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Keywords:

  • γ-peptides;
  • cyclohexyl constraint;
  • helix foldamers;
  • solvation effect;
  • density functional calculations

ABSTRACT

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

The conformational preferences of helix foldamers having different sizes of the H-bonded pseudocycles have been studied for di- to octa-γ2,3-peptides based on 2-(aminomethyl)cyclohexanecarboxylic acid (γAmc6) with a cyclohexyl constraint on the Cα–Cβ bond using density functional methods. The helical structures of the γAmc6 oligopeptides with homochiral configurations are known to be much stable than those with heterochiral configurations in the gas phase and in solution (chloroform and water). In particular, it is found that the (P/M)−2.514-helices are most preferred in the gas phase and in chloroform, whereas the (P/M)−2.312-helices become most populated in water due to the larger helix dipole moments. As the peptide sequence becomes longer, the helix propensities of 14- and 12-helices are found to increase both in the gas phase and in solution. The γAmc6 peptides longer than octapeptide are expected to exist as a mixture of 12- and 14-helices with the similar populations in water. The mean backbone torsion angles and helical parameters of the 14-helix foldamers of γAmc6 oligopeptides are quite similar to those of 2-aminocyclohexylacetic acid oligopeptides and γ2,3,4-aminobutyric acid tetrapeptide in the solid state, despite the different substituents on the backbone. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 87–95, 2014.


INTRODUCTION

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

Mimicking the structural features of the biomolecules such as proteins, nucleic acids, and polysaccharides with non-natural sequences has been a challenge for chemists. Peptide foldamers are non-natural oligomers that have well-defined structural motifs similar to those of natural peptides and proteins.[1-4] Oligomers composed of β- or γ-amino acid residues (i.e., β- or γ-peptides) as well as their hybrids with α-amino acid residues have been considerably studied over the past decade and are found to adopt the secondary structures such as α-helix, β-sheet, β-turn, or β-hairpin as those of natural α-peptides, even though the degrees of conformational flexibility are increased by introducing the additional CH2 groups into the backbone of each residue of α-peptides.[5-12]

In particular, helices, which are one of the major structural motifs in α-peptides, are the most frequently characterized secondary structure for β- and γ-peptides to date. Five and two distinct helices have been identified experimentally in β- and γ-peptides, respectively, namely, 14-,[13, 14] 12-,[15, 16] 10-,[17, 18] 8-,[19] and mixed 12/10-helices[20-23] for β-peptides and 14-24–28 and 9-helices[29, 30] for γ-peptides, which are different in the size and orientation of the H-bonded pseudocycle. The important features of the β- and γ-peptide helices are that they can fold into helices with a chain length of as short as six and four residues when compared with about 10–12 residues for natural α-peptides in organic solvents, respectively, and that the helix type, the helicity [right-handed (P) and left-handed (M)], and the direction of the helix macrodipole (i.e., the orientation of H-bonds) can readily be controlled by the substitution pattern or/and stereochemistry of residues. Besides experimental measurements, considerable molecular dynamics simulations and ab initio calculations have also been performed to obtain the conformational preferences and the effects of substituents on folding propensities of β-peptides[31-36] and all possible periodic structures having the characteristic sizes and patterns of the H-bonded pseudocycles for hexapeptides of γ-aminobutyric acid (γAbu) and its vinylogous derivatives.[37-39] In particular, it is found that the 14- and 9-helices of the γAbu hexapeptide are most preferred in the gas phase; however, its 12- and 14-helices become most probable in water.[37, 39]

