Addition of a Peptide Fragment on an α-Helical Depsipeptide Induces α/310-

Conjugated Helix: Synthesis, Crystal Structure, and Circular Dichroism

Spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt

Hiroyuki Oku, Takafumi Ohyama, Akihiro Hiroki, Keiichi Yamada,

Keiichi Fukuyama,† Hiroyuki Kawaguchi,

†† and Ryoichi Katakai*

Department of Chemistry, Gunma University, Kiryu, Gunma 376-8515, JAPAN.

†Department of Biology, Graduate School of Science, Osaka University, Toyonaka,

Osaka 560-0043, JAPAN. ††

Institute for Molecular Science, Okazaki, Aichi 444-

8585, JAPAN

Running title: Crystal Structure of a Depsipeptide

Corresponding author: Ryoichi Katakai; e-mail, katakai@chem.gunma-u.ac.jp;

Phone & Fax, +81-277-30-1343.

1

Abstract: The depsipeptide Boc1-Leu2-Leu3-Ala4-Leu5-Leu6-Lac7-Leu8-Leu9-Lac10-

Leu11-Leu12-Lac13-Leu14-Leu15-OEt16 (1) (Boc = tert-butyloxycarbonyl, Lac = L-

lactic acid residue) has been synthesized from a peptide, Boc-Leu-Leu-Ala-OEt (2)

and a depsipeptide, Boc-(Leu-Leu-Lac)3-Leu-Leu-OEt (3). Single crystals of 1 were

successfully obtained and the structure has been solved by direct methods (such as

Sir2002 and Shake-and-Bake). Interestingly, 1 adopts a α/310-conjugated helix

containing a kink at the junction of peptide and depsipeptide segments, Leu3~Lac7.

This is significantly different from the conformation of 3, which has a straight α-

helical structure with standard φ and ψ angles. Microcrystalline circular dichroism

(CD) spectra were also studied to compare structural properties of 1 and 3. The

difference of α/310 and α helices has been appeared in these CD spectra.

Keywords: depsipeptide; α-helix; 310-helix; leucine; lactic acid; nano-material;

crystal structure; liquid-phase peptide synthesis; segment condensation.

2

Abbreviations Used: Aib = α-aminoisobutyric acid, n-BuOH = n-butanol, CCDC =

Cambridge Crystallographic Data Centre, CD = circular dichroism, Boc = tert-

butyloxycarbonyl, DCC = dicyclohexylcarbodiimide, DMAP =

dimethylaminopyridine, DMF = dimethylformamide, Hea = 1-hydroxy ethanoic acid,

Hmb = (S)-2-hydroxy-3-methylbutanoicacid, Hmp = L-leucic acid, (S)-2-hydroxy-4-

methylpentanoicacid, HONSu = N-hydroxysuccinimide, Lac = L-lactic acid, MeOH =

methanol, NMM = N-methymorpholine, TFA = trifluoroacetic acid, TFE = 1,1,1-

trifluoroethamol, TLC = thin layer chromatography.

3

INTRODUCTION

Depsipeptides are oligomers and polymers composed of hydroxy- and amino-

acids linked by amide and ester bonds. In nature, the depsipeptides are found in

antibacterials. In some cases, the depsipeptides are applied for cancer therapeutics

such as actinomycin D, FK-228, and FR 901228.1-3

Except naturally occurring compounds, Goodman et al. first reported the

usefulness of the depsipeptides for conformational studies.4-8 They have prepared

sequential polymers, such as poly(Ala-Ala-Lac) and poly(Val-Pro-Hea-Val-Gly).

