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.     

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.     

Structural versatility of peptides from Cα,α-dialkylated glycines. II. An IR absorption and 1H-nmr study of homo-oligopeptides from Cα,α-diethylglycine

The conformational preferences of the N-trifluoroacetylated homo-peptides of C^α,α-diethylglycine from monomer to pentamer in chloroform solution were determined by using ir absorption and ¹H-nmr. Intramolecular hydrogen bonding was found to be the dominant factor for all NH groups. The likely absence of a conformational transition upon increasing main-chain length, and the remarkable stability to dilution, heating, and addition of perturbing agents, are additional relevant findings of this study. These results are in agreement with those of the fully extended, C₅-conformation-forming homo-peptides from the higher homolog C^α,α-di-n-propylglycine, but contrast dramatically to those of the homo-peptides from the lower homolog C^α,α-dimethylglycine, which have been shown to adopt the 3₁₀-helical structure.     

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.     

Structural versatility of peptides from Cα,α-dialkylated glycines. I. A conformational energy computation and x-ray diffraction study of homo-peptides from Cα,α-diethylglycine

Conformational energy computations on a derivative and a homo-dipeptide of C^α,α-diethylglycine were performed. In both cases the N- and C-terminal groups are blocked as acetamido and methylamido moieties, respectively. It was found that the C^α,α-diethylglycine residues are conformationally restricted and that the minimum energy conformation corresponds to the fully extended C₅ structure when the N? C^α? C′ bond angle is smaller than 108° (as experimentally observed). The results of the theoretical analysis are in agreement with the crystal-state structural propensity of the complete series of N-trifluoroacetylated homo-peptides of this C^α,α-dialkylated residue from monomer to pentamer, determined by x-ray diffraction and also described in this work. Interestingly, for the first time, a crystallographically planar peptide backbone was observed (in the protected tripeptide). A comparison with peptides of C^α,α-dimethylglycine, C^α-methyl, C^α-ethylglycine, and C^α,α-di-n-propylglycine indicates that the fully extended conformation becomes more stable than the helical structures when both amino acid side-chain C^β atoms are substituted.     

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 conformations of peptides containing α,α-disubstituted α-amino acids

The conformational preferences of linear peptides containing α,α-disubstituted α-amino acids, derived from the crystal structures of 28 compounds, are reviewed. In particular, the sensitivity of peptide conformation to the geometry of these unusual amino acids is underlined. We also consider possible future directions of research, which, we hope, will result in a complete understanding of the structures adopted by peptaibol antibiotics.     

Relationship between conformation and geometry as evidenced by molecular dynamics simulation of Cα,α-dialkylated glycines

The relationship between the local backbone conformation and bond angles at C^α of symmetrically substituted C^α,α-dialkylated glycines (C^α,α-dimethylglycine or α-aminoisobutyric acid, Aib; C^α,α-diethylglycine, Deg; C^α,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the C^α bond angles. The MD simulations show that the C^α bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-C^α-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239–244, 1998     

Conformations of peptides containing a chiral cyclic α, α‐disubstituted α‐amino acid within the sequence of Aib residues

A single chiral cyclic α,α‐disubstituted amino acid, (3S,4S)‐1‐amino‐(3,4‐dimethoxy)cyclopentanecarboxylic acid [(S,S)‐Ac₅c^dOM], was placed at the N‐terminal or C‐terminal positions of achiral α‐aminoisobutyric acid (Aib) peptide segments. The IR and ¹H NMR spectra indicated that the dominant conformations of two peptides Cbz‐[(S,S)‐Ac₅c^dOM]‐(Aib)₄‐OEt ( 1) and Cbz‐(Aib)₄‐[(S,S)‐Ac₅c^dOM]‐OMe (2) in solution were helical structures. X‐ray crystallographic analysis of 1 and 2 revealed that a left‐handed (M) 3₁₀‐helical structure was present in 1 and that a right‐handed (P) 3₁₀‐helical structure was present in 2 in their crystalline states. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Mixed conformation in Cα,α-disubstituted tripeptides: X-ray crystal structures of Z-Aib-Dph-Gly-Ome and Bz-Dph-Dph-Gly-Ome

We report here the synthesis and molecular structure in the solid state of fully protected tripeptides containing C^α,α-diphenylglycine (Dph), namely Z-Aib-Dph-Gly-OMe (Aib: C^α,α-dimethylgrycine) and Bz-Dph-Dph-Gly-OMe. The molecular conformation around the Dph residue, containing two bulky substituents, is fully extended, while the Aib residue, containing two smaller groups on the C^α atom, adopts the typical 3₁₀/α-helical conformation. Gly residues, without substituents on the C^α atom, show different conformational preferences. Each residue seems to behave, from a conformational point of view, independently from the presence of the other residues, and thus mixed local conformations (folded and extended) are present in the crystals. The nonconventional peptide synthesis, using the Ugi reaction, is also reported. © 1994 John Wiley & Sons, Inc.     

