Peptide mimics for structural features in proteins

The crystal structure determination of three heptapeptides containing α-aminoisobutyryl (Aib) residues as a means of helix stabilization provides a high-resolution characterization of 6→1 hydrogen-bonded conformations, reminiscent of helix-terminating structural features in proteins. The crystal parameters for the three peptides, Boc-Val-Aib-X-Aib-Ala-Aib-Y-OMe, where X and Y are Phe, Leu (I), Leu, Phe (II) and Leu, Leu (III) are: (I) space group P1, Z= 1, a= 9.903 Å, b 10.709 Å, c= 11.969 Å, α= 102.94°, β=103.41°, γ= 92.72°, R= 4.55%; (II) space group P2₁, Z= 2, a=10.052 Å, b=17.653 Å, c= 13.510 Å, β=108.45°. R= 4.49%; (III) space group P1, Z= 2 (two independent molecules IIIa and IIIb in the asymmetric unit). a=10.833 Å, b=13.850 Å, c=16.928 Å, α=99.77°, β=105.90°, γ= 90.64°, R= 8.54%. In all cases the helices form 3_10/α-helical (or 3l₁₀-helical) structures, with helical columns formed by head-to-tail hydrogen bonding. The helices assemble in an all-parallel motif in crystals I and III and in an antiparallel motif in II. In the four crystallographically characterized molecules, I, II, IIIa and IIIb, Aib(6) adopts a left-handed helical (ht) conformation with positive φψ values, resulting in 6→1 hydrogen-bond formation between Aib(2) CO and Leu(7)/Phe(7) NH groups. In addition a 4→1 hydrogen bond is seen between Aib(3) CO and Aib(6) NH groups. This pattern of hydrogen bonding is often observed at the C-terminus of helices in proteins, with the terminal π-type turn being formed by four residues adopting the h_Rh_Rh_Rh_L conformation.     

Observation of a mixed antiparallel and parallel β-sheet motif in the crystal structure of Boc-Ala-Ile-Aib-OMe

A diastereomeric mixture of the tripeptide Boc-Ala-Ile-Aib-OMe crystallized in the space group Pl from CH₃OH/H₂O. The unit cell parameters are a= 10.593(2) Å, b= 14.377(3) Å, c= 17.872(4) Å, α= 104.41(2)°, β= 90.55(2)°, γ= 106.91(2)°, V= 2512.4 ų, Z=4. X-Ray crystallographic studies shows the presence of four molecules in the asymmetric unit consisting of two pairs of diastereomeric peptides, Boc-l -Ala-l -Ile-Aib-OMe and Boc-l -Ala-d -Ile-Aib-OMe. The four molecules in the asymmetric unit form a rarely found mixed antiparallel and parallel β-sheet hydrogen bond motif. The Ala and (l ,d )-Ile residues in all the four molecules adopt the extended conformations, while the φ, ψ values of the Aib residues are in the right-handed helical region. In one of the molecules the Ile sidechain adopts the unusual gauche conformation about the C^β-C^γ bond. © Munksgaard 1996.     

Conformational investigation of α, β-dehydropeptides

The crystal structure of Ac-Pro-ΔVal-NHCH₃ was examined to determine the influence of the α,β-dehydrovaline residue on the nature of peptide conformation. The peptide crystallizes from methanol-diethyl ether solution at 4° in needle-shaped form in orthorhombic space group P2₁2₁2₁ with a= 11.384(2) Å, b = 13.277(2) Å, c = 9.942(1) Å. V = 1502.7(4) ų Z = 4, D_m= 1.17 g cm^?3 and D_c=1.18 g cm^?3 The structure was solved by direct methods using SHELXS-86 and refined to an R value of 0.057 for 1922 observed reflections. The peptide is found to adopt a β-bend between the type I and the type III conformation with φ₁=?68.3(4)°, ψ₁=? 20.1(4)°, φ₂=?73.5(4)°= and Ψ₂=?14.1(4)°=. An intramolecular hydrogen bond between the carbonyl oxygen of ith residue and the NH of (i+ 3)th residue stabilizes the β-bend. An additional intermolecular N.,.O hydrogen bond joins molecules into infinite chains. In the literature described crystal structures of peptides having a single α,β-dehydroamino acid residue in the (i+ 2) position and forming a β-bend reveal a type II conformation.     