Although cyclic side chains substituted at the backbone strongly affect the secondary structure formation in γ-peptide foldamers, there are only limited works on γ-peptide-containing foldamers with a cycloalkyl constraint on the Cα–Cβ or Cβ–Cγ bonds of the backbone due to the lack of efficient synthetic methods for chirospecific building blocks and their couplings until now.[12, 40, 41] An infinite parallel sheet structure with intermolecular bifurcated H-bonds was observed in the crystal structure of the three-residue trans-2-(aminomethyl)cyclopropanecarboxylic acid (γAmc3; Figure 1a), in which the Cα- and Cβ-atoms are incorporated in a cyclopropane ring.[42] Homochiral and heterochiral tetrapeptides of γ2,3-trans-dioxolane-constrained residues led to a strand-like structure in benzene, which is stabilized by seven-membered intermolecular N[BOND]H···O H-bonds.[43] It has been shown that tri- to hexa-γ-peptides of the 2-aminocyclohexylacetic acid (γAc6a; Figure 1b) derivative possessing a cis cyclohexyl constraint on the Cβ–Cγ bond adopt the 14-helical structure both in the solid state and in organic solvent,[44] as found for other γ-peptides.[6, 7, 10, 12] Recently, Guo et al.[45] and we[46] have shown that helix and β-turn foldamers can be obtained using 2-(aminomethyl)cyclohexanecarboxylic acid (γAmc6; Figure 1c) residues containing a cyclohexyl constraint on the Cα–Cβ bond, respectively. Tetra- and hexa-α/γ-peptides containing the (2S,3R)-γAmc6 residue adopt the 12/10- and 12-helical conformations stabilized by two intramolecular and four C[DOUBLE BOND]O(i)···H[BOND]N(i + 3) H-bonds in the solid state, respectively.[45] However, the (2S,3S)-(2R,3R)-γAmc6 dipeptide forms a stable β-turn structure in water, resembling a type II′ turn of α-peptides, which can be used as a β-turn motif in β-hairpins of Ala-based α-peptides.[46]

image

Figure 1. Chemical structures of γ-peptides with cycloalkanes in backbone: (a) trans-2-(aminomethyl)cyclopropanecarboxylic acid (γAmc3) with a cyclopropyl constraint on the Cα–Cβ bond; (b) 2-aminocyclohexylacetic acid (γAc6a) with a cyclohexyl constraint on the Cβ–Cγ bond; and (c) 2-(aminomethyl)cyclohexanecarboxylic acid (γAmc6) with a cyclohexyl constraint on the Cα–Cβ bond and their backbone torsion angles.

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Here, we extensively studied the conformational preferences of various helix foldamers for the oligomers of γAmc6 residues with a cyclohexyl constraint on the Cα–Cβ bond using density functional methods in the gas phase and in solution (chloroform and water) and compared them with the relevant experimental results.

COMPUTATIONAL METHODS

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

Chemical structure and torsion angles for the γAmc6 residue are defined in Figure 1c. All density functional calculations were carried out using the hybrid-meta-GGA M06-2X functional method[47] and the Solvation Model based on Density (SMD) method[48] implemented in the Gaussian 09 program.[49] GaussView[50] was used in editing the peptide structures.

Because of the rigidity imposed by a cyclohexyl ring, the torsion angle ζ about the Cα–Cβ bond of the γAmc6 residue is chirospecific depending on the chiralities at Cα and Cβ atoms and the puckering of cyclohexyl ring (Figure 2).[46] For the torsion angle ζ, residues 1–3 have the gauche+ (g+) conformation, whereas residues 4–6 have the gauche− (g) conformation. According to the helical structures of the γ2,3,4-tetrapeptide with (2R,3R,4R) configuration in the solid state[27, 28] and the hexapeptide of γAbu optimized at the HF/6-31G(d) level of theory,[37] the torsion angle ζ for the γAmc6 residue should have a gauche conformation to form helical structures.

image

Figure 2. Chirospecific γAmc6 residues depending on the chiralities at Cα and Cβ atoms and the puckering of cyclohexyl ring. The values of torsion angle ζ are those optimized at the M06-2X/6-31G(d) level of theory.

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Four helix types having different sizes of the H-bonded pseudocycles are considered in this study (Figure 3). For the γ-peptides, the 14- and 9-helices are featured by 14- and 9-membered H-bonded pseudocycles in the backward direction along the sequence between C[DOUBLE BOND]O(i − 3) and N[BOND]H(i) and between C[DOUBLE BOND]O(i − 2) and N[BOND]H(i), respectively, whereas the 12- and 7-helices are defined by 12- and 7-membered H-bonded pseudocycles in the forward direction between N[BOND]H(i) and C[DOUBLE BOND]O(i + 1) and between N[BOND]H(i) and C[DOUBLE BOND]O(i), respectively. In particular, it has been reported that various γ-peptides adopt H7, H9, and H14 helical structures in solution and in the crystal.[11] Although other helical structures with larger 17-, 19-, 22-, and 24-membered H-bonded pseudocycles can be formed for γ-Abu oligopeptides,[37, 39] they are not considered in this work because of much higher relative electronic energies.

image

Figure 3. Feasible H-bonding patterns in γAmc6 peptides.