Conformational behavior of α,α-dialkylated peptides

The preferred conformations of N-acetyl-N′-methyl amides of some dialkylglycines have been determined by empirical conformational-energy calculations; minimum-energy conformations were located by minimizing the energy with respect to all the dihedral angles of the molecules. The conformational space of these compounds is sterically restricted, and low-energy conformations are found only in the regions of fully extended and helical structures. Increasing the bulkiness of the substituents on the C^α, the fully extended conformation becomes gradually more stable than the helical structure preferred in the cases of dimethylglycine. This trend is, however, strongly dependent on the bond angles between the substituents on the C^α atom: In particular, helical structures are favored by standard values (111°) of the N-C^α-C′ angle, while fully extended conformations are favored by smaller values of the same angle, as experimentally observed, for instance, in the case of α,α-di-n-propylglycine.     

β-Turn conformations in crystal structures of model peptides containing α,α-Di-n-propylglycine and α,α-Di-n-butylglycine

The crystal state conformations of three peptides containing the α,α-dialkylated residues. α,α-di-n-propylglycine (Dpg) and α,α-di-n-butylglycine (Dbg), have been established by x-ray diffraction. Boc-Ala-Dpg-Alu-OMe (I) and Boc-Ala-Dbg-Ala-OMe (III) adopt distorted type II β-turn conformations with Ala (1) and Dpg/Dbg (2) as the corner residues. In both peptides the conformational angles at the Dxg residue (I: ? = 66.2°, ψ = 19.3°; III: ? = 66.5°. ψ = 21.1°) deviate appreciably from ideal values for the i + 2 residue in a type II β-turn. In both peptides the observed (N…O) distances between the Boc CO and Ala (3) NH groups are far too long (1: 3.44 Å: III: 3.63 Å) for an intramolecular 4 → 1 hydrogen bond. Boc-Ala-Dpg-Ata-NHMe (II) crystallizes with two independent molecules in the asymmetric unit. Both molecules HA and HB adopt consecutive β-turn (type III-III in HA and type III-I in IIB) or incipient 3₁₀-helical structures, stabilized by two intramolecular 4 → 1 hydrogen bonds. In all four molecules the bond angle N-C^α-C′ (τ) at the Dxg residues are ≥ 110°. The observation of conformational angles in the helical region of ?,ψ space at these residues is consistent with theoretical predictions. © 1995 John Wiley & Sons, Inc.     

Synthesis and conformational studies of peptides containing TOAC,a spin-labelled Cα,α-disubstituted glycine

A variety of host L -alanine homo-peptides (to the pentamer) containing one or two spin-labelled TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) residues were synthesized by solution methods and fully characterized. The conformational features of the terminally blocked, doubly spin-labelled–TOAC–(Ala)₂–TOAC–Ala– pentapeptide were examined in the crystal state by X-ray diffraction and in solution using a combination of techniques (Fourier transform infrared, circular dichroism, cyclic voltammetry and electron spin resonance) in comparison with singly labelled shorter peptides. The 3₁₀-helical structure of the pentapeptide, promoted by the two C^α,α-disubstituted glycines under favourable experimental conditions, allows an interaction to take place between the two nitroxide TOAC side chains spaced by one turn of the helix. Taken together, these results suggest that TOAC is an excellent probe for exploring bends and helices in doubly labelled peptides.     

Contrasting solution conformations of peptides containing α,α-dialkylated residues with linear and cyclic side chains

The conformational properties of α,α-dialkylated amino acid residues possessing acyclic (diethylglycine, Deg: di-n-propylglycine, Dpg; di-n-butylglycine, Dbg) and cyclic (1-amino-cycloalkane-1-carboxylic acid, Ac_nc) side chains have been compared in solution. The five peptides studied by nmr and CD spectroscopy are Boc-Ala-Xxx-Ala-OMe, where Xxx = Deg(I). Dpg (II), Dbg (III), Ac₆c (IV), and Ac₇c (V). Delineation of solvent-shielded NH groups have been achieved by solvent and temperature dependence of NH chemical shifts in CDCl₃ and (CD₃)₂SO and by paramagnetic radical induced line broadening in pepiide III. In the Dxg peptides the order of solvent exposure of NH groups is Ala(1) > Ala(3) > Dxg(2), whereas in the Ac_nc peptides the order of solvent exposure of NH groups is Ala(1) > Ac_nc(2) > Ala(3). The nmr results suggest that Ac_nc peptides adopt folded β-turn conformations with Ala(1) and Ac_nc(2) occupying i + 1 and i + 2 positions. In contrast, the Dxg peptides favor extended C₅ conformations. The conformational differences in the two series are clearly borne out in CD studies. The solution conformations of peptides I-III are distinctly different from the β-turn structure observed in crystals. Low temperature nmr spectra recorded immediately after dissolution of crystals of peptide II provide evidence for a structural transition. Introduction of an additional hydrogen-bonding function in Boc-Ala-Dpg-Ala-NHMe (VI) results in a stabilization of a consecutive β-turn or incipient 3₁₀-helix in solution. © 1995 John Wiley & Sons, Inc.     

