Helix-helix interconversion rates of short13C-labeled helical peptides as measured by dynamic NMR spectroscopy

Acceleration and deceleration of chirality inversion speeds in a dynamic helical metallocryptand by alkali metal ion binding

We report that the chirality inversion kinetics of a trinickel(II) cryptand can be controlled by guest recognition in the cryptand cavity. When the guest was absent, the nickel(II) cryptand underwent a dynamic interconversion between the P and M forms in solution, preferring the M form, with a half-life of t1/2 = 4.99 min. The P/M equilibrium is reversed to P-favored by binding with an alkali metal ion in the cryptand cavity. The timescale of this M→P inversion kinetics was both notably accelerated and decelerated by the guest binding (t1/2 = 0.182 min for K+ complex; 186 min for Cs+ complex); thus, the equilibration rate constants differed by up to 1000-fold depending on the guest metal ions. This acceleration/deceleration can be explained in terms of the virtual binding constants at the transition state of the P/M chirality inversion; K+ binding more stabilizes the transition state rather than the P and M forms to result in the acceleration.

Stapling strategy for slowing helicity interconversion of α-helical peptides and isolating chiral auxiliary-free one-handed forms

In nature, α-helical peptides adopt right-handed conformations that are dictated by L-amino acids. Isolating one-handed α-helical peptides composed of only achiral components remains a significant challenge. Here, this goal is achieved by optical resolution of the corresponding racemic (quasi-)static α-helical peptide with double stapling, which effectively freezes the interconversion between the right-handed (P)- and left-handed (M)-α-helices. An as-obtained doubly stapled analogue having an unprotected L-valine residue at the C-terminus transforms from a kinetically trapped (M)-α-helix to a thermodynamically stable (P)-α-helix upon heating. In contrast, the corresponding singly stapled α-helical peptide undergoes an acid/base-triggered and solvent-induced reversible inversion of its preferred helicity within minutes. The interconversion rates of the singly and doubly stapled α-helical peptide foldamers are approximately 106 and 1012 times slower, respectively, than that of a non-stapled dynamic helical peptide. Therefore, the enantiopure doubly-stapled (quasi-)static α-helical peptide would retain its optical activity for several years at 25 °C.

Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp)

The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 "Polymers under multiple constraints: restricted and controlled molecular order and mobility" this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.

Introducing the Chiral Constrained α-Trifluoromethylalanine in Aib foldamers to Control, Quantify and Assign the Helical Screw-Sense

Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that adopt 3 10 helical structures with equal population of left- and right-handed conformers. Yet, the screw-sense preference of the helical chain may be controlled by a single chiral residue located at one terminus. 1 H and 19 F NMR, X-ray crystallography and circular dichroism studies on new Aib oligomers show that the incorporation of a chiral quaternary α-trifluoromethylalanine at their N -terminus induces a reversal of the screw-sense preference of the 3 10 -helix compared to that of a non-fluorinated analogue having an l-α-methyl valine residue. This work demonstrates that, among the many particular properties of introducing a trifluoromethyl group into foldamers, its stereo-electronic properties are of major interest to control the helical screw sense. Its use as an easy-to-handle 19 F NMR probe to reliably determine both the magnitude of the screw-sense preference and its sign assignment is also of remarkable interest.

Cα-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds

In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 3₁₀- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by C^α-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and ¹H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.

Distance-Dependent Chiral Communication between Two Quinoline Oligoamide Foldamers Connected by Alkyl Chains

A series of macrocycles that contain two quinoline oligoamide foldamers (QOFs) using various length of alkyl chains as linkers (2, 3, 6, 8 or 12 hydrocarbons) were synthesized. The two QOFs interact with each other through the linkers and the intramolecular helix chiral communications between the two QOFs were studied by ¹ H NMR spectroscopy and crystal structures. Investigations show that the intensity of the intramolecular helix chiral communications between the two QOFs is dependent on the length of the linkers, and the interaction between the two QOFs increases with decreasing length of the linkers. When the length of the linkers decreased to C2 linkers, only one conformer is present in solution. Moreover, increasing the length of the foldamers would enhance the intramolecular helix chiral communication if the linkers are short, indicating that the length of the foldamers also has significant impact on intramolecular helix chiral communication.