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The initial structures of terminally blocked di-γAmc6 peptides [i.e., Ac-(γAmc6)2-NHMe] with Hn-14, Hn-12, Hn-9, and Hn-7 (n = 16) helix types were generated using the mean backbone torsion angles of the γAbu residue for its most stable hexapeptide with the same helix types optimized at the HF/6-31G(d) level of theory in the gas phase.[37] In the case of 7-helical structures, the mean backbone torsion angles of the H7II structure of γAbu hexapeptide were used as the initial values for optimization, although the H7II structure is less stable than the H7I structure at the HF/6–31G(d) level of theory.[37] However, the H1-7 foldamer of di-γAmc6 peptide generated from the H7I structure is found to be less stable than that from the H7II structure at the M06-2X/6–31+G(d) level of theory, of which the former is the local minimum d17 (Supporting Information Table SVIII). All right-handed (P)- or left-handed (M)-type counterparts were generated by changing the signs of the given torsion angles with each other except for the torsion angle ζ. From residues 1, 2, and 3, we obtained the (P)-type helices of Hn-14, Hn-9, and Hn-7 and the (M)-type helix of Hn-12. We generated the (M)-type helices of Hn-14, Hn-9, and Hn-7 and the (P)-type helix of Hn-12 from residues 4, 5, and 6. For each helix type, the initial extended conformation with the backbone torsion angles of 180° except for the torsion angle ζ was also built as a reference in estimating the helix propensity. These initial structures were optimized at the HF/3–21G(d) level of theory in the gas phase. Further optimizations were carried out at the M06-2X/6-31G(d) level of theory and followed by the optimizations at the M06-2X/6-31+G(d) level of theory in the gas phase. The same procedures were also applied to all H1, H2, H4, and H5 helices of tetra-, hexa-, and octa-γAmc6 peptides. This is because all H3 (or H6) helices of the di-γAmc6 peptide have relative electronic energies higher by ∼8 to 12 kcal/mol than the most stable H1-9 (or H4-9) helix at the M06-2X/cc-pVTZ//M06-2X/6-31+G(d) level of theory in the gas phase (see Supporting Information Table SI). In the case of hexapeptides and octapeptides of heterochiral residues 2 and 5, we obtained the ribbon-like extended structures at the HF/6-31G(d) level of theory, which were transformed into ring-like structures at the M06-2X/6-31G(d) and M06-2X/6-31+G(d) levels of theory. Thus, the helix propensities per residue were calculated only for H1 and H4 foldamers with the homochiral configurations.

For all local minima of helices and extended structures at the M06-2X/6-31+G(d) level of theory, the relative energies (ΔEc and ΔEw) of each local minimum in chloroform and water were calculated as the sum of the relative single-point energy (ΔE0) at the M06-2X/cc-pVTZ level of theory and the relative solvation free energies (ΔΔGs,c and ΔΔGs,w) obtained at the SMD M06-2X/6-31+G(d) level of theory in chloroform and water. The helical parameters of each helix foldamer for tetra-, hexa-, and octa-γAmc6 peptides were calculated from a set of consecutive β-carbons with the HELFIT program,[51] which uses total least squares algorithm for helix fitting and requires minimum four data points for the analysis.

RESULTS AND DISCUSSION

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

Relative Stabilities

The thermodynamic properties and the dipole moments of the helix foldamers for di- to octa-γAmc6 peptides of residues 1 and 2 with the torsion angle ζ in the g+ conformation in the gas phase and in solution (chloroform and water) are listed in Table 1 and those of residues 4 and 5 with the torsion angle ζ in the g conformation are listed in Supporting Information Table SII. In the gas phase and in solution, it is known that each of the H1 (or H4) foldamers with the homochiral (2S,3S) [or (2R,3R)] configuration is more preferred than the corresponding H2 (or H5) foldamer with the heterochiral (2S,3R) [or (2R,3S)] configuration and the relative stability of the former to the latter increases as the peptide sequence becomes longer and the solvent polarity increases.

