Design and synthesis of novel nonpolar host peptides for the determination of the 310- and α-helix compatibilities of α-amino acid buildig blocks: An assessment of α,α-disubstituted glycines

Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides

Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R₂ ) ≅ [θ]₂₂₂ /[θ]₂₀₈ ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R₁ ) ≅ [θ]₁₉₂ /[θ]₂₀₈ ), may be utilized towards identifying the peptide/protein conformation (especially 3₁₀ - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R₁ parameter can characterize better the individual helices, while the other parameter R₂ and the signal intensity do not always converge. We emphasize the use of the R₁ ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources.

Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines

Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report how the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure of a DFNKF derivative. Computational studies suggest that both the iodinated and the wild-type peptides populate very similar conformations. Furthermore, the conformer found in the solid-state structure is one of the most populated in solution, making the crystal structure a reliable model for the peptide in solution. The crystal structure of DFNKF(I) confirms the overall features of the amyloid cross-β spine and highlights how aromatic-aromatic interactions are important structural factors in the self-assembly of this peptide. A detailed analysis of such interactions is reported.

The ‘CαNN’ motif: an intrinsic lover of sulfate and phosphate ions

The ‘C^αNN’ motif has an intrinsic affinity for the anions and can recognize anion through local interactions along with augmentation of the helical conformation at the motif segment.

Stable right- and left-handed peptide helices containing C(alpha)-tetrasubstituted alpha-amino acids

Short peptidomimetics with stable secondary structures in solution are of interest for applications in chemistry, biology, and medicine. One way to rigidify the backbone of a peptide is the use of cyclic C(alpha)-tetrasubstituted alpha-amino acids (TAAs) like compound 14. The structures resulting from the incorporation of this unnatural amino acid into peptides were investigated. In total, 13 different peptides with a length of up to eight residues and alternating sequences of TAA 14 and (S)- or (R)-valine were synthesized. Their structures were characterized by X-ray diffraction analysis and NMR and CD measurements showing that the all-S-backbone-configured peptides 5 and 6 (SS)(2-3) form right-handed 3(10)-helices, while the all-R-configured peptides 11-13 (RR)(2-4) form left-handed 3(10)-helices in the solid state and solution.

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.

Distributed Drug Discovery, Part 2: global rehearsal of alkylating agents for the synthesis of resin-bound unnatural amino acids and virtual D(3) catalog construction

Distributed Drug Discovery (D³) proposes solving large drug discovery problems by breaking them into smaller units for processing at multiple sites. A key component of the synthetic and computational stages of D³ is the global rehearsal of prospective reagents and their subsequent use in the creation of virtual catalogs of molecules accessible by simple, inexpensive combinatorial chemistry. The first section of this article documents the feasibility of the synthetic component of Distributed Drug Discovery. Twenty-four alkylating agents were rehearsed in the United States, Poland, Russia, and Spain, for their utility in the synthesis of resin-bound unnatural amino acids 1, key intermediates in many combinatorial chemistry procedures. This global reagent rehearsal, coupled to virtual library generation, increases the likelihood that any member of that virtual library can be made. It facilitates the realistic integration of worldwide virtual D³ catalog computational analysis with synthesis. The second part of this article describes the creation of the first virtual D³ catalog. It reports the enumeration of 24 416 acylated unnatural amino acids 5, assembled from lists of either rehearsed or well-precedented alkylating and acylating reagents, and describes how the resulting catalog can be freely accessed, searched, and downloaded by the scientific community.

Control of peptide conformation by the Thorpe-Ingold effect (C alpha-tetrasubstitution)

The preferred conformations of peptides heavily based on the currently extensively exploited achiral and chiral alpha-amino acids with a quaternary alpha-carbon atom, as determined by conformational energy computations, crystal-state (x-ray diffraction) analyses, and solution ((1)H-NMR and spectroscopic) investigations, are reviewed. It is concluded that 3(10)/alpha-helical structures and the fully extended (C(5)) conformation are preferentially adopted by peptide sequences characterized by this family of amino acids, depending upon overall bulkiness and nature (e.g., whether acyclic or C(alpha) (i) <--> C(alpha) (i) cyclized) of their side chains. The intriguing relationship between alpha-carbon chirality and bend/helix handedness is also illustrated. gamma-Bends and semiextended conformations are rarely observed. Formation of beta-sheet structures is prevented.

Direct evidence for alteration of unfolding profile of a helical peptide by far-ultraviolet circular dichroism aromatic side-chain contribution

Aromatic side-chains are known to contribute to the far-UV circular dichroism (CD) spectra of peptides and proteins. Among other things, this can significantly affect the measured helix propensities of amino acids [Chakrabartty et al., Biochemistry 32 (1993) 5560-5565]. In order to address how interfering side-chain contributions can affect the backbone unfolding transition of a helical peptide, as monitored by [theta;](222) (molar ellipticity at 222 nm), we have studied the unfolding transition of a short designed (alpha-amino isobutyric acid/alanine-based) helical peptide containing an interacting Tyr residue. The guanidinium hydrochloride-induced unfolding of the peptide, as monitored by [theta;](222), showed the presence of a sharp transition superposed over a much broader transition. When the same experiment was performed with a similar peptide that lacked the interacting Tyr residue, the sharp transition disappeared and only the broad transition remained. The sharp transition was assigned to originate from the interacting Tyr side-chain. This demonstrates that conformationally restricted aromatic side-chains that interact with the helical backbone not only can alter the backbone far-UV CD signal, they may also alter the unfolding profiles, monitored by far-UV CD, rendering them unfit for a simple analysis for extracting the appropriate unfolding thermodynamic parameters.

High-performance liquid chromatographic separation of the enantiomers of unusual alpha-amino acid analogues

The direct and indirect stereochemical resolution of the enantiomers of ring- and alpha-methyl-substituted phenylalanines and phenylalanine amides was attempted by high-performance liquid chromatographic methods. The direct separation was carried out on two chiral stationary phases, the crown-ether-based Crownpak CR(+), and the teicoplanin-based Chirobiotic T, while the indirect resolution was performed by applying pre-column derivatization with 2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl isothiocyanate (GITC) and Nalpha-(2,4-dinitro-5-fluorophenyl)-L-alanine amide (Marfey's reagent, FDAA). The Chirobiotic T column was efficient in the separation of ring- and alpha-methyl-substituted phenylalanine analogues, but was ineffective for the amides of these analogues. The Crownpak CR(+) column separated the ring-substituted phenylalanines and amides, whereas the alpha-methylated analogues were coeluted. Of the two indirect methods, GITC derivatization seemed more effective than FDAA derivatization.