Structural versatility of peptides from Cα, α-disubstituted glycines: Crystal-state conformational analysis of homopeptides from Cα-methyl,Cα-benzylglycine [(αMe)Phe]n

The molecular and crystal structures of one derivative and three homopeptides (from the di-to the tetrapeptide level) of the chiral, C^{α, α}-disubstituted glycine C^α-methyl, C^α-benzylglycine [(αMe)Phe], have been determined by x-ray diffraction. The derivative is mClAc-D -(αMe)Phe-OH, and the peptides are pBrBz-[D -(αMe)Phe]₂-NHMe, pBrBz-[D -(αMe)Phe]₃-OH hemihydrate, and pBrBz-[D -(αMe)Phe]₄-OtBu sesquihydrate. All (αMe)Phe residues prefer ?,ψ torsion angles in the helical region of the conformational map. The dipeptide methylamide and the tripeptide carboxylic acid adopt a β-turn conformation with a 1 ← 4 C?O…?H? N intramolecular H bond. The structure of the tripeptide carboxylic acid is further stabilized by a 1 ← 4 C?O…?H? O intramolecular H bond, forming an “oxy-analogue” of a β-turn. The tetrapeptide ester is folded in a regular (incipient) 3₁₀-helix. In general, the relationship between (αMe)Phe chirality and helix screw sense is opposite to that exhibited by protein amino acids. A comparison is made with the conclusions extracted from published work on homopeptides from other C^α-methylated α-amino acids. © 1993 John Wiley & Sons, Inc.     

Preferred conformation of peptides rich in Ac8c,a medium-ring alicyclic Cα,α-disubstituted glycine

A complete series of terminally blocked, monodispersed homo-oligopeptides (to the pentamer level) from the sterically demanding, medium-ring alicyclic C^α,α-disubstituted glycine 1-aminocyclooctane-1-carb oxylic acid (Ac₈c), and two Ala/Ac₈c tripeptides, were synthesized by solution methods and fully characterized. The preferred conformation of all the oligopeptides was determined in deuterochloroform solution by IR absorption and ¹H-NMR. The molecular structures of the amino acid derivative Z-Ac₈c-OH, the dipeptide pBrBz- (Ac₈c)₂-OH and the tripeptide pBrBz-(Ac₈c)₃-OtBu were assessed in the crystal state by X-ray diffraction. Conformational energy computations were performed on the monopeptide Ac-Ac₈c-NHMe. Taken together, the results obtained strongly support the view that the Ac₈c residue is an effective β-turn and helix former. A comparison is also made with the conformational preferences of α-aminoisobutyric acid, the prototype of C^{α, α}-disubstituted glycines, and of the other members of the family of 1-aminocycloalkane-1-carboxylic acids (Ac_nc, with n=3, 5–7) investigated so far. The implications for the use of the Ac₈c residue in peptide conformational design are considered.     

Helical screw sense of peptide molecules: The pentapeptide system (Aib)4/L-Val[L-(αMe)Val] in the crystal state

The crystal-state preferred conformations of six N^α-blocked pentapeptide esters, each containing four helicogenic, achiral α-aminoisobutyric acid (Aib) residues followed by one chiral L -valine (L -Val) or C^α-methyl-L -valine [(αMe)Val] residue at the C-terminus, have been assessed by x-ray diffraction analysis. In all of the compounds the  (Aib)₄ sequence is folded in a regular 3₁₀-helical conformation. In the four pentapeptides characterized by the L -(αMe)Val residue two conformationally distinct molecules occur in the asymmetric unit. Conversely, only one molecule is observed in the asymmetric unit of two pentapeptides with the C-terminal L -Val residue. In the L -Val based peptides the helical screw sense of the  (Aib)₄ sequence is right-handed, whereas in the L  (αMe)Val analogues both right- and left-handed helical screw senses concomitantly occur in the two crystallographically independent molecules. © 1998 John Wiley & Sons, Inc. Biopoly 46: 433–443, 1998     

Synthesis and conformational study of poly(0,0′-dicarbobenzoxy-L-β-3,4-dihydroxyphenyl-α-alanine)