Until today, various depsipepides have been reported from the viewpoint of structural

interest: (1) stabilization and destabilization of β-turn conformation,9,10 (2) the

stability of helical structures consisting of β-amino acids,11,12 (3) peptide compounds

having 2-hydroxy-2,3-dimethylbutanoic acid residues,13 and (4) replacement with a

Lac residue in -Val-Ala-Leu-Aib- based helices.14,15 We have also studied

sequential oligo- and poly-depsipeptides composed of non-polar amino-acid residues

(Leu, Val, Ala, and Gly) and the corresponding hydroxy-acid residues (Hmp, Hmb,

Lac, and Hea).16-30 Hydroxy acid mutation is also useful for the studies of native

proteins.31-38 For example, a coiled-coil structure in GCN4 has been tested for the

difference of thermal denaturation energy.31 As a model of amyloidgenesis,

depsipeptides have been applied to prevent β-sheet aggregation.32

A practical application of polydepsipeptides is for biodegradable and bio-

absorbable materials.39-44 In those polymers, ester linkages can be hydrolyzed by

esterases at each implanted site and can be decomposed into oligomers. As an

example, we have developed a material for a drug delivery system42 where we can

modulate degradation period from days to a year depending on their hydrophobicity.

4

Recently we have found that a series of Leu and Lac based depsipeptides are

suitable for nano-structural materials due to the solubility,17 conformational

stability,21,22,24,25 and crystallinity.18-23,27 For example, by the crystallographic

analysis we have realized that Boc-(Leu-Leu-Lac)3-Leu-Leu-OEt (3)19 still have α-

helix conformation even with three Lac residues. In the helical structure of 3, a

slight distortion was observed at the level of the Lac residues. We have also

prepared a composite sequence, Boc-(Leu-Leu-Ala)2-(Leu-Leu-Lac)3-OEt (4)27,18

which is made of two units -Leu-Leu-Ala- and -Leu-Leu-Lac-. The crystal structure

of 4 is an α-helix with a 310-helical part at the connective region between the peptide

and the depsipetide moieties, -Ala7-Leu8-Leu9-Lac10-Leu11-Leu12-. These two

examples have indicated that the local structure around Lac residues is probably

flexible compared with those of Leu residues.

In this report, we describe the synthesis and geometrical parameters of a novel

sequence, Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (1), which is a block

oligomer prepared from a peptide, Boc-Leu-Leu-Ala-OEt (2) and a depsipeptide Boc-

(Leu-Leu-Lac)3-Leu-Leu-OEt (3).

EXPERIMENTAL

Peptide Synthesis

The depsipeptide 1 was synthesized by a condensation of a peptide and a depsipeptide

fragments. These fragments were synthesized by stepwise elongation of peptide

chains. Couplings between the segments were mediated by

dicyclohexylcarbodiimide-N-hydroxysuccinimide (DCC/HONSu) in CHCl3.

5

HCl.H-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (HCl.5). Boc-(Leu-Leu-Lac)3-

Leu-Leu-OEt19 (37.2g, 0.1 mol) was dissolved in 2.5 N HCl/dioxane (100 mL). The

solution was allowed to stand for 1 h at room temperature, and then the solvent was

evaporated under reduced pressure. Addition of diethyl ether and hexane gave

crystals of the hydrochloride salt HCl.5, which were collected on a glass filter and

washed with hexane. Yield, 29.4 g (95%).

Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (1). HCl.5 (29.4 g, 0.095 mol)

was dissolved in CHCl3. To the solution were added NMM (10.45 mL, 0.095 mol),

Boc-Leu-Leu-Ala-OH (39.6 g, 0.095 mol), and HONSu (21.9 g, 0.19 mol). The

solution was cooled at 0 ˚C, and DCC (19.6 g, 0.095 mol) was added. The solution

was stirred for one hour at 0 ˚C and allowed to stand at room temperature for 12h.

The solution was diluted with ethyl acetate and the crystals of dicyclohexylurea were

removed by filtration, and the filtrate was concentrated in vacuo to give a solid, which

was dissolved in ethyl acetate. The solution was washed with 10% citric acid, water,

saturated NaHCO3, water, and saturated NaCl solution, and dried over Na2SO4,

successively. The solvent was then evaporated again. Addition of hexane into the

residue gave a colorless solid. The crude product was purified by a silica gel column

chromatography, eluting with a solvent system, chloroform-ethyl acetate (2:1 (= v/v)).