Table 1. Thermodynamic Properties (kcal/mol) and Dipole Moments (D) of Ac-(γAmc6)n-NHMe Peptides
  Gas PhaseChloroformWater Gas PhaseChloroformWater
  ΔE0aμbΔΔGs,ccΔEcdμbΔΔGs,wcΔEwdμb ΔE0aμbΔΔGs,ccΔEcdμbΔΔGs,wcΔEwdμb
  1. a

    Relative single-point energies at the M06-2X/cc-pVTZ level of theory in the gas phase.

  2. b

    Dipole moment at the (SMD) M06-2X/6-31+G(d) level of theory in the gas phase and in solution.

  3. c

    Relative solvation free energies at the SMD M06-2X/6-31+G(d) level of theory in solution.

  4. d

    Relative energies at the M06-2X/cc-pVTZ//SMD M06-2X/6-31+G(d) level of theory in solution.

  5. e

    Extended structure.

  6. f

    Calculated for the hexa-γAmc6 peptide, which is obtained by removing both terminal residues from H1-9 helical foldamers for the octa-γAmc6 peptide at the M06-2X/6-31+G(d) level of theory.

n = 2H1-141.219.34−1.210.0011.520.371.5813.58H2-144.229.020.284.5111.222.056.2812.76
 H1-123.0410.05−2.540.5012.77−3.040.0015.50H2-128.379.98−0.817.5612.82−0.577.8015.67
 H1-90.009.040.250.2510.863.683.6812.45H2-94.398.311.275.6610.274.588.9614.10
 H1-73.548.11−0.792.759.811.324.8611.29H2-77.268.28−0.167.109.681.999.2512.62
 E1e8.884.69−3.914.975.86−4.754.136.96E2e15.628.21−3.9711.6511.20−6.089.546.16
n = 4H1-140.0015.700.000.0019.381.041.0422.77H2-145.0414.872.677.7118.625.3810.4222.30
 H1-122.6918.90−2.450.2423.30−2.690.0027.16H2-1215.1118.970.8315.9423.420.9316.0427.27
 H1-92.9816.361.824.7918.808.0911.0720.84H2-912.0115.393.2615.2718.239.1321.1520.88
 H1-711.2214.20−0.8610.3616.562.3113.5318.61H2-717.9515.360.2818.2317.124.7822.7318.57
 E1e22.346.16−7.6914.657.54−9.2413.108.83E2e35.115.54−7.7727.348.51−9.0326.0811.74
n = 6H1-140.0024.160.000.0028.801.791.7932.84H2-148.1022.482.8710.9727.385.8914.0032.04
 H1-124.9328.33−4.140.7933.87−4.930.0038.54H2-1224.5528.780.7725.3134.27−0.1624.3838.95
 H1-9f12.5124.570.6713.1927.488.2120.7330.01H2-923.1822.832.6425.8226.379.8433.0229.79
 H1-722.1222.49−4.2017.9225.461.1123.2328.17H2-732.1823.45−1.8630.3225.573.0735.2627.49
 E1e39.827.73−13.7726.069.25−16.8422.9910.66         
n = 8H1-140.0031.350.000.0036.650.060.0641.31H2-1410.7030.353.0613.7636.126.5717.2841.56
 H1-126.6738.85−5.920.7545.23−6.670.0050.57H2-1233.2839.210.5833.8645.50−1.0332.2550.90
 H1-915.8032.67−0.2915.5135.869.1824.9838.82H2-934.2330.441.7535.9834.5610.2744.5038.71
 H1-733.8328.44−6.7327.0931.82−3.1630.6735.06H2-746.9031.45−4.4842.4233.701.4448.3435.86
 E1e57.549.62−21.3436.2011.33−26.9230.6212.92         