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     

Design of peptides using α,β-dehydro-residues: Synthesis,crystal structure and molecular conformation of Boc-L-Val- ΔPhe-ΔPhe-L-Val-OCH3

The peptide Boc-L-Val-ΔPhe-ΔPhe-L-Val-OCH₃ was synthesized by the azlactone method in solution phase, and its crystal and molecular structures were determined by x-ray diffraction method. Single crystals were grown by slow evaporation from a methanol/water solution at 6°C. The crystals belong to an orthorhombic space group P2₁2₁2₁ with a = 10.478 (6) Å, b = 13.953 (1), c = 24.347 (2) and Z = 4. The structure was determined by direct methods and refined by least squares procedure to an R value of 0.052. The structure consists of a peptide and a water molecule. The peptide adopts two overlapping β-turn conformations of Types II and I′ with torsion angles: ϕ₁ = -54.8 (6), ψ₁ = 130.5 (4), ϕ₂ = 65.8 (5), ψ₂ = 12.8 (6), ϕ₃ = 79.4 (5), ψ₃ = 3.9 (7)°. The conformation is stabilized by intramolecular hydrogen bonds involving Boc CO and NH of ΔPhe³ and CO of Val¹ and NH of Val⁴. The molecules are tightly packed in the unit cell. The crystal structure is stabilized by hydrogen bonds involving NH of ΔPhe² and CO of a symmetry related (x-½, ½ -y, -z) ΔPhe². The solvent-water molecule forms two hydrogen bonds with peptide molecule involving NH of Val¹ as an acceptor and another with CO of a symmetry related (1 -x, y-½, ½ -z) ΔPhe³ as a donor. These studies indicate that a tetrapeptide with two consecutive ΔPhe residues sequenced with valines on both ends adopts two overlapping β-turns of Types II and I′. © 1996 John Wiley & Sons, Inc.     

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

The present work describes three novel nonpolar host peptide sequences that provide a ready assessment of the 3₁₀- and α-helix compatibilities of natural and unnatural amino acids at different positions of small- to medium-size peptides. The unpolar peptides containing Ala, Aib, and a C-terminal p-iodoanilide group were designed in such a way that the peptides could be rapidly assembled in a modular fashion, were highly soluble in solvent mixtures of triflouroethanol and H₂O for CD- and two-dimensional (2D) nmr spectroscopic analyses, and showed excellent crystallinity suited for x-ray structure analysis. To validate our approach we synthesized 9-mer peptides 79a–96 (Table IV), 12-mer peptides 99–110c (Table V), and 10-mer peptides 120a–125d and 129–133 (Table VI and Scheme 8) incorporating a series of optically pure cyclic and open-chain (R)- and (S)-α,α-disubstituted glycines 1–10 (Figure 2). These amino acids are known to significantly modulate the conformations of small peptides. Based on x-ray structures of 9-mers 79a, 80, and 87 (Figures 4–7), 10-mers 124c, 131, and 132 (Figures 9–12), and 12-mer peptide 102b (Figure 13), CD spectra of all peptides recorded in acidic, neutral, and basic media and detailed 2D-nmr analyses of 9-mer peptide 86 and 12-mer 102b, several interesting conformational observations were made. Especially interesting results were obtained using the convex constraint CD analysis proposed by Fasman on 9-mer peptides 79a–d, 80, 81, 86, and 87, which allowed us to determine the relative content of 3₁₀- and α-helical conformations. These results were fully supported by the corresponding x-ray and 2D-nmr analyses. As a striking example we found that the (S)- and (R)-β-tetralin derived amino acids (R)- and (S)-1 show excellent α-helix stabilisation, more pronounced than Aib and Ala. These novel reference peptide sequences should help establish a scale for natural and unnatural amino acids concerning their intrinsic 3₁₀- and α-helix compatibilities at different positions of medium-sized peptides and thus improve our understanding in the folding processes of peptides. © 1997 John Wiley & Sons, Inc. Biopoly 42: 575–626, 1997     

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.     

Noncoded residues as building blocks in the design of specific secondary structures: Symmetrically disubstituted glycines and β-alanine

Structural changes can be induced in a peptide by selective substitution of coded α-amino acid residues by noncoded α-amino acid residues and the consequent production of analogues with modified structure and conformational preferences. In this review article we summarize the solid state structural results and the conformational preferences of two classes of “building blocks”: (a) the linear and cyclic symmetrically α, α-disubstituted glycines in which either two identical n-alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side-chain system is formed by linking the two α-carbon side chains, respectively; and (b) the β-alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given. © 1993 John Wiley & Sons, Inc.     

Synthetic studies toward labionin,a new α,α‐disubstituted amino acid from type III lantibiotic labyrinthopeptin A2

The labyrinthopeptins are a new class of lantibiotics containing two identical quaternary α,α‐disubstituted amino acids, named labionin (Lab). The synthetic formation of this unique structural feature represents the key step in the total synthesis of these polycyclic peptides. In this report we describe the synthesis of an orthogonally protected α,α‐disubstituted amino acid building block serving as labionin precursor for the future assembly of labyrinthopeptin A2 and of other labyrinthopeptin derivatives. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.