The product was recrystallized from ethyl acetate to give 42.0 g (65 % yield) of 1.

Mp 216–217 ˚C; [α]20D = -40.5˚ (c = 0.1, CHCl3); IR (KBr) 3305, 2959, 2872, 1745,

1685, 1661, 1648, 1541, 1470, 1388, 1369, 1283, 1241, 1166, 1101, 1036, 949, 865,

701, 666, 588, 468 cm-1; 1H NMR (CDCl3, 500 MHz) δ 7.67 (d, J = 5.49 Hz 1H, NH),

7.57 (d, J = 6.53 Hz 1H, NH), 7.50 (d, J = 6.41 Hz 1H, NH), 7.49 (d, J = 7.94 Hz 1H,

NH), 7.46 (d, J = 5.19 Hz 1H, NH), 7.41 (d, J = 5.49 Hz 1H, NH), 7.38 (d, J = 6.41

6

Hz 1H, NH), 7.37 (d, J = 5.80 Hz 1H, NH), 7.24 (d, J = 7.33 Hz 1H, NH), 6.77 (d, J =

3.36 Hz 1H, NH), 5.38 (br, 1H, NH), 5.10 (q, J = 7.02 Hz 1H, CαH), 5.01 (q, J = 7.02

Hz 1H, CαH), 4.94 (q, J = 7.02 Hz 2H, CαH), 4.49 (m, 1H, CαH), 4.43 (m, 1H, CαH),

4.24 (m, 2H, CαH), 4.16 (m, 2H, CαH), 4.13 (q, J = 7.02 Hz 2H, CH3CH2), 4.07 (m,

1H, CαH), 3.88 (m, 1H, CαH), 1.98–1.56 (m, 30H, CβH, CγH), 1.53 (d, J = 7.02 Hz

3H, CβH), 1.52 (d, J = 7.02 Hz 3H, CβH), 1.52 (d, J = 7.02 Hz 3H, CβH), 1.47 (d, J =

7.02 Hz 3H, CβH), 1.47 (s, 9H, Boc), 1.23 (t, J = 7.02 Hz 3H, CH3CH2), 1.02–0.83 (m,

60H, CδH); ESI-MS m/z(M+) calcd for C79H141N11O20 1564.0, obsd 1587.2 (M +

Na+); Anal. Calcd for C79H141N11O20: C, 60.63; H, 9.08; N, 9.84. Found: C, 60.34; H,

8.94; N, 9.39.

X-Ray Crystallography

To obtain single crystals suitable for crystallographic analysis, 10 mg of 1 was

dissolved in 1 mL of MeOH and equilibrated via vapour phase diffusion against 1 mL

of water, resulting in fine needle crystals after 1-2 weeks at 15 °C. X-ray diffraction

data were collected on a Rigaku RAXIS-RAPID imaging plate area detector with

graphite monochromated Cu-Kα radiation. The data collection conditions and

crystallographic parameters were listed in Table I. We have successfully solved the

structure of 1 by direct methods for macromolecular crystals (such as Shake-and-

Bake45 and SIR200246). An empirical absorption collection program, DIFABS,47

was applied which resulted transmission factors ranging from 0.72 to 1.10. Nitrogen

and oxygen atoms were refined anisotropically. Carbon atoms were refined with

isotropic displacement parameters due to the limited numbers reflections. Hydrogen

atoms were placed in calculated positions and refined with a riding model, and with

Uiso constrained to be 1.2 times Uiso of the carrier atom. The final cycles of full-

7

matrix least squares refinement was based on 8232 observed reflections, and 737

variable parameters and converged with R1 = 0.081 and wR2 = 0.192. Refinement

calculations were performed on the Crystal Structure 3.50 (RIGAKU/MSC, 2003).

The final atomic parameters are deposited into CCDC database (no. 236273).

FT-IR, CD, and 1H-NMR Spectroscopic Measurements

FT-IR spectra were taken on a JASCO FT/IR-660-plus spectrometer equipped with a

TGS detector at 273 K.

