Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data

Analysis of nuclear Overhauser enhancement (NOE) intensities data of interc onverting microstates of a peptide is a difficult problem in nmr. A new sta tistical mechanics methodology has been proposed recently, consisting of se veral steps: (1) potential energy wells on the energy surface of the molecu le ave identified (the corresponding regions are called wide microstates); (2) each wide microstate is then spanned by a Monte Carlo (MC) or molecular dynamics simulation starting rom a representative structure, and the corre sponding relative populations are obtained from the free energy calculated with the local states method; and (3) the overall NOEs and (3)J coupling co nstants are obtained as averages over the corresponding contributions of th e samples, weighted by the populations. Extending this methodology to cycli c peptides, we are treating here the hexapeptide cyclo(D-Pro(1)-Phe(2)-Ala( 3)-Ser(4)-Phe(5)-Phe(6)) in DMSO, which was studied by Kessler et al. using nmr (Journal of the American Chemical Society, 1992, Vol. 114, pp. 4805-48 18). They found that at least two structures are required to explain their NOE data, a conclusion also corroborated by our analysis (Journal of the Am erican Chemical Society 1998 Vol. 120 pp. 800-812) and led to a novel deriv ation of atomic solvation parameters (ASPs) for DMSO. Thus, the overall int eractions within the peptide-solvent system are described approximately by E-tot = E-GRO + Sigma sigma(i)A(i), where E-GRO is the energy of the GROMOS force field, Ai is the solvent-accessible surface area of atom i, and sigm a(i) is the ASP. In the present paper the validity of these ASPs within the framework of the entire methodology is verified. This requires taking into account 23 microstates. A very good agreement is obtained between experime ntal and calculated NOEs and (3)J coupling constants. The free energy based populations lead to the best results, which means that entropic effects sh ould not be ignored. We have also studied the behavior of the internal angu lar fluctuations of the proton-proton vectors and discovered that they have a negligible effect on the calculated NOEs; this is due to the relatively concentrated wide microstates spanned by the MC simulations. The applicabil ity of our ASPs to other cyclic peptides in DMSO is being studied in anothe r work and preliminary results are discussed. (C) 1999 John Wiley & Sons, I nc.