Solution NMR structure of aD,L-alternating oligonorleucine as a model of ?-helix

Abstract

β‐Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of β‐helices configurations does not allow a direct conformational analysis of β‐helical oligopeptides. A synthetic alternating D,L‐oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of β‐helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR experimental data and theoretical calculations clearly indicate that the XIIMe adopts a single β4.4‐helix‐type conformation in nonpolar solvents. © 2001 John Wiley & Sons, Inc. Biopolymers 59: 110–119, 2001

Synthesis and structural study of carbocyclic analogues of 1,2-disubstituted nucleosides

“…2), it was possible to obtain a chart of NOE intensities that could easily be transformed to interproton distance intervals with a lower limit of 2 Åand an upper limit of 3, 4, or 5 Å, depending on the intensity of the NOEs (Table 1)-as described in the literature [17][18][19].…”

Foldamers Based on Remote Intrastrand Interactions

“…The a-Oligopeptide Precedent: from Antibiotic Gramicidin A to Poly-Gln Aggregates in Huntington's Disease Mixed helices, also termed b-helices by virtue of this similarity to b-sheet type structures, were proposed in the early 1970s independently by Ramachandran and Chandrasekharan [129], and Urry [130] [131][132][133][134][135]. They can be either right-or left-handed depending on parameters such as sequence, length and environment.…”

Study of peptide fingerprints of parasite proteins and drug–DNA interactions with Markov-Mean-Energy invariants of biopolymer molecular-dynamic lattice networks

“…[19][20][21][22][23][24][25][26][27][28][29][30][31][32] and a comprehensive review [33]). In fact, since the advent of MD with the work of Karplus et al [37][38][39][40][41][42], MD has become a computational technique to investigate structure and function of biomolecules and their respective complexes and interactions. In view of this, to understand really the interaction mechanism of drugs with proteins or DNA, we should consider not only the static structures concerned but also the dynamical information obtained by simulating their interactions through a dynamic process.…”