CD spectra were recorded on a JASCO J-720 spectropolarimeter at 273 K. A

cylindrical fused quartz cells with path lengths of 0.01 cm was used for all the

experiments. Sample concentrations for CD experiments were 1.00 mg/mL.

Microcrystalline CD spectra were taken under the same condition as in

solution. The nujol-mull sample was prepared from 1 mL of spectro-grade nujol and

1.00 mg of peptide crystals, which were carefully mixed and ground on an agate

mortar and by a pestle.

1H-NMR studies were carried out on JEOL α-500 and λ-500 spectrometers.

Peptide concentrations were in 5 mM and the probe temperature was maintained at

308 or 303 K.

RESULTS

Crystal Structure of 1

A stereo view of the molecular structure and a packing diagram are shown in

Figures 1 and 2, respectively.

8

The torsion angles of main- and side-chains are listed in Tables II. The φ and

ψ torsional angles of the helical residues from Leu2 to Leu14 have shown various

pairs of angles ranging from -49 ~ -93˚ and -18 ~ -44˚, respectively. We can not

simply classify each pair of φ and ψ data to either α- or 310-helical conformations. 46-48

In these cases, hydrogen bond pattern is suitable to assign helical classes as discussed

below. For the side chains of Leu residues, the torsion angle data have suggested a

stable orientation, g-(t, g-),50-54 except Leu2 and Leu11 which adopt the other stable

form, t(g+, t).

The intramolecular and intermolecular hydrogen bonds are listed in Tables III

and IV, respectively. The molecules are packed into infinite chains by the three

intermolecular bonds. The connecting residues are found at the head-to-tail

positions, Lac13....Leu2, Leu14....Leu2, and Leu14....Leu3. The dotted lines in Figure

2 show interactions by three hydrogen bonds, NH...O=C, although the Leu14-Leu3

hydrogen bond is not clearly to be seen by the overlapping of atoms.

For intramolecular interactions, total 13 hydrogen bonds are found for

carbonyl oxygens and amide NHs. Among them, eight interactions are of [i, i+4]

types, which form α-helical segments. The observed pairs are

O12(Boc1)…N51(Leu5), O21(Leu2)…N61(Leu6), O41(Ala4)…N81(Leu8),

O51(Leu5)…N91(Leu5), O72(Lac7)…N111(Leu11), O81(Leu8)…N121(Leu12),

O102(Lac10)…N141(Leu14), and O111(Leu11)…N151(Leu15). The rest of five

interactions are of [i, i+3] types, which forms 310-helical segments. These are found

in the pairs of O12(Boc1)…N41(Leu4), O21(Leu2)…N51(Leu5), O51(Leu5)…N81(Leu8),

O81(Leu8)…N111(Leu11), and O111(Leu11)…N141(Leu14). The N…O lengths of

NH…C=O hydrogen bonds are in the range of 3.02(2)~3.31(1) Å. All [i, i+3]

hydrogen bonds are expected to have very weak interactions except one, which have a

9

bond length of 3.02(2) Å. These values are well corresponding to the reported data

(mean ~3.0 Å) observed in the peptide structures.55-58

The connections between Leu6-Lac7, Leu9-Lac10, and Leu12-Lac13 residues

are ester linkages and do not have NHs. Therefore both α- and 310-helical

interactions can not be expected for the carbonyls of Leu3, Leu6, and Leu9 (α-type)

and for those of Ala4, Lac7, and Lac9 (310-type). Interestingly, any ester C=Os do

not contribute to the hydrogen bonding. For example, O91…N121 distance is

4.00(2) Å. This length is far beyond the range of bonding interaction.

The other oxygen atoms in those ester moieties (–O–) are found to contribute

to the hydrogen bonding with amide NHs. The bonding pairs are O71…N81,

O101…N111, O131…N141, and O161…N151.

CD spectra of 1 and 3

Solution spectra.