High-molecular-weight poly(0,0′-dicarbobenzoxy-L -β-3,4-dihydroxyphenyl-α-alanine) was prepared by the N-carboxyanhydride method. From the results obtained by a study of the optical rotation, nuclear magnetic resonance, and solution infrared absorption, the conformation of poly(0,0′-dicarbobenzoxy-L -β-3,4-dihydroxyphenyl-α-alanine) depended greatly on the solvent taking a right-handed helix with [θ]₂₂₅ = ?13,600 ～ ?18,900 in alkyl halides, a left-handed helix with [θ]₂₂₈ = 22,100 ～ 24,800 in cyclic ethers or trimethylphosphate, and a random coil structure in dichloroacetic acid, trifluoroacetic acid, or hexafluoroacetone sesquihydrate. The polypeptide underwent a right-handed helix-coil transition in chloroform/dichloroacetic acid (or trifluoroacetic acid) mixed solvents and a left-handed helix-coil transition in dioxane/dichloroacetic acid (or trifluoroacetic acid) mixed solvents. The results were compared with those of poly(0-carbobenzoxy-L -tyrosine).     

Reverse Relationship between α-Carbon Chirality and Helix Handedness in (αMe)Phe Peptides

Abstract

The crystal-state preferred conformations of two tripeptides, one tetrapeptide, and one pen- tapeptide, each containing a single residue of the chiral, C^α,α-disubstituted glycine C^α-methyl, C^α-benzylglycine [(αMe)Phe], have been determined by X-ray diffraction. The tripeptides are Z-L-(αMe)Phe-(Aib)₂-OH dihydrate and Z-Aib-D-(αMe)Phe-Aib-OtBu, the tetrapeptide is Z-(Aib)₂-D-(αMe)Phe-Aib-OtBu, and the pentapeptide is pBrBz-(Aib)₂-DL-(αMe)Phe-(Aib)₂-OtBu. While the two tripeptides are folded in a β-bend conformation, two such conformations are consecutively formed by the tetrapeptide. The pentapeptide adopts a regular 3₁₀-helix promoted by three consecutive β-bends. This study confirms the strong propensity of short peptides containing C^α-methylated α-aminoacids to fold into β-bends and 3₁₀-helical structures. Since Aib is achiral, the handedness of the observed bends and helices is dictated by the presence of the (αMe)Phe residue. In general, we have found that the relationship between (αMe)Phe chirality and helix handedness is opposite to that exhibited by protein aminoacids. A comparison with the preferred conformation of other extensively investigated C^α-methylated aminoacids is made.     

Sweet and bitter taste: Structure and conformations of two aspartame dipeptide analogues

The synthesis and X-ray diffraction analysis of two dipeptide taste ligands have been carried out as part of our study of the molecular basis of taste. The compounds L -aspartyl-D -α-methylphenylalanine methyl ester [L -Asp-D -(αMe)Phe-OMe] and L -aspartyl-D -alanyl-2,2,5,5-tetramethylcyclopentanyl ester [L -Asp-D -Ala-OTMCP] elicit bitter and sweet taste, respectively. The C-terminal residues of the two analogues adopt distinctly different conformations in the solid state. The aspartyl moiety assumes the same conformation found in other dipeptide taste ligands with the side-chain carboxylate and the amino groups formaing a zwitterionic ring with a conformation defined by ψ,χX1 = 157.7°, ?61.5° for L -Asp-D -Ala-OTMCP and 151.0°, ?68.8° for L -Asp-D -(αMe)Phe-OMe. In the second residue, a left-handed helical conformations is observed for the (αMe)Phe residue of L -Asp-D -(αMe)Phe-OMe with ?₂ = 49.0° and ψ₂ = 47.9°, while the Ala residue of L -Asp-D -Ala-OTMCP adopts a semi-exextended conformation characterized by dihedral angles ?₂ = 62.8° and ψ₂ = ?139.9°. The solid-state structure of the bitter L -Asp-D -(αMe)Phe-OMe is extended; while the crystal structure of the sweet L -Asp-D -OTMCP roughly adopts the typical L-shaped structure shown by other sweeteners. The data of L -Asp-D -(αMe)Phe-OMe are compared with those of its diastereoisomer L -Asp-L -(αMe)Phe-OMe. Conformational analysis of the two taste ligands in solution by NMR and computer simulations agrees well with our model for sweet and bitter tastes.     

Heterochiral Ala/(αMe)Aze sequential oligopeptides: Synthesis and conformational study

α‐Amino acid residues with a ?,ψ constrained conformation are known to significantly bias the peptide backbone 3D structure. An intriguing member of this class of compounds is (αMe)Aze, characterized by an N^α‐alkylated four‐membered ring and C^α‐methylation. We have already reported that (S)‐(αMe)Aze, when followed by (S)‐Ala in the homochiral dipeptide sequential motif ‐(S)‐(αMe)Aze‐(S)‐Ala‐, tends to generate the unprecedented γ‐bend ribbon conformation, as formation of a regular, fully intramolecularly H‐bonded γ‐helix is precluded, due to the occurrence of a tertiary amide bond every two residues. In this work, we have expanded this study to the preparation and 3D structural analysis of the heterochiral (S)‐Ala/(R)‐(αMe)Aze sequential peptides from dimer to hexamer. Our conformational results show that members of this series may fold in type‐II β‐turns or in γ‐turns depending on the experimental conditions.     