Bis-pyrene probes of foldamer conformation in solution and in phospholipid bilayers

Exploring the detailed structural features of synthetic molecules in the membrane phase requires sensitive probes of conformation. Here we describe the design, synthesis and characterization of bis(pyrene) probes that report conformational changes in membrane-active dynamic foldamers. The probes were designed to distinguish between left-handed (M) and right-handed (P) screw-sense conformers of 3₁₀-helical α-aminoisobutyric acid (Aib) peptide foldamers, both in solution and in bilayer membranes. Several different bis(pyrene) probes were synthesized and ligated to the C-terminus of Aib tetramers that had different chiral residues at the N-terminus, residues that favored either an M or a P screw-sense in the 3₁₀-helix. The readily synthesized and conveniently incorporated N-acetyl-1,2-bis(pyren-1'-yl)ethylenediamine probe proved to have the best properties. In solution, changes in foldamer screw-sense induced substantial changes in the ratio of excimer/monomer fluorescence emission (E/M) for this reporter of conformation, with X-ray crystallography revealing that opposite screw-senses produce very different interpyrene distances in the reporter. In bilayers, this convenient and sensitive fluorescent reporter allowed, for the first time, an investigation of how the chirality of natural phospholipids affects foldamer conformation.

Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids

The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by (13)C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer-ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a "proton-counting" molecular device capable of providing a tunable, pH-dependent conformational response to its environment.

Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.

Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids

The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.

Screw sense alone can govern enantioselective extension of a helical peptide by kinetic resolution of a racemic amino acid

Helical secondary structure alone, even in the absence of local chiral residues, can direct the enantioselectivity of peptide coupling.

Left-handed helical preference in an achiral peptide chain is induced by an L-amino acid in an N-terminal type II β-turn

Oligomers of the achiral amino acid Aib adopt helical conformations in which the screw-sense may be controlled by a single N-terminal residue. Using crystallographic and NMR techniques, we show that the left- or right-handed sense of helical induction arises from the nature of the β-turn at the N terminus: the tertiary amino acid L-Val induces a left-handed type II β-turn in both the solid state and in solution, while the corresponding quaternary amino acid L-α-methylvaline induces a right-handed type III β-turn.

Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature

The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To characterize helical and unfolded states adopted by water-soluble Aib-containing peptides, the conformational preference of Ac-Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Tyr-NH(2) was determined by CD, NMR and MD simulations as a function of temperature. Temperature-dependent CD data indicated the contribution of two major components, each an admixture of helical and extended/polyproline II structures. Both right- and left-handed helical conformations were detected from deconvolution of CD data and (13)C NMR experiments. The presence of a helical backbone, more pronounced at the N-terminal, and a temperature-induced shift in alpha-helix/3(10)-helix equilibrium, more pronounced at the C-terminal, emerged from NMR data. Starting from polyproline II, the N-terminal of the peptide folded into a helical backbone in MD simulations within 5 ns at 60 degrees C. Longer simulations showed a mixed-helical backbone to be stable over the entire peptide at 5 degrees C while at 60 degrees C the mixed-helix was either stable at the N-terminus or occurred in short stretches through out the peptide, along with a significant population of polyproline II. Our results point towards conformational heterogeneity of water-soluble Aib-based peptide helices and the associated subtleties. The problem of analyzing CD and NMR data of both left- and right-handed helices are discussed, especially the validity of the ellipticity ratio [theta](222)/[theta](207), as a reporter of alpha-/3(10)- population ratio, in right- and left-handed helical mixtures.

Antiamoebin I in Methanol Solution: Rapid Exchange between Right-Handed and Left-Handed310-Helical Conformations

Antiamoebin I (Aam-I) is a membrane-active peptaibol antibiotic isolated from fungal species belonging to the genera Cephalosporium, Emericellopsis, Gliocladium, and Stilbella. Antiamoebin I has the amino acid sequence: Ac-Phe(1)-Aib-Aib-Aib-Iva-Gly-Leu-Aib(8)-Aib-Hyp-Gln-Iva-Hyp-Aib-Pro-Phl(16). By using the uniformly (13)C,(15)N-labeled sample of Aam-I, the set of conformationally dependent J couplings and (3h)J(NC) couplings through H-bonds were measured. Analysis of these data along with the data on magnetic nonequivalence of the (13)C(beta) nuclei (Deltadelta((13)C(beta))) in Aib and Iva residues allowed us to draw the univocal conclusion that the N-terminal part (Phe(1)-Gly(6)) of Aam-I in MeOH solution is in fast exchange between the right-handed and left-handed 3(10)-helical conformations, with an approximately equal population of both states. An additional conformational exchange process was found at the Aib(8) residue. The (15)N-NMR-relaxation and CD-spectroscopy measurements confirmed these findings. Molecular modeling and Monte Carlo simulations revealed that both exchange processes are correlated and coupled with significant hinge-bending motions around the Aib(8) residue. Our results explain relatively low activity of Aam-I with respect to other 15-amino acid residue peptaibols (for example, zervamicin) in functional and biological tests. The high dynamic 'propensity' possibly prevents both initial binding of the antiamoebin to the membrane and subsequent formation of stable ionic channels according to the barrel-stave mechanism.