Solution conformations of the depsipeptides 1 (Figure 3a) and 3 (Figure 3b)

were examined in n-BuOH, TFE and MeOH by using CD spectra. The spectrum of

1 in n-BuOH is characterized by a positive band at 192 nm and a negative band at 203

nm, accompanied by an indistinct shoulder near 220 nm with mean residue ellipticity

[θ]203 = -20,500 and [θ]220 = -4,800 deg.cm2.dmol-1, respectively. The ellipticity of

amide n −> π* transition at 220 nm59 was smaller than that of π −> π* at 203 nm.

This spectral pattern is often observed for short helical-peptides and -depsipeptides

having 14-16 residues.17,60 In the case of a typical α-helix, the spectrum is

characterized by a positive ellipticity at 190 nm and a double minimum at about 208

and 222 nm with equal intensity.61-64 In polar solvents, TFE and MeOH, the peptide

10

have shown CD spectra with a negative ellipticity at around 190-203 nm which is

characteristic of unordered structure in oligopeptides.61,62,65-67

The spectra of 3 show weaker negative bands at around 190-203 nm even in n-

BuOH solvent, which is less polar than TFE and MeOH and can stabilize the helical

structure. These spectra are corresponding to unordered structure61,62,65-67 that is

often observed for the sequences having short chain length (< 12 residues).

The CD spectra of 1 and 3 have indicated that the solution conformation of 1

was significantly stabilized by the addition of a peptide fragment, -Leu-Leu-Ala-, into

the depsipeptide sequence of 3. The stability is probably attributable to the

difference of (1) chain length (14 and 11 residues for 1 and 3, respectively) and (2)

the number of possible intramolecular N-H...O=C hydrogen bonds. Actually in the

crystalline state of 1, there are 13 intramolecular hydrogen bonds as revealed by the

X-ray diffraction study. On the contrary, there are only six hydrogen bonds in that

of 3. Therefore we can estimate that the increased number of hydrogen bonds also

stabilizes the helical conformation in solution states.

Microcrystalline spectra.

Figure 4 shows microcrystalline CD spectra of 1 and 3 by using the nujol-

mulls. The ellipticity was normalized by residual molar concentration to compare

band intensity. Full scale of the ordinate axis is formally corresponding to +12,000

~ -12,000 mdeg.cm-2.mol-1.

Solid-state CD using microcrystalline and thin-film samples has been widely

used in the field of inorganic complexes and small organic molecules, and peptides.68-

76 Especially, microcrystalline technique is powerful to obtain crystalline-specific

information. The measurements can be done either in nujol or in a KBr disk form

11

where grounded crystal particles are dispersed homogeneously in each matrix.

Although the spectral measurement is quite simple, we should treat the spectra very

carefully. The most important artifact is the scattering effect. The incident

polarized light can be partially reflected by the suspended peptide crystals, and

probably broaden the band width and weaken the band intensity compared with an

idealized spectrum. Many good examples are available in the published papers such

as by Kuroda et al73-76 and Bosnich et al.68 In our case, all the samples were

prepared very thoroughly to achieve homogeneous states. Each spectrum was

confirmed by using four different samples to test reproducibility of the spectral shape.

The spectrum of 1 has a positive band at 193 nm and a negative shape

consisting of broad bands at 211 and 219nm with similar intensity. The broad

spectra are probably come from the scattering effect of the incident light in the

spectrometer, although the samples were prepared with careful treatment and no

distinct crystals can be seen in the nujol suspensions. The spectrum of 3 has a

positive band at 193 nm, a negative shoulder near 211 nm, and a negative peak at 223

nm. The band at 223 nm shows stronger intensity than that at 211 nm. Both

spectra is similar to the α-helical pattern having a positive band at 190 nm and a

double negative bands at about 208 and 222 nm.61-64 A minor dissimilarity, the

intensity difference at 223 nm is attributable to the conformational properties of α-

helix (3) and α/310 conjugated helix (1) in crystal states.