Structural versatility of peptides from Cα,α-disubstituted glycines: Preferred conformation of the chiral isovaline residue

The molecular structures of four protected isovaline- (Iva-) containing peptides to the pentamer level have been determined by x-ray diffraction. The peptides are t-Boc-Ala-(S)-Iva-Ala-OMe (t-Boc : tert-butyloxycarbonyl; OMe : methoxy) and its (R)-Iva diastereomer, and t-Boc-[Ala-(R)-Iva]₂-Ala-OH and its (S)-Iva diastereomeric methyl ester analogue. The two tripeptides are folded in an open type II β-bend conformation. The fully developed right-handed 3₁₀-helix formed by the (R)-Iva pentapeptide, which includes an unusual intramolecular (acid) O? H ?O?C(peptide) H bond, is partially unfolded (near the C-terminus) in the (S) -Iva pentapeptide. ¹H-nmr and Fourier transform ir absorption studies suggest that in CDCl₃ solution (a) the two tripeptides maintain a type II β-bend conformation of comparable stability and (b) both diastereomeric pentapeptide sequences adopt a fully developed 3₁₀-helix. A comparison with the preferred conformation of other extensively investigated C^α,α-disubstituted glycines is made and the implications for the use of the Iva residue in designing conformationally constrained analogues of bioactive peptides are briefly discussed.     

Conformational characterization of peptides rich in the cycloaliphatic Cα,α-disubstituted glycine 1-amino-cyclononane-1-carboxylic acid

A series of N- and C-protected, monodispersed homo-oligopeptides (to the pentamer level) from the cycloaliphatic C^α,α,-dialkylated glycine 1-aminocyclononane-1-carboxylic acid (Ac₉c) and two Ala/Ac₉c tripeptides have been synthesized by solution methods and fully characterized. The conformational preferences of all the model peptides were determined in deuterochloroform solution by FT-IR absorption and ¹H-NMR. The molecular structures of the amino acid derivatives mClAc-Ac₉c-OH and Z-Ac₉c-OtBu, the dipeptide pBrBz-(Ac₉c)₂-OtBu, the tetrapeptide Z-(Ac₉c)₄-OtBu, and the pentapeptide Z-( Ac₉c)₅-OtBu were determined in the crystal state by X-ray diffraction. Based on this information, the average geometry and the preferred conformation for the cyclononyl moiety of the Ac₉c residue have been assessed. The backbone conformational data are strongly in favour of the conclusion that the Ac₉c residue is a strong β-turn and helix former. A comparison with the structural propensity of α-aminoisobutyric acid, the prototype of C^α,α-dialkylated glycines, and the other extensively investigated members of the family of 1-aminocycloalkane-1-carboxylic acids (Ac_nc, with n=3−8) is made and the implications for the use of the Ac₉c residue in conformationally constrained analogues of bioactive peptides are briefly examined. © 1997 European Peptide Society and John Wiley & Sons, Ltd. J. Pep. Sci. 3: 367–382 No. of Figures: 10. No. of Tables: 6. No. of References: 62     

Conformational behaviour of Cα,α-diphenylglycine: folded vs. extended structures in DϕG-containing tripeptides

The crystal structures of three fully protected tripeptides containing the Dϕg residue (C^α,α-diphenylglycine) in the central position are reported, namely Z-Gly-Dϕg-Gly-OMe ( a ), Z-Gly-Dϕg-Aib-OMe ( b ) and Z-Aib-Dϕg-Aib-OMe ( c ). The molecular conformations are quite unusual because the Dϕg residue adopts a folded conformation in the 3₁₀-helical region when the following residue adopts a folded conformation of opposite handedness (peptides b and c ). In contrast, the Dϕg residue adopts the more frequently observed fully extended conformation when the following residue adopts a semi-extended conformation (peptide a ). These findings are in agreement with the theoretical calculations on Ac-Dϕg-Aib-NHCH₃ and Ac-Aib-Dϕg-NHCH₃ also reported in this work. © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Structural versatility of peptides from Cα,αdialkylated glycines: Linear Ac3c homo-oligopeptides