In the gas phase, the most stable helix foldamer of di-γAmc6 peptides is H1-9 with the helix propensity of −4.4 kcal/mol per residue to the corresponding extended structure, which is equivalent to the C7 structure (γ-turn) stabilized by a 3 [RIGHTWARDS ARROW] 1 H-bond between C[DOUBLE BOND]O(i − 1) and N[BOND]H(i + 1) in natural α-peptides and proteins[52, 53] and followed by H1-14, H1-12, and H1-7. These are consistent with the results of a systematic conformational study on the hexa-γAbu peptide to form helix foldamers at the B3LYP/6-31G(d) level of theory in the gas phase.[37] For the H2 helix foldamers of di-γAmc6 peptide, however, H2-9 is less stable by 0.16 kcal/mol than H2-14.

In the case of tetra- to octa-γAmc6 peptides, the conformational stabilities of the H1 helix foldamers are calculated to be in the order H1-14 > H1-12 > H1-9 > H1-7 in the gas phase. As the peptide sequence becomes longer, the energy difference between each H1 helix foldamer and its extended structure increases, indicating that the propensity to form each helix foldamer increases. In particular, ongoing from tetra- to hexa- to octa-γAmc6 peptides, the helix propensities per residue of the H1-14 foldamer are calculated to be −5.6, −6.6, and −7.2 kcal/mol, respectively. In addition, the relative stability of H1-14 to H1-12 is found to increase with the increase of sequence length, despite the same number of H-bonds for both foldamers.

In chloroform, the H1-14 foldamer is found to be most preferred for di-γAmc6 peptides with the helix propensity of −2.5 kcal/mol per residue and followed by H1-9, H1-12, and H1-7 foldamers with ΔEc = 0.25, 0.50, and 2.75 kcal/mol, respectively. For tetra- to octa-γAmc6 peptides in chloroform, the conformational stabilities of the H1 helix foldamers are calculated to be in the order H1-14 > H1-12 > H1-9 > H1-7, as found in the gas phase. However, there are the decreases of 0.24, 0.79, and 0.75 kcal/mol in ΔEc of H1-12 relative to H1-14 for tetra-, hexa-, and octa-γAmc6 peptides, respectively. Ongoing from tetra- to hexa- to octa-γAmc6 peptides in chloroform, the helix propensities of the H1-14 foldamer per residue are calculated to be −3.7, −4.3, and −4.5 kcal/mol, respectively, which are quite similar to −3.6, −4.2, and −4.4 kcal/mol of the H1-12 foldamer, respectively.

In water, the conformational preferences of H1 helix foldamers for di- to octa-γAmc6 peptides are calculated to be in the order H1-12 > H1-14 >> H1-9 > H1-7, whereas those of H2 helix foldamers are in the order H2-14 > H2-12 > H2-9 > H2-7. Although the H1-12 foldamer of each peptide is found to be preferred over the corresponding H1-14 one in water, the difference in their ΔEws for each peptide is not remarkable. For di- to octa-γAmc6 peptides, the helix propensities of H1-12 foldamers per residue are −2.1, −3.3, −3.8, −3.8 kcal/mol, respectively, whereas those of the H1-14 foldamers are −1.3, −3.0, −3.5, −3.8 kcal/mol, respectively. This indicates that the helix propensities of both H1-12 and H1-14 foldamers increase as the peptide sequence becomes longer and that those of both foldamers become equally probable when the sequence is equal to octapeptide and longer in water. However, the helix propensities of both the foldamers in water are lower by 0.3–0.8 kcal/mol than those in chloroform.

In particular, we found the increase of populations for the H1-12 foldamers as the solvent polarity increases. This can be ascribed to that H1-12 has the preferred solvation per residue over H1-14 by 0.7 and 1.2 kcal/mol in chloroform and water, respectively, because of the larger dipole moments of the former (Table 1), as pointed out for the hexa-γAbu peptide in water.[37] In contrast to H1-12 and H1-14, H1-9 and H1-7 are a little more stable or even less stable than the corresponding extended structures in water, indicating that γAmc6 oligopeptides are not likely to form H1-9 and H1-7 structures in water. 1H NMR experiments for γAbu derivatives showed that the formation of the nine-membered H-bond between nearest neighboring amide groups is enthalpically favorable than the formation of the seven-membered H-bond in methylene chloride.[54] We found that H1-9 is favorable for the γAmc6 dipeptide with ΔEc = 0.25 kcal/mol relative to H1-14 in chloroform (Table 1).