Crystal structures of a nonapeptide helix containing α, α-di-n-butylglycine (Dbg), Boc-G1y-Dbg-Ala-Val-Ala-Leu-Aib-Val-Leu-OMe

Two crystal structures of a nonapeptide (anhydrous and hydrated) containing the amino acid residue α,α-di-n-butylglycyl, reveal a mixed 3₁₀-α-helical conformation. Residues 1-7 adopt φ, ψ values in the helical region, with Val(8) being appreciably distorted. The Dbg residue has φ, ψ values of -40, -37° and -46, -407° in the two crystals with the two butyl side chains mostly extended in each. Peptide molecules in the crystals pack into helical columns. The crystal parameters are: C₅₀ H₉₁ N₉ O₁₂, space group P2₁, with a= 9.789(1)Å;, b= 20.240(2) Å. c= 15.998(3) Å. β= 103.97(1): Z= 2, R=10.3% for 1945 data observed < 3σ(F) and C₅₀H₉₁N₉O₁₂· 3H₂O, space group P2₁ with a= 9.747(3)Å, b= 21.002(8) Å, c= 15.885(6) Å, β= 102.22(3). Z= 2. R=13.6% for 2535 data observed < 3σ(F) The observation of a helical conformation at Dbg suggests that the higher homologs in the α,α-dialkylated glycine series also have a tendency to stabilize peptide helices. © Munksgaard 1996.     

Structure of N-Boc-L-Pro-dehydro-Leu-NHCH3

The peptide N-Boc-L-Pro-dehydro-Leu-NHCH₃ was synthesized to examine the nature of β-bend as a result of dehydro-Leu in the sequence. The peptide crystallizes from methanol-water mixture at 4° in orthorhombic space group P22₁2₁ with a = 5.726(1)Å, b = 14.989(4) Å, c = 24.131(9) Å, V = 2071(1) ų, Z = 4, dm = 1.064(5)gcm^-3 and dc = 1.0886(5)gcm^-3. The structure was solved by direct methods using SHELXS 86 and it was refined by full-matrix least-squares procedure to an R value of 0.059 for 957 observed reflections. The peptide is found to adopt a β-bend type II conformation with φ₁=– 51(1)°, ψ₁= 133(1)°, φ₂= 74(2)° and ψ₂= 8(2)°. The β-bend is stabilized by an intra-chain hydrogen bond between the carbonyl oxygen of ith residue and the NH of (i + 3)th residue. The five-membered pyrrolidine ring of Pro-residue adopts an ideal C^γ-exo conformation with torsion angles of χ₁¹=– 25(1)°, χ₁²= 38(1)°, χ₂=– 34(1)°, χ₁⁴= 20(1)° and χ₁⁰= 2(1)°. The side chain conformation angles of dehydro-Leu residue are χ₂= 12(2)°, χ₂^2.1=– 112(2)° and χ₂^2.2= 136(2)°. The crystal structure is stabilized by a network of hydrogen bonds and van der Waals interactions.     

Backbone—side-chain interactions in serine Synthesis,crystal structure and solution conformation of a linear model peptide N-Boc-l-Ser-l-Phe-OCH3

The peptide Boc-Ser-Phe-OCH₃ was synthesised by a solution-phase method using the usual workup procedure. The peptide was crystallized from a 70:30 (v/v) methanol-water mixture. The crystals are monoclinic, space group P2₁ with a= 5.128(2), b=17.873(2), c=11.386(2) Å, and β=98.03(3)°. The structure was determined by direct methods and refined by a structure factor least-squares procedure. The final R-value for 1499 observed reflections was 0.041. The structure contains one peptide and one solvent water molecule. The peptide adopts a β-strand-like conformation with φ₁=- 100.3(5), ψ_l= 99.9(5), φ₂= - 122.2(5), ψ^T₂= -172.5(6)°. The Ser side-chain assumes an extended conformation with χ¹₁= - 177.0(4)°. The O^γH group of serine acts as a proton donor in an intramolecular weak hydrogen bond with (Ser) O′₁; [O^γ₁;-H^γ₁?O′₁= 3.253(6) Å]. The Phe side-chain adopts a staggered conformation with χ¹₂= -70.9(6), χ²_2,1= 88.4(7)°, χ^2,2₂= -89.2(6)°. The water molecule generates a loop through two hydrogen bonds with O^γ₁ [OW?O^γ₁= 2.893(5) Å] and O′₂ [OW-O′₂= 2.962(7) Å] atoms. The unit-translated peptide molecules along the α-axis are held by hydrogen bonds: N₁-H₁?O₂ (x-1, y, z) = 2.954(4) Å and N₂-H₂?O′₁ (x+1, y, z) = 2.897(6) Å in a manner similar to those observed in parallel β-pleated sheet structures. There is an additional interaction involving O^γ₁ and the water molecule [OW?O^γ₁ (x= 1, y, z) = 2.789(4) Å]. The strong NOE peak of C_i(H)?N_i+1 (H) and a simultaneous weak NOE peak of N_i(H)?N_i+l (H) in the ROESY spectra of two-dimensional NMR in dimethyl sulfoxide indicate a β-strand-like conformation for the peptide in solution. © Munksgaard 1996.     