The crystal-state molecular structures of five linear Ac₃c homo-oligopeptides to the tetramer were determined by x-ray diffraction. The oligomers are H-(Ac₃c)₂-OMe, Fmoc-(Ac₃c)₂-OMe MeOH, Ac-(Ac₃c)₂-OMe, pBrBz-(Ac₃c)₃-OMe · H₂O, and t-Boc-(Ac₃c)₄-OMe · 2H₂O. The results indicate the propensity of the tri- and tetrapeptides to fold into type I β-bends and distorted 3₁₀-helices, respectively, in partial contrast to Aib, Ac₅c, and Ac₆c homo-peptides of comparable main-chain length, where regular type III β-bends and 3₁₀-helical structures were found. When the influence of the constraints produced by the intramolecular H bonds of the C₁₀-type is absent, other less common structural features may be observed. The average geometry of the cyclopropyl group of the Ac₃c residue is found to be asymmetric and the N? C^α? C′ bond angle significantly expanded from the regular tetrahedral value.     

Defect peptide chemistry: Perturbations in the structure of a homopentapeptide induced by a guest residue interrupting side-chain regularity

The fully blocked pentapeptide Tfa-(Deg)₂-L -Abu-(Deg)₂-OtBu (Tfa:triflouroacetyl; Deg: C^α,α-diethylglycine; OtBu: tert-butoxy) adopts in the crystal state a regular, right-handed 3₁₀-helical structure stabilized by three N ? H …? O ? C intramolecular 1 ← 4 (or C₁₀) H bonds, as determined by an x-ray diffraction analysis. However, a Fourier transform ir absorption and ¹H-nmr study strongly supports the view that in deuterochloroform solution the four Deg residues at both termini of the peptide main chain are involved in successive, fully extended C₅ forms. A comparison with the stable, fully developed, multiple C₅ conformation of Tfa-(Deg)₅-OtBu indicates that incorporation of an Abu guest residue, interrupting the side-chain uniformity of the host (Deg)₅ homopeptide, while altering only marginally the conformation in a solvent of low polarity, is responsible for a dramatic perturbation of the crystal-state structure. © 1994 John Wiley & Sons, Inc.     

Synthesis and Solid State Conformation of Tetrapeptide Amides Containing two Aib and two (αMe)Phe Residues – Use of Enantiomerically Pure 2‐Benzyl‐2‐methyl‐2H‐azirin‐3‐amines as (αMe)Phe‐Synthons

A series of tetrapeptide amides containing two aminoisobutyric acids (Aib) and two α‐methylphenylalanine ((αMe)Phe) units were prepared through the ‘azirine/oxazolone method’. New 2‐benzyl‐2‐methyl‐2H‐azirin‐3‐amines have been used for the selective introduction of (S)‐ and (R)‐(αMe)Phe, respectively. The solid‐state conformations of five tetrapeptide amides were determined by X‐ray crystallography. In all cases, two β‐turns stabilize 3₁₀‐helical conformations and it was confirmed that, in contrast to proteinogenic amino acids, the configuration of (αMe)Phe does not determine the screw sense of the helix.     

The polypeptide 310-helix as a template and a spacer

Summary X-ray diffraction analyses have provided detailed structural information on the 3₁₀-helices of (i) pBrBz-d-(Me)Phe-(Aib)₂-d-(Me)Phe-Aib-OtBu and Ac-(Aib)₂-l-Lys(Bz)-(Aib)₂-l-Lys(Bz)-(Aib)₂-NHMe as suitable templates for molecular recognition studies, and (ii) pBrBz-TOAC-(l-Ala)₂-TOAC-l-Ala-NHtBu as an appropriate spacer for an ESR study of side chain to side chain interactions. In addition, in Ac-TOAC-(Aib)₂-l-Trp-Aib-OMe, forming a 3₁₀-helix, the TOAC residue plays the role of an effective quencher of the fluorescence of the tryptophan residue located one turn apart.     

Preferred conformation of the terminally blocked (Aib)10 homo-oligopeptide: A long,regular 310-helix

The decapeptide pBrBz- (Aib)₁₀-OtBu, synthesized by the 5(4H)-oxazolone method, crystallizes in the monoclinic space group C2/c with a = 43.901(2), b = 9.289(2), and c = 34.746(3) A; β = 114.69(3)°; and Z = 8. The crystals contain one molecule of water associated with each peptide. The structure has been solved by the Patterson method and refined to an R value of 0.073 for 6819 observed reflections. The peptide adopts a regular 3₁₀-helical structure stabilized by eight N? H …? O?C intramolecular 1 ← 4 (or C₁₀) H bonds. This study has allowed us to characterize this important peptide secondary structure in great detail. The crystal-state conformation agrees well with proposals made on the basis of an ir absorption and ¹H-nmr study in solution.     

