Solution structure determination of oligoureas using methylene spin state selective NMR at ¹³C natural abundance

Abstract

Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons.

The Canonical Helix of Urea Oligomers at Atomic Resolution: Insights Into Folding‐Induced Axial Organization

“…The similarity between the structures reported herein and those deduced earlier from NMR studies in solution is striking and underlines the excellent complementarities of the two techniques to analyze urea‐based foldamers 22–25. 31, 38 Our study also demonstrates the robustness of the folding process: four acyclic residues are sufficient to drive complete helix formation with all complementary H‐bonding sites being satisfied. Overall, this crystallographic data set provides the ground for the structure‐guided development of urea foldamers with function, such as recognition of biomolecules and catalysis,20, 39, 40 and also for the elaboration of new tertiary and quaternary structural motifs.…”

“…Although three‐centered H‐bonding between CO( i ) and urea HN( i −3) and HN′( i −2) to form 12‐ and 14‐membered pseudo rings is likely to occur, detailed NMR investigations provided some evidence for H‐bond dissymmetry with d(O( i )N( i −3))<d(O( i )N′( i −2)). Notwithstanding the high quality of structure calculations recently achieved using NMR spectroscopy at 13 C natural abundance,31 structural data at atomic resolution are clearly needed to precisely describe the H‐bonding pattern of the 2.5 helix and facilitate the design of functionally active oligoureas and more complex structures. Herein, we report the first crystal structures of enantiopure N , N ′‐linked oligoureas with from 5 to 9 urea groups and containing exclusively acyclic residues with proteinogenic side chains (that is, Me, i Pr, i Bu, and Bn).…”

“…b) Detail of the three‐centered H‐bonding. O(7)⋅⋅⋅HN(4) and O(7)⋅⋅⋅HN′(5) distances in Å. c) Overlay with the 20 best NMR structures (in gray) of a related nona‐urea 31. Side chains are omitted for clarity.…”

“…Overlay of the X‐ray structure of octamer 3 and the optimized structure of a related nona‐urea determined by NMR spectroscopy31 provides precise insight into the behavior of this helical fold in solution (Figure 1 c). First, the helix in solution is clearly distorted at both ends, which is a direct consequence of an incomplete H‐bond network.…”

Applications of spin-spin couplings

“…Solution structure of the nonamer of N,N 0 -linked oligourea has been determined with the help of 3 J HH couplings by Miclet and co-workers. 52 3 J HH couplings have been used by Va´zquez and co-workers 184 in the studies of conformational domino effect in a series of b-D-glucopyranosyl- a the number of amino acid residues. b the total number of vicinal backbone and side chain proton-proton couplings measured.…”