Design of peptides with αβ-dehydro residues: Synthesis,crystal structure and molecular conformation of N-Boc-L-Ile-ΔPhe-L-Trp-OCH3

The dehydro-peptide Boc-L-Ile-ΔPhe-L-Trp-OCH₃ was synthesized by the azlactone method in the solution phase. The peptide was crystallized from methanol in an orthorhombic space group P2₁2₁2₁ with a = 10.777(2), b= 11.224(2), c= 26.627(10) Å. The structure was determined by direct methods and refined to an R value of 0.069 for 3093 observed reflections [l≥ 2σ(l)].The peptide failed to adopt a folded conformation with backbone torsion angles: φ₁, = 90.8(8)°, ψ₁= -151.6(6)°, φ₂= 89.0(8)°, ψ₂= 15.9(9)°, φ₃= 165.7(7)°, ψ^T₃= -166.0(7)°. A general rule derived from earlier studies indicates that a three-peptide unit sequence with a ΔPhe at the (i+ 2) position adopts a β-turn II conformation. Because the branched β-carbon residues such as valine and isoleucine have strong conformational preferences, they combine with the ΔPhe residue differently to generate a unique set of conformations in such peptides. The presence of β-branched residues simultaneously at both (i+ 1) and (i+ 3) positions induces unfolded conformations in tetrapeptides, but a β-branched residue substituted only at (i+ 3) positron can not prevent the formation of a folded β-turn II conformation. On the other hand, the present structure shows that a β-branched residue substituted at the (i+ 1) position prevents the formation of a β-turn II conformation. These observations indicate that a β-branched residue at the (i+ 1) position prevents a folded conformation whereas it cannot generate the same degree of effect from the (i+ 3) position. This may be because of the trans disposition of the planar ΔPhe side-chain with respect to the C=O group in the residue. The molecules are packed in an anti-parallel manner to generate N₂-H₂…O₂ (-x,y-1/2, -z+ 3/2) and N^ε1₃-H^ε1₃…O₁(-x,y -1/2, -z+ 3/2) hydrogen bonds.     