In organic solvents and in the solid state, it has been known that the oligopeptides of γ4-, γ2,4-, and γ2,3,4-Abu residues[24-28] and γAc6a residues[44] (Figure 1b) form 14-helical structures, whereas the dipeptides of γ2,3,4-Abu[28] and γAc6a residues[44] adopt a 9-helical structure, which are consistent with our calculated results for the oligopeptides of γAmc6 residues in the gas phase and in chloroform. However, it was suggested that a γ2,3,4-Abu tetrapeptide forms a 14-helix in the solid state, but probably not to a larger extent in methanol or acetonitrile solution.[28] This may suggest the possibility of the depopulation of 14-helix into other helical forms as the solvent polarity increases. We found that the H1-14 foldamers of γAmc6 oligopeptides are preferred over the corresponding H1-12 ones in chloroform, although there are small differences in their helix propensities per residue. However, the populations of the H1-14 foldamers are decreased and the H1-12 foldamers become more populated for di-, tetra-, and hexa-γAmc6 oligopeptides in water. In particular, the populations of H1-14 and H1-12 foldamers become almost the same for octapeptide in water, as described earlier.

Helix Structures

The mean backbone torsion angles of γAmc6 residues 1 and 4 with homochiral (2S,3S) and (2R,3R) configurations, respectively, for optimized helical and extended structures of tetra-, hexa-, and octapeptides are listed in Table 2. The backbone torsion angles for each of optimized helical and extended structures of oligopeptides are listed in Supporting Information Table SIII. The helical and extended structures of octapeptide with residue 1 are shown in Figure 4 and those of other oligopeptides with residue 1 are shown in Supporting Information Figure S1. The corresponding structures of oligopeptides with residue 4 are shown in Supporting Information Figure S2. The mean backbone torsion angles of helical structures with residues 2 and 5 with heterochiral (2S,3R) and (2R,3S) configurations, respectively, are listed in Supporting Information Table SIV.

Table 2. Mean Backbone Torsion Angles (°) of γAmc6 Residues for Helical and Extended Structures
PeptideFoldamerϕθζψ
  1. a

    Extended structure.

  2. b

    Ref. [44].

  3. c

    Ref. [27].

  4. d

    Ref. [37].

γAmc6 (1) (2S,3S)H1-14−135.260.959.8−139.1
H1-12−79.6−77.163.0−125.2
 H1-9−94.475.067.7−107.3
 H1-798.146.248.390.3
 E1a−102.3−176.760.1−142.1
γAmc6 (4) (2R,3R)H4-14135.2−60.9−59.8139.1
H4-1279.677.1−63.0125.2
 H4-994.4−75.0−67.7107.3
 H4-7−98.1−46.2−48.3−90.3
 E4a102.3176.7−60.1142.1
γAc6abH-14−154.560.259.5−126.8
γ2,3,4AbucH-14140.4−67.1−54.6133.6
γAbudHI14131.2−61.9−66.3145.4
 HI1284.769.1−76.7145.3
 HI997.8−69.8−75.197.9
 HI7−93.2−48.5−50.4−103.2
image

Figure 4. The optimized helical and extended structures of octapeptides with residue 1: (top) viewing perpendicular to the helical axes and (bottom) views along the helical axes.

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The H1-14, H1-9, and H1-7 helix foldamers are the right-handed (P)-helical structures, whereas the H1-12 helix foldamer is the left-handed (M)-helical structure, although these four helix foldamers have in common the torsion angle ζ in the g+ conformation. Each of the H4 helix foldamers is an enantiomer to the H1 helix foldamer with the same helix type and energy. The mean backbone torsion angles of γAmc6 residue 1 for the optimized 14-helical oligopeptides are ϕ = −135°, θ = 61°, ζ = 60°, and ψ = −139°, which are close to those in X-ray structures of γAc6a oligopeptides,[44] although there are some differences of 19° and 12° in ϕ and ψ, respectively, which seem to be due to the difference in the location of the cyclohexane constraints on backbone. However, those of residue 4 for the optimized 14-helical structures are consistent with those of X-ray structure of γ2,3,4-Abu tetrapeptide[27] and those of the H14I helical structure of the hexa-γAbu peptide optimized at the HF/6-31G* level of theory in the gas phase.[37] Recently, Guo et al. reported that the hexa-α/γ-peptide containing the γAmc6 residue 2 with the (2S,3R) configuration adopts the 12-helical conformations stabilized by four C[DOUBLE BOND]O(i)···H[BOND]N(i + 3) H-bonds in the solid state, whose mean backbone torsion angles of γAmc6 residues are ϕ = −129°, θ = 57°, ζ = 56°, and ψ = −121°,[45] which are similar to those of ϕ = −136°, θ = 67°, ζ = 55°, and ψ = −136° for the H2-14 helix foldamer (Supporting Information Table SIV).

We monitored the distances d(C[DOUBLE BOND]O···H[BOND]N) and angles ∠N[BOND]H···O for the C[DOUBLE BOND]O···H[BOND]N H-bonds of helix foldamers, whose mean values are listed in Supporting Information Table SVI. For H1-14 foldamers of tetra- to octapeptides, the mean H-bond distance and angle are obtained to be 2.00 Å and 168°, respectively, whereas the corresponding values for H1-12 foldamers are 1.88 Å and 156°, respectively. This indicates that the latter has a shorter distance but somewhat a larger deviation from linearity than the former. The mean H-bond distance and angle for H1-14 foldamers are consistent with the values of 2.09 Å and 154° for the second H-bond in X-ray structure of γ2,3,4-Abu tetrapeptide[27] and the mean values of 2.06 Å and 155° for the α-helices in proteins.[55]

The helical parameters for each helix foldamer of tetra-, hexa-, and octa-γAmc6 peptides are listed in Supporting Information Table SVII and their mean values are listed in Table 3. The H1-14 helix foldamers have a mean pitch of 5.3 Å and 2.5 residues per turn, whereas those of the H1-12 helix foldamers are 5.3 Å and 2.3, respectively. The mean radii for these two foldamers are 3.0 and 2.4 Å, respectively. The calculated mean helical parameters of the H1-14 foldamers are similar to the values of a pitch of 5.5 Å and 2.5 residues per turn for the 14-helices of γAc6a oligopeptides in the solid state,[44] despite the different location of the cyclohexyl substituent on the backbone, but they are a little different from the values of a pitch of 5.7 Å and 2.6 residues per turn for X-ray structure of γ2,3,4-Abu tetrapeptide.[27] In particular, as the size of the H-bonded pseudocycle decreases, that is, ongoing from H1-14 to H1-12 to H1-9 to H1-7, the rise per residue increases and the radius of helix decreases, as shown in Figure 4.

Table 3. Mean Helical Parameters for Helix Foldamer of Oligo-γAmc6 Peptides
Peptidemapbdcrd
  1. a

    Number of residues per turn.

  2. b

    Rise per turn (pitch) (Å).

  3. c

    Rise per residue (Å).

  4. d

    Radius of helix (Å).

H1-142.55.32.13.0
H1-122.35.32.42.4
H1-92.48.43.52.0
H1-72.610.54.01.5
     
H4-142.55.32.13.0
H4-122.35.32.42.4
H4-92.48.43.52.0
H4-72.610.54.01.5

Conformational Preferences of γAmc6 Dipeptides

Conformational analysis of the terminally blocked (2S,3S)-γAmc6 (1) dipeptide, Ac-(γAmc6 (1))2-NHMe, has been carried out to confirm whether the helical structures are preferred in the gas phase and in solution (Supporting Information Table SVIII). In addition, conformational analysis of Ac-(γAmc6 (4))2-NHMe, which has an enantiomer to the γAmc6 (1) residue, has been carried out. For each of the dipeptides at the M06-2X/cc-pVTZ//SMD M06-2X/6-31+G(d) level of theory, we identified the 38, 58, and 60 local minima with ΔE < 10 kcal/mol in the gas phase, in chloroform, and in water, respectively, of which one, eight, and one local minima have ΔE < 1 kcal/mol, respectively. The representative conformations d1, d3, Hd-14, and Hd-12 for the (2S,3S)-γAmc6 (1) dipeptide are shown in Supporting Information Figure S3.