The conformational properties of α,β‐dehydroamino acids with a C‐terminal ester group

α,β‐Dehydroamino acid esters occur in nature. To investigate their conformational properties, a systematic theoretical analysis was performed on the model molecules Ac‐ΔXaa‐OMe [ΔXaa = ΔAla, (E)‐ΔAbu, (Z)‐ΔAbu, ΔVal] at the B3LYP/6‐311+ + G(d,p) level in the gas phase as well as in chloroform and water solutions with the self‐consistent reaction field‐polarisable continuum model method. The Fourier transform IR spectra in CCl₄ and CHCl₃ have been analysed as well as the analogous solid state conformations drawn from The Cambridge Structural Database. The ΔAla residue has a considerable tendency to adopt planar conformations C5 (?, ψ ≈ ? 180°, 180°) and β2 (?, ψ ≈ ? 180°, 0°), regardless of the environment. The ΔVal residue prefers the conformation β2 (?, ψ ≈ ? 120°, 0°) in a low polar environment, but the conformations α (?, ψ ≈ ? 55°, 35°) and β (?, ψ ≈ ? 55°, 145°) when the polarity increases. The ΔAbu residues reveal intermediate properties, but their conformational dispositions depend on configuration of the side chain of residue: (E)‐ΔAbu is similar to ΔAla, whereas (Z)‐ΔAbu to ΔVal. Results indicate that the low‐energy conformation β2 is the characteristic feature of dehydroamino acid esters. The studied molecules constitute conformational patterns for dehydroamino acid esters with various side chain substituents in either or both Z and E positions. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

The crystal state conformation of Aib-rich segments of peptaibol antibiotics

Ac-(Aib-Ala)₃-OH (a protected segment of the peptaibols gliodeliquescin and paracelsin), Z-Leu-Aib-Val-Aib-Gly-OtBu (a segment of [Leu]⁷-gliodeliquescin), Z-Val-Aib-Aib-Gln-OtBu (a common segment of alamethicin, paracelsin, and hypelcin), and Ac-Aib-Pro-(Aib-Ala)₂-OMe and Z-Aib-Pro-(Aib-Ala)₂-OMe, which represent differently N^α-protected 1–6 segments of alamethicin and hypelcin, have been synthesized by solution methods. The crystal-state conformations of these five Aib-containing peptides have been determined by X-ray diffraction analysis. We have confirmed that the 3₁₀-helical structure is preferentially adopted by Aib-rich short peptides. An experimentally unambiguous proof for the 3₁₀→α-helix conversion has been provided by the two differently N-blocked -Aib-Pro-(Aib-Ala)₂-OMe hexapeptides. The β-bend ribbon conformation, commonly observed in the (Aib-Pro)_n sequential oligopeptides, is not found in the -Aib-Pro-Aib-Ala-Aib-Ala- sequence. As expected on the basis of the l -configuration of the C^α-monoalkylated residues, a right-handed helix screw sense was found in all peptides investigated. © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Synthesis,conformational study,and spectroscopic characterization of the cyclic Cα,α‐disubstituted glycine 9‐amino‐9‐fluorenecarboxylic acid

A series of terminally blocked peptides (to the pentamer level) from l ‐Ala and the cyclic C^α,α‐disubstituted Gly residue Afc and one Gly/Afc dipeptide have been synthesized by solution method and fully characterized. The molecular structure of the amino acid derivative Boc‐Afc‐OMe and the dipeptide Boc‐Afc‐Gly‐OMe were determined in the crystal state by X‐ray diffraction. In addition, the preferred conformation of all of the model peptides was assessed in deuterochloroform solution by FT‐IR absorption and ¹H‐NMR. The experimental data favour the conclusion that the Afc residue tends to adopt either the fully‐extended (C₅) or a folded/helical structure. In particular, the former conformation is highly populated in solution and is also that found in the crystal state in the two compounds investigated. A comparison with the structural propensities of the strictly related C^α,α‐disubstituted Gly residues Ac₅c and Dϕg is made and the implications for the use of the Afc residue in conformationally constrained analogues of bioactive peptides are briefly examined. A spectroscopic (UV absorption, fluorescence, CD) characterization of this novel aromatic C^α,α‐disubstituted Gly residue is also reported. Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd.