-ns simulation. The less-ordered state observed at 270 K is mor e compact than the disordered state observed at 278 K; the former may represent a folding intermediate. The folded state is stabilized prima rily by a number of transient hydrogen bonding interactions, including hydrogen bonds between Tyr-1 O and Ala-9 HN, between Asn-3 HN and Ser -7 O, and between the side chain of Asn-3 and backbone groups of Asp-5 , Gly-6, and Ser-7. The 270 K simulation was restarted at 2.10 ns, wit h a single loose nuclear Overhauser effect (NOE) upper-bound distance restraint of 5.5 Angstrom added between Gln-2 H-alpha and Gln-8 H-alph a. This single restraint maintained folded conformations for the remai ning 10.50 ns of the trajectory. The restraint was frequently violated (i.e., the restraint potential frequently took on nonzero values) dur ing the period between about 0.24 and 6.51 ns of the restrained trajec tory. Between about 6.51 and 8.04 ns of the restrained trajectory, the restraint remained well-satisfied, demonstrating a transiently stable , alternate-folded conformational state during this period. These resu lts indicate that even long (by today's standards), similar to 1 ns ti mescale trajectories may not always be sufficient to prove the long-te rm stability of the native state in simulations of biomolecules, and t hat apparently converged states may only be metastable. (C) 1996 John Wiley & Sons, Inc.