Heterochiral N-formyl methionyl peptides

Crystal and molecular structures for the heterochiral sequence N-formyl-l -methionine-d -phenylalanine, 1, and its tertiary butyl ester, 2, are reported. The solid-state peptide conformation is compared to that observed in solution by n.m.r. techniques. For N-f-Met-d -Phe, 1, the crystal was orthorhombic, space group P2₁ 2₁2₁ with a cell of dimensions a = 5.061(3), b = 16.575(5) and c = 19.656(6) Å at ambient temperature of 293K; V = 1649(2)ų, Z = 4, D_m= 1.31(2)gcm^?3, D_x= 1.307gcm^?3, μ(Mokx) = 2.047cm^?1. For N-f-Met-d -Phe-OtBu. 2, the crystal was monoclinic, space group P2₁ with a cell of dimensions a = 9.963(2), b = 11.147(2), c = 19.166(3)Å. β= 102.31(1) at 273K; V = 2080(2) ų Z = 4, D_m= 1.22(2)gcm^?3, D_x= 1.215gcm^?3μ(MoKx) = 1.714cm^?1. The structures were solved from diffractometer data and refined to conventional final R = 0.046, R_w= 0.053 for F-Met-d -Phe (1301 observations. I ≥ 3σ(I)) and to R = 0.056, R_w= 0.064 for the t-butylester (2411 observations. I ≥ 3σ(I)). The l-d acid, 1, crystallizes in an extended β-sheet conformation with trans-planar peptide bond; the principal torsion angle values are φ₁=– 141.2(4).Ψ₁= 149.6(4)³, φ₂= 157.4(4)°. The methionine side chain adopts a common coiled conformation with x¹₁= - 58.0(5).x²¹= 175.1(4), x³₁= 76.5(5). The Phe side chain adopts the statistically least favored g orientation in contrast to the most populated rotamer in solution. The crystal structure is composed of parallel β-sheets held together by four weak intermolecular contacts including two C-H O contacts from the alpha carbons to the formyl and peptide carbonyl oxygens. Sheet layers are joined in a head-to-tail fashion through a very short (2.569(4) Å) contact between the carboxyl OH and the formyl oxygen and may be further stabilized by a C-H—O interaction between the formyl proton and the carboxyl OH. Two crystallographically independent molecules are observed in the crystal structure of N-f-l -Met-d -Phe-OtBu, 2. These are distinct conformational isomers differing principally at both the N and C termini. Particularly noteworthy is the synplanar orientation of the ester C = O with respect to the peptide nitrogen in molecule A. which contrasts to the antiplanar orientation in molecule B. Additionally, the formyl group is coiled more towards the C-terminus in molecule B. Principal torsion angles are φ₁(A) = - 120.6(5), Ψ₁(A) = 102.0(6)°, φ₂(A) = 128.1(6), φ₁(B) = - 94.6(5), Ψ₁(B) = 91.9(6)°. 121.7(6)°. The peptide bond is trans-planar in both molecules. Side chain dispositions are essentially identical in both structures. The Met side chain adopts the zig-zag trans-planar conformation while the Phe residue adopts an orientation near + 60° in agreement with rotamer populations observed by solution n.m.r. Typical peptide intermolecular H-bonding is observed in the ester crystal structure; both the peptide and formyl groups participate in the proposed H-bonding scheme.     

Cystine peptides Antiparallel β-sheet conformation of the cyclic biscystine pep tide [Boc-Cys-Ala-Cys-NHCH3]2

The crystal structure analysis of the cyclic biscystine peptide [Boc-Cys¹-Ala²-Cys³-NHCH₃]₂ with two disulfide bridges confirms the antiparallel β-sheet conformation for the molecule as proposed for the conformation in solution. The molecule has exact twofold rotation symmetry. The 22-membered ring contains two transannular NH ? OC hydrogen bonds and two additional NH ? OC bonds are formed at both ends of the molecule between the terminal (CH₃)₃COCO and NHCH₃ groups. The antiparallel peptide strands are distorted from a regularly pleated sheet, caused mainly by the L-Ala residue in which φ=– 155° and ψ= 162°. In the disulfide bridge C^α (1)-C^β (1)-S(1)-(3′)-C^β(3′)-C^α(3′), S—S = 2.030 Å, angles C^β SS = 107° and 105°, and the torsional angles are –49, –104, +99, –81, –61°, respectively. The biscystine peptide crystallizes in space group C2 with a = 14.555(2) Å, b = 10.854(2) Å, c = 16.512(2)Å, and β= 101.34(1) with one-half formula unit of C₃₀H₅₂N₈O₁₀S₄· 2(CH₃)₂SO per asymmetric unit. Least-squares refinement of 1375 reflections observed with |F| > 3σ(F) yielded an R factor of 7.2%.     

Conformations of peptides containing 1-aminocyclohexanecarboxylic acid (Acc6). Crystal structures of two model peptides

The crystal structures of two peptides containing 1-aminocyclohexanecarboxylic acid (Acc⁶) are described. Boc-Aib-Acc⁶-NHMe · H₂O adopts a β-turn conformation in the solid state, stabilized by an intramolecular 4 → 1 hydrogen bond between the Boc CO and methylamide NH groups. The backbone conformational angles (φ_Aib = – 50.3°, ψ_Aib = – 45.8°; φ_Acc6 = – 68.4°, ψ_Acc6 = – 15°) lie in between the values expected for ideal Type I or III β-turns. In Boc-Aib-Acc⁶-OMe, the Aib residue adopts a partially extended conformation (φ_Aib = – 62.2°, ψ_Aib = 143°) while the Acc⁶residue maintains a helical conformation (φ_Acc6 = 48°, ψ_Acc⁶= 42.6°). ¹H n.m.r. studies in CDCl₃ and (CD₃)₂SO suggest that Boc-Aib-Acc⁶-NHMe maintains the β-turn conformation in solution.     

Crystal structure of tert.-butyloxycarbonyl-L-prolyl-D-alanyl-D-alanyl-N-methylamide Dimeric β-sheet formation

The crystal structure of the tripeptide t-Boc-L-Pro-D-Ala-D-Ala-NHCH₃, monohydrate, (C₁₇H₃₀N₄O₅·H₂O, molecular weight = 404.44) has been determined by single crystal X-ray diffraction. The crystals are mono-clinic, space group P2₁, a = 9.2585(4), b = 9.3541(5). c = 12.4529(4) Å, β= 96.449(3)°, Z = 2. The peptide units are in the trans and the tBoc-Pro bond in the cis orientation. The first and third peptide units show significant deviations from planarity (Δω=5.2° and Δω=3.7°, respectively). The backbone torsion angles are: φ¹, = -60°, ψ_1/= 143.3°, ω₁= -174.8°, φ₂= 148.4°, ψ₂= -143.1°, ω₂= -179.7°, φ₃= 151.4°, ψ₃= -151.9°, ω₃= -176.3°. The pyrrolidine ring of the proline residue adopts the C₂— C^γ conformation. The molecular packing gives rise to an antiparallel β-sheet structure formed of dimeric repeating units of the peptide. The surface of the dimeric β-sheet is hydrophobic. Water molecules are found systematically at the edges of the sheets interacting with the urethane oxygen and terminal amino groups. Surface catalysis of an L-Ala to D-Ala epimerization process by water molecules adsorbed on to an incipient β-sheet is suggested as a mechanism whereby crystals of the title peptide were obtained from a solution of tBoc-Pro-D-Ala-Ala-NHCH₃.     

Crystal structure and conformation of polypeptides: L-leucylglycylglycylglycine

Crystals of L-leucylglycylglycylglycine, LGGG (C₁₂H₂₂N₄O₅), grown from an ethanol-water solution, are orthorhombic, space groups P2₁2₁2₁, with unit cell dimensions (at 22 ± 3°) a = 9.337(1), b = 10.995(1), c = 15.235(1)Å, v = 1563.4 ų, Z = 4 with a density of D_obs= 1.29 g-cm^-3 and D_calc= 1.279 g°cm^-3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.029 for 1018 reflections with I ± 2s?. The molecule exists as a zwitterion in the crystal. The trans peptide backbone takes up a folded conformation at the middle glycylglycyl link accompanied by a significant nonplanarity up to Δω of 8° at the middle peptide and is relatively more extended at the two ends. The molecules are linked together intermolecularly in an infinite sequence of head to tail 1–4′ hydrogen bonds, as is typical of charged peptides. It is interesting to note that while glycylglycylglycine takes up an extended β-sheet conformation, addition of Leu to the N-terminal results in a bent conformation.     

Crystal and molecular structure of Boc-Phe-Val-OMe; comparison of the peptide conformation with its dehydro analogue

The crystal structure of the peptide Boc-Phe-Val-OMe determined by X-ray diffraction methods is reported in this paper. The crystals grown from aqueous methanol are orthorhombic, space group P 2₁2₁ 2₁, a= 11.843(2), b= 21.493(4), c= 26.676(4) A and V= 6790 ų. Data were collected on a CAD4 diffractometer using MoK_α radiation (λ= 0.7107 Å) up to Bragg angle θ=26°. The structure was solved by direct methods and refined by a least-squares procedure to an R value of 6.8% for 3288 observed reflections. There are three crystal-lographically independent peptide molecules in the asymmetric unit. All the three molecules exhibit extended conformation. The sidechain of the Val² residue shows two different conformations. The conformation of the peptide Boc-Phe-Val-OMe is compared with the conformation of Ac-ΔPhe-Val-OH. It is observed that while Boc-Phe-Val-OMe exhibits an extended conformation, Ac-ΔPhe-Val-OH shows a folded conformation. The results of this comparison highlight the conformation constraining property of the ΔPhe residue. Interestingly, even though Boc-Phe-Val-OMe and Ac-ΔPhe-Val-OH are conformation ally different, they exhibit similar packing patterns in the solid state. © Munksgaard 1995.     

Molecular design of peptides

The peptide N-Boc-l -Phe-dehydro-Abu-NH-CH₃ was synthesized by the usual workup procedure. The crystals grown from methanol at 4°C belong to the space group P2₁2₁2₁ with a= 7.589(2), b= 13.690(4), c= 21.897(6) Å, Z= 4 and d_c= 1.149(5) g cm^?3 for C₁₉H₂₉N₃O₅·CH₃OH. The peptide crystals were highly sensitive to radiation. The final agreement factor R was 0.055 for 1109 observed reflections (I > 2σ) with data extending to a 2θ value of 103°. The methanol oxygen atom is split into two occupancies. Both sites are involved in identical hydrogen bonding. As a result of substitution of a dehydro-Abu residue at the (i+ 2) position the peptide adopts an ideal β-turn II′ conformation with torsion angles of corner residues as φ₁=63(1)°, ψ₁= - 127(1)°, φ₂= -66(1)° and ψ₂= - 10(1)°, and an intramolecular hydrogen bond N—H ? O of length 3.01(1) Å. This shows that the conformational constraints produced by dehydro-Abu are similar in nature to but different in magnitude than those produced by dehydro-Phe and dehydro-Leu. The methanol–peptide interactions show characteristic features of multiple hydrogen-bond formations involving polar sites of participating peptide and methanol molecules. The packing of the molecules in the unit cell is stabilized by interactions through methanol molecules with the help of several hydrogen bonds.     

Influence of hydrophobic interactions on the conformational adaptability of the β‐Ala residue

Abstract: The chemical synthesis and X‐ray crystal structure analysis of a model peptide incorporating a conformationally flexible β‐Ala residue: Boc‐β‐Ala‐Pda, 1 (C₂₃H₄₆N₂O₃: molecular weight = 398.62) have been described. The peptide crystallized in the crystal system triclinic with space group P2₁: a = 5.116(3) Å, b = 5.6770(10) Å, c = 21.744(5) Å; α = 87.45°, β = 86.87°, γ = 90.0°; Z = 1. An attractive feature of the crystal molecular structure of 1 is the induction of a reasonably extended backbone conformation of the β‐Ala moiety, i.e. the torsion angles φ ≈ ?115°, µ ≈ 173° and ψ ≈ 122°, correspond to skew^?, trans and skew⁺ conformation, respectively, by an unbranched hydrophobic alkyl chain, Pda, which prefers an all‐anti orientation (θ₁ ≈ ?153°, θ₂ ≈ … θ₁₄ ≈ ±178°). The observation is remarkable because, systematic conformational investigations of short linear β‐Ala peptides of the type Boc‐β‐Ala‐Xaa‐OCH₃ (Xaa = Aib or Acc⁶) have shown that the chemical and stereochemical characters of the neighboring moieties may be critical in dictating the overall folded and/or unfolded conformational features of the β‐Ala residue. The overall conformation of 1 is typical of a ‘bar’. It appears convincing that, in addition to a number of hydrophobic contacts between the parallel arranged molecules, an array of conventional N‐H…O=C intermolecular H‐bonding interactions stabilize the crystal molecular structure. Moreover, the resulting 14‐membered pseudo‐ring motif, generated by the amide–amide interactions between the adjacent molecules, is completely devoid of nonconventional C?H…O interaction. The potentials of the conformational adaptation of the β‐Ala residue, to influence and stabilize different structural characteristics have been highlighted.     

Channel‐forming,self‐assembling,bishelical amphiphilic peptides: design,synthesis and crystal structure of Py(Aibn)2, n = 2, 3, 4

