Theoretical Prediction of Substituent Effects on the Intrinsic Folding Properties of β-Peptides

Abstract

Dedicated to Prof. Dr. Peter Welzel on the occasion of his 65th birthday A systematic conformational analysis on blocked b-amino acids as constituents of b-peptides by ab initio MO theory reveals that the conformer pool of b-peptide monomers is essentially determined by the conformation of simple submonomer fragments. The influence of single and multiple substitutions at the C(a) and C(b) backbone atoms on the intrinsic folding properties of the monomers was estimated both in the singlemolecule approximation and in a polar solvent continuum, applying a quantum-chemical SCRF model. Substitution at C(b) has a higher impact on the b-amino acid conformation than a substitution at C(a). It can be shown that the conformations of important periodic secondary structures in b-peptides belong to the conformer pool of the monomers, even for those secondary-structure elements where H-bond formation appears only in longer sequences. Rules for design of special secondary-structure types by selection of an actual substituent pattern in the b-amino acid constituents have been derived within the monomer approach.1. Introduction. ± In recent years, oligomers of b-amino acids, called b-peptides, have gained much attraction because of their ability to form well-ordered secondary structures [1 ± 6], e.g., b-strand-like conformers [7 ± 9], reverse turns [10 ± 14], and, in particular, helices with differing H-bonding patterns [15 ± 34]. Some representatives are stable against proteases [35 ± 37] and can be translocated across the cell membrane [38] [39], which makes b-peptides possible candidates for pharmacological applications [40 ± 49]. In comparison to a-amino acid constituents, b-amino acids offer a much greater number of different substituent patterns, which should influence the secondarystructure formation in peptide sequences. Therefore, it might be useful to look for the intrinsic folding properties in b-peptide models with substituents in various positions.It is a tempting approach to derive the characteristic secondary structures in peptide sequences from the conformational properties of the monomer constituents (monomer approach). Numerous systematic conformational analyses on blocked a-amino acids and unnatural amino acids have been reported [50 ± 74]. These theoretical studies, employing molecular-orbital (MO) theory and empirical force fields, indicate that most of the typical secondary structures found in peptides and proteins already belong to the conformer pool of the monomers. This concerns even those secondary-structure elements that are characterized by H-bond formation between amino acid residues that are more or less distant in the sequence. Obviously, H-bonds may significantly influence the stability relationships between competing folding alternatives, but they are not the driving force for the formation of the corresponding conformers themselves.

Theoretical prediction of the basic helix types in α,β‐hybrid peptides

“…From the very beginning, the synthetic efforts in the field of peptide foldamers were successfully accompanied by theoretical conformational analyses employing the methods of ab initio molecular orbital (MO) theory. On the basis of theoretical calculations, it was possible to obtain a complete overview on the characteristic secondary structure elements in several classes of peptide foldamers as, for instance, in β, γ, δ, aminoxy, and hydrazino peptides 11–22. The most stable structures determined by the theoretical calculations agree very well with the typical secondary structures found in experimental studies.…”

Side‐chain control of folding of the homologous α‐, β‐, and γ‐peptides into “mixed” helices (β‐helices)

“…Gramicidin A itself is a good example for the substituent influence on the secondary structure formation, since an alternating sequence of D ‐ and L ‐amino acids seems to be a basic requirement for the formation of the channel‐like structure. Like in gramicidin A, experimental and theoretical data for β‐peptides demonstrate the sensitivity of secondary structure formation to substituents 21–24. Thus, folding into the two most important periodic folding patterns of β‐peptides with 14‐ and 12‐membered hydrogen‐bonded rings (H 14 , H 12 ) is clearly influenced by the substitution type of the backbone 21, 23, 25.…”

“…Like in gramicidin A, experimental and theoretical data for β‐peptides demonstrate the sensitivity of secondary structure formation to substituents 21–24. Thus, folding into the two most important periodic folding patterns of β‐peptides with 14‐ and 12‐membered hydrogen‐bonded rings (H 14 , H 12 ) is clearly influenced by the substitution type of the backbone 21, 23, 25. There are also hints that the mixed helix found in β‐peptide sequences is favored by alternating β 2 ‐ and β 3 ‐substituted amino acids 11, 22, 24, 26…”

On the flexibility of β‐peptides

“…The need for tackling larger and larger units and yet preserving as high level of quantum mechanics (QM) as possible is foremost in current expectations 25. Due to developments in computational technology, theoretical examination of blocked β‐amino acids and short peptides (i.e., β‐peptides) has become possible in recent years 26–32. In addition to structural information derived from experimental results, Hofmann et al recognized, that values of the central torsion angle μ (also called θ) are usually in the regions of syn‐clinal and anti‐periplanar, when studying β‐peptides using quantum chemical calculations 32.…”