Ensemble fits of restrained peptides’ conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3

Abstract

Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr- d-Daa-Phe-Daa-NH 2 (Daa = diamino acid): 1 combining d-Dab 2 (α,γ-diaminobutyryl) with Lys 4, and 2 – d-Dap 2 (α,β-diaminopropionyl) with Orn 4. The ω-amino groups of d-Daa 2 and Daa 4 are coupled with 〉C O into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and impotent μ/δ opioid peptides, respectively. To the current task, we took from an earlier work ( Filip et al, J. Pept. Sci. 11 (2005) 347–352) the NMR NOE- and J-data in H 2O/D 2O; and the selection of the ensembles of 1 and 2, 822 and 788 conformational families, respectively, obtained by using the EDMC/ECEPP3 method. Here, we generated ensembles of 1 and 2 using AMBER molecular dynamics in explicit water to eventually selected 686 and 761 conformers for 1 and 2, respectively. We did numbers of fits for both types of the conformational ensembles of 1 and 2 to their NOE- and J-data using a common method i.e. maximum entropy approach ( Groth et al, J. Biomol. NMR 15 (1999) 315–330). Both types of the well structurally diversified ensembles fit to quite different equilibria in regressions to common experimental NOE- and J-restraints using maximum entropy principle, which is a disappointing message. Intriguing is startlingly small standard deviation in J-couplings: σ J NH α H ≈ 0.01 Hz for LES-MD/AMBER ensemble, contrary to σ J NH α H = 0.8 − 1.1 Hz for the EDMC/ECEPP ensemble, over the wide range of entropy, i.e. relatively insensitive to it. A similar feature is not the case when comparing σ NOE in both methods. Hence, at minute entropy contributions, it follows that J does or does not transpose “overfitted” into the final σ J in the AMBER or ECEPP ensemble, respectively. Could this be an effect of softness of the AMBER flexible-valence force field compared to ECEPP rigid-geometry, and its effect on ensemble sampling? We do not know an answer.