Abstract: The design, synthesis, characterization and self‐assembling properties of a new class of amphiphilic peptides, constructed from a bifunctional polar core attached to totally hydrophobic arms, are presented. The first series of this class, represented by the general structure Py(Aib_n)₂ (Py = 2,6‐pyridine dicarbonyl unit; Aib = α, α′‐dimethyl glycine; n = 1–4), is prepared in a single step by the condensation of commercially available 2,6‐pyridine dicarbonyl dichloride with the methyl ester of homo oligoAib peptide (Aib_n‐OMe) in the presence of triethyl amine. ¹H NMR VT and ROESY studies indicated the presence of a common structural feature of 2‐fold symmetry and an NH…N hydrogen bond for all the members. Whereas the Aib3 segment in Py(Aib3)₂ showed only the onset of a 3₁₀‐helical structure, the presence of a well‐formed 3₁₀‐helix in both Aib4 arms of Py(Aib4)₂ was evident in the ¹H NMR of the bispeptide. X‐ray crystallographic studies have shown that in the solid state, whereas Py(Aib2)₂ molecules organize into a sheet‐like structure and Py(Aib3)₂ molecules form a double‐stranded string assembly, the tetra Aib bispeptide, Py(Aib4)₂, is organized to form a tetrameric assembly which in turn extends into a continuous channel‐like structure. The channel is totally hydrophobic in the interior and can selectively encapsulate lipophilic ester (CH₃COOR, R = C₂H₅, C₅H₁₁) molecules, as shown by the crystal structures of the encapsulating channel. The crystal structure parameters are: 1b , Py(Aib2)₂, C₂₅H₃₇N₅O₈, sp. gr. P2₁2₁2₁, a = 9.170(1) Å, b = 16.215(2) Å, c = 20.091(3) Å, R = 4.80; 1c , Py(Aib3)₂, C₃₃H₅₁N₇O₁₀·H₂O, sp. gr. P, a = 11.040(1) Å, b = 12.367(1) Å, c = 16.959(1) Å, α = 102.41°, β = 97.29°, γ = 110.83°, R₁ = 6.94; 1 da, Py(Aib4)₂?et ac, C₄₁H₆₅N₉O₁₂?1.5H₂O·C₄H₈O₂, sp. gr. P, a = 16.064(4) Å, b = 16.156 Å, c = 21.655(5) Å, α = 90.14(1)°, β = 101.38(2)°, γ = 97.07(1)°, Z = 4, R₁ = 9.03; 1db, Py(Aib4)₂?amylac,C₄₁H₆₅N₉O₁₂?H₂O ·C₇H₁₄O₂, P2₁/c, a = 16.890(1) Å, b = 17.523(1) Å, c = 20.411(1) Å, β = 98.18 °, Z = 4, R = 11.1 (with disorder).     

Design of peptides withα,β-dehydro-residues: synthesis,and crystal and molecular structure of a310-helical tetrapeptide Boc-l-Val-ΔPhe-ΔPhe-l-Ile-OCH3

Abstract: The peptide Boc-l -Val-ΔPhe-ΔPhe-l -Ile-OCH₃ was synthesized using the azlactone method in the solution phase, and its crystal and molecular structures were determined by X-ray diffraction. Single crystals were grown by slow evaporation from solution in methanol at 25°C. The crystals belong to an orthorhombic space group P2₁2₁2₁ with a = 12.882(7) Å, b = 15.430(5) Å, c = 18.330(5) Å and Z = 4. The structure was determined by direct methods and refined by a least-squares procedure to an R-value of 0.073. The peptide adopts a right-handed 3₁₀-helical conformation with backbone torsion angles: φ₁ = 56.0(6)°, ψ₁ = –38.0(6)°, φ₂ = –53.8(6)°, ψ₂ = 23.6(6)°, φ₃ = –82.9(6)°, ψ₃ = –10.6(7)°, φ₄ = 124.9(5)°. All the peptide bonds are trans. The conformation is stabilized by intramolecular 4→1 hydrogen bonds involving Boc carbonyl oxygen and NH of ΔPhe³ and CO of Val¹ and NH of Ile⁴. It is noteworthy that the two other chemically very similar peptides: Boc-Val-ΔPhe-ΔPhe-Ala-OCH₃ (i) and Boc-Val-ΔPhe-ΔPhe-Val-OCH₃ (ii) with differences only at the fourth position have been found to adopt folded conformations with two overlapping β-turns of types II and III′, respectively, whereas the present peptide adopts two overlapping β-turns of type III. Thus the introduction of Ile at fourth position in a sequence Val-ΔPhe-ΔPhe-X results in the formation of a 3₁₀-helix. The crystal structure is stabilized by intermolecular hydrogen bonds involving NH of Val¹ and carbonyl oxygen of a symmetry related (–x, y – 1/2, 1/2 + z) ΔPhe² and NH of ΔPhe² with carbonyl oxygen of a symmetry related (x, y1/2, 1/2 + z) Ile⁴. This gives rise to long columns of helical molecules linked head to tail running along [010] direction.     