Conformation d1 is most preferred with the population of 83% in the gas phase, which has three H-bonds such as two seven-membered H-bonds with the distance d(C[DOUBLE BOND]O⋯ H[BOND]N) = 2.08 and 2.05 Å in the first and second residues, respectively, and a 14-membered H-bond with the distance of 1.97 Å between the C[DOUBLE BOND]O of the acetyl group and the H[BOND]N of the C-terminal NHMe group. Helix foldamers Hd-9, Hd-14, Hd-12, and Hd-7 are less stable than d1 by 2.64, 3.84, 5.68, and 6.18 kcal/mol in ΔE0, respectively. However, conformation d3 (26%) becomes most preferred in chloroform, which has a bifurcated H-bond of the C[DOUBLE BOND]O of the acetyl group with the H[BOND]N of the second residue (i.e., a nine-membered H-bond with the distance of 2.10 Å) and the H[BOND]N of the C-terminal NHMe group (i.e., a 14-membered H-bond with the distance of 1.97 Å), and is followed by conformations Hd-14 (13%) and d1 (12%) with ΔEc = 0.42 and 0.48 kcal/mol, respectively. In water, the Hd-12 helix foldamer is found to be most preferred with the population of 68%, which is ascribed to the favored solvation by −3.01 and −8.22 kcal/mol over conformations d3 (5%) and d1 (1%) with ΔEw = 1.52 and 2.54 kcal/mol, respectively, which can be ascribed to the higher dipole moment of 15.5 D for the former than those of 13.2 and 1.46 D for the latter, respectively. The population of the Hd-14 helix foldamer is calculated to be 5% by ΔEw = 1.58 kcal/mol in water. The optimized H-bond distances of d(C[DOUBLE BOND]O⋯H[BOND]N) is 1.95 and 1.99 Å for Hd-12 and Hd-14 foldamers, respectively, which are a little longer than and similar to the mean value of its oligopeptides, respectively, as described earlier.

CONCLUSIONS

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

The chirospecific di- to octa-γ2,3-peptides based on γAmc6 with a cyclohexyl constraint on the Cα–Cβ bond adopt well-defined helix structures with different characteristic H-bonding patterns. The conformational analyses on the γAmc6 peptides with homochiral (2S,3S) or (2R,3R) configurations revealed that the (P/M)−2.514-helices are most preferred in the gas phase and in chloroform, whereas the (P/M)−2.312-helices are most stable in water due to the larger helix dipole moments. However, the negligible difference in electronic energy between 12- and 14-helix for octa-γAmc6 peptides in water indicates that both foldamers become equally probable when the sequence is equal to octapeptide and longer. As the peptide sequence becomes longer, the helix propensities of 14- and 12-helices are also found to increase both in the gas phase and in solution. The mean backbone torsion angles and helical parameters of the 14-helix foldamers of γAmc6 oligopeptides are consistent with those of X-ray structures for oligopeptides of 2-aminocyclohexylacetic acid and tetrapeptide of γ2,3,4-aminobutyric acid, despite the different substituents on the backbone. In particular, as the size of the H-bonded pseudocycle decreases, the rise per residue increases and the radius of helix decreases.

The conformational preferences of the γAmc6 oligopeptides obtained here are expected to provide useful information for structure-based designs of biologically active γ-peptides with specific functions. In particular, the incorporation of hydrophobic or charged groups into the cyclohexane rings may increase the resistance of helical structures to proteolysis or the antimicrobial activity and provide the surface and cavity of the helical structures suitable for molecular recognition and catalysis.

REFERENCES

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

Supporting Information

  1. Top of page
  2. ABSTRACT
  3. INTRODUCTION
  4. COMPUTATIONAL METHODS
  5. RESULTS AND DISCUSSION
  6. CONCLUSIONS
  7. REFERENCES
  8. Supporting Information

Additional Supporting Information may be found in the online version of this article.

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bip22287-sup-0001-suppinfo.doc2412KSupplementary Information

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