NMR‐Solution Structures in Methanol of an α‐Heptapeptide, of a β³/β²‐Nonapeptide, and of an all‐β³‐Icosapeptide Carrying the 20 Proteinogenic Side Chains

Abstract

Herrn Professor Rolf Huisgen zum 85. Geburtstag gewidmetThe NMR-solution structure of an a-heptapeptide with a central Aib residue was investigated in order to verify that, in contrast to b-peptides, short a-peptides do not form a helical structures in MeOH. Although the central Aib residue was found to induce a bend in the experimentally determined structure, no secondary structure typical for longer a-peptides or proteins was found. A b 2 /b 3 -nonapeptide with polar, positively charged side chains was subjected to NMR analysis in MeOH and H 2 O. Whereas, in MeOH, it folds into a 10/12-helix very similar to the structure determined for a corresponding b 2 /b 3 -nonapeptide with only aliphatic side chains, no dominant conformation could be determined in H 2 O. Finally, the NMR analysis of a b 3 -icosapeptide containing the side chains of all 20 proteinogenic amino acids in MeOH is described. It revealed that this 20mer folds into a 3 14 -helix over its whole length forming six full turns, the longest 3 14 -helix found so far. Together, our findings confirm that, in contrast to a-peptides, b-peptides not only form helices with just six residues, but also form helices that are longer than helical sections usually observed in proteins or natural peptides. The higher helix-forming propensity of long b-peptides is attributed to the conformation-stabilizing effect of the staggered ethane sections in b-peptides which outweighs the detrimental effect of the increasing macrodipole.

Secondary Structure Dependent Self‐Assembly of β‐Peptides into Nanosized Fibrils and Membranes

“…However, the synthesis of a 20-residue-long helical chain was recently accomplished. [9] Through observation of the packing of the secondary structural units in the solid state, tertiary structural motifs potentially available for b-peptides were identified; Xray crystallographic studies revealed a H14 helix-bundle motif [10] and a polar pleated sheet. [3] As a further step towards tertiary structures, designed b-peptide helices have been observed to exhibit self-association in solution, [11][12][13][14] but the creation of distinct tertiary structures with specific morphologies still remains a challenge.…”

Simulation of an all‐β3‐icosapeptide containing the 20 proteinogenic side chains: Effect of temperature, pH, counterions, solvent, and force field on helix stability

“…In methanol at 298 K, the salt bridge between Asp 11 and Lys 14 is marginally more present than the one between Glu 6 and Arg 9 in agreement with the fact that only the first one was detected experimentally. 23 The very small differences in population between the two saltbridges increase when the simulation of the -peptide is done in water. The presence of the Cl À counterions promotes the formation of both salt bridges.…”

“…NOE distance bound violations were obtained by comparing the nonlinearly averaged protonproton distances (direct r À6 averaging, appropriate for small molecules) 31,32 from the simulation with the upper bound distances derived from the experimental NOE intensities. 23 Pseudoatom corrections (0.09 nm for CH 2 , 0.10 nm for CH 3 , 0.22 nm for (CH 3 ) 2 and (CH 3 ) 3 ) were applied to the experimental upper bounds, and the virtual atom creation technique 15,24 was used to obtain positions for the hydrogen atoms attached to carbon atoms, because a united-atom force field was used. Figure 1 shows the atom-positional RMSD for the backbone atoms with respect to the initial ideal 3 14 helix.…”

“…They are shown above the amino acid names for high pH and below the amino acid names for low pH conditions. This peptide had been synthesized and studied experimentally by NMR 22,23 and found to adopt a stable 3 14 -helix in methanol but no dominant structure in water. It has been constructed to have all hydrophobic side chains close together at the same side of the helix and to form at least two salt bridges, one between Glu 6 and Arg 9 and the other between Asp 11 and Lys 14, although only for the latter experimental indications could be found.…”

“…It has been constructed to have all hydrophobic side chains close together at the same side of the helix and to form at least two salt bridges, one between Glu 6 and Arg 9 and the other between Asp 11 and Lys 14, although only for the latter experimental indications could be found. 23 Here, we analyze the stability of the 3 -icosapeptide in methanol and in water at different temperatures, for different charge configurations (pH) and number of counterions, and using different force-field parameter sets. We analyze hydrogen-bond and salt-bridge formation and compare the NOE distances and 3 J-values calculated from the simulation trajectories with those derived or obtained from experiment.…”