Ten-membered cyclotripeptides

The 10-membered cyclotripeptide cyclo(-MeβAla-Phe-Pro) 3 and its diastereoisomer cyclo(-MeβAla-Phe-d Pro-) 4 have been synthesized under mild cyclization conditions starting from linear precursors containing C-terminal proline. The crystal and molecular structure of the two models has been determined by X-ray crystallography. Analysis of the NMR spectra supported by NOE data clearly indicates that the conformations found in the crystals are retained in solution. Both cyclotripeptides exhibit a cis-cis-trans backbone conformation. The two tertiary peptide bonds, at the proline and MeβAla nitrogen atoms, adopt a cis conformation whereas the CO—NH junctions are trans in both the models. The deviations from planarity of the peptide units vary from Δω values of ca. 18° for the Pro-MeβAla and d Pro-MeβAla bonds to ca. 7° for Phe-Pro and Phe-d Pro bonds. Relevant conformational details of 3 and 4, as revealed by X-ray and NMR analysis, are reported. Crystals of 3 are monoclinic: P2₁, a= 5.317(2), b= 17.059(6), c= 9.514(3)Å, β= 99.18(3), Z = 2. The final R and Rw are 0.054 and 0.071 respectively. Crystals of 4 are orthorhombic: P2₁2₁2₁, a= 8.797(2), b= 19.440(9), c= 21.605(10)Å, Z = 8. The final R and Rw are 0.069 and 0.104 respectively.     

Crystal structure of Boc-LAla-ΔPhe-ΔPhe-ΔPhe-ΔPhe-NHMe: a left-handed helical peptide

αβ-Dehydrophenylalanine residues constrain the peptide backbone to β-bend conformation. A pentapeptide containing four consecutive (APhe) residues has been synthesised and crystallised. The peptide Boc-LAla-ΔPhe-ΔPhe-ΔPhe-ΔPhe-NHMe (C₄₅H₄₆N₆O₇, MW = 782.86) was crystallised from an acetonitrile/ methanol mixture. The crystal belongs to the orthorhombic space group P2₁2₁2₁ with a = 19.455(6), b = 20.912(9), c = 11.455(4) Å and Z = 4. The X-ray (MoK_α, lD = 0.7107 Å) intensity data were collected using the Rigaku-AFC7 diffractrometer. The crystal structure was determined by direct methods and refined using the least-squares technique, R = 8.41% for 1827 reflections with ‖F₀‖ > 4σ‖F_o‖. The molecule contains the largest stretch of consecutive dehydrophenylalanine residues whose crystal structure has been determined so far. The peptide adopts left-handed 3₁₀-helical conformation despite the presence of LAla at the N-terminus. The mean ø, Ψ values, averaged across the last four residues are 56.8° and 17.5°, respectively. There are four 41 intramolecular hydrogen bonds, characteristic of the 3₁₀-helix. In the crystal each molecule interacts with four crystallographically symmetric molecules with one hydrogen bond each.     

Structure and conformation of linear peptides

The crystal structure of a dipeptide tert-butyloxycarbonyl-l -alanylglycine monohydrate (C₁₀H₁₈N₂O₅·H₂O), molecular weight 264, has been determined. The crystals are monoclinic, space group P2₁, with a= 10.767(1), b= 6.317(1), c= 10.981(2) Å, β= 109.15(2)°, and Z= 2, D_c= 1.24 g cm^?3. The structure was solved by direct methods and refined to 3 final R-index of 0.045 for 856 reflections (sin θ/λ < 0.55 Å^?1) with I > 2 σ. The N-terminus of the molecule blocked with the t-Boc group is uncharged and the C-terminus exists in an unionized state. The peptide unit is trans and shows slight deviations from planarity. (Δω= 3.1°). The peptide backbone is folded, with torsion angles of φ₁= -76.0(5), ψ₁= 164.3(4), ω₁= 176.9(5), φ₂= 116.1(5), ψ₂₁= - 2.8(7) and ψ₂₂= 177.8(4)°. The conformation about the urethane bond (C5–N1) is trans. The urethane group is essentially planar. The conformation of the boc group is trans–trans.