Spectral difference between solution and microcrystalline states

CD spectroscopy is particularly useful to examine structural changes. By the

spectral comparison between solution and crystalline states, we have realized that the

spectral shapes are significantly dissimilar for the compounds, 1 and 3. In the

crystalline states, both depsipeptides have shown single positive (at 193 nm) and

12

double negative (at 208 and 220 nm) bands, which are a typical pattern for helical

structure. On the contrary, in the solution states, we have observed a positive (193

nm) –negative (203 nm) shape for 1 and a weak-negative signal (200 nm) for 3 in n-

BuOH. In the case of 3, the observed spectral differences between both solution and

microcrystalline states have suggested that the helical structure will be loosen when

dissolving the depsipeptide even in n-BuOH, which is known as a helix-promoting

solvent. In the case of a n-BuOH solution of 1, a negative band (at 220 nm) was

disappeared, although the helical property (positive-negative spectrum) is still

remained. One possible explanation is the structural change from α/310 (crystalline)

to 310 (solution). By using CD spectroscopy, many attempts have been done to

distinguish 310- and α-helical conformations.61,77,78 A criterion proposed by

Manning & Woody61 is that 310-helices would have weaker 222-nm bands relative to

their 208-nm bands based on the CNDO/S calculations of N-methylacetamide.

Therefore in our case, the disappearing of the 220-nm band of 1 has suggested a slight

conformational transition occurs in an n-BuOH solution. The structural change is

probably an energetically favorable process where a helical compound accommodates

to the solvent environment from the crystal packing state.

DISCUSSION

Figures 5 and 6 show the side and the top views of 1 and 3 to compare the folding

geometries. The structure of 1 contains both 310 and α helical interactions. The

whole helical chain is not straight and slightly bent at the junction of a peptide and a

depsipeptide segments, Leu3~Lac7. This is significantly different from the

13

conformation of 3, which has a straight α-helical structure with standard φ and ψ

angles.

Here we will discuss three interesting points by the comparison of folding

geometries of 1 and 3: (1) Does ester groups stabilize or destabilize the helical

structure? (2) What makes the α/310 conjugated helical structure? (3) What kind of

force bends (approximately 40˚) the overall helical fold of 1? For the first question,

the answer is both. In the crystal structure of depsipeptides, we have observed

evidences that represent the stabilization and/or destabilization of helices by the ester

groups as discussed below.

The destabilization effect is found in the repulsive interaction between the

ester oxygen, –O–, and the carbonyl oxygen, C=O. The repulsion has been deduced

from the inter-atomic distances observed both in 1 and 3 as shown in Table V. The

distances are in the range of 3.11(1) ~ 3.52(1) Å for [i, i+3] pairs, and 3.61(1) ~

4.19(1) Å for [i, i+4] pairs as shown in Table V. The angles, –O–...O=C, are in the

range of 100.5(2) ~ 111.1(2) ˚ for [i, i+3] pairs, and 114.4(2) ~ 125.9(2) ˚ for [i, i+4]

pairs. The [i, i+3] pairs have shorter O...O distances and smaller angles of O...O=C

than those of the [i, i+4] pairs. If there is no interaction between two oxygen atoms,

the inter-atomic length is expected to be in the range of 2.8-3.1 Å, which is

corresponding to the N...O length in an α-helix. Therefore, the O...O distance values

are significantly greater and clearly suggest the repulsive force between the

electronegative oxygen atoms. The long O...O distances have been found in our

helical depsipeptide, Boc-(Leu-Leu-Ala)2-(Leu-Leu-Lac)3-OEt (4) as listed in Table

V.18 The distance values in 4 are 3.24(2) and 3.30(2) Å for [i, i+3], and 3.80(2) and

3.87(2) Å for [i, i+4] interactions.18 Similar phenomena have been observed in the

compounds,15 Boc-Val-Val-Ala-Leu-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe and Boc-

14

Val-Ala-Leu-Aib-Val-Ala-Leu-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe. In both

helices, the O...O distances of [i, i+3] types are 3.47 and 3.24 Å, respectively. These

of [i, i+4] types are 3.81 and 3.87 Å, respectively.15 Relatively short distance is

found in the crystal structure of Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Ala-

Leu-OMe. In this case, the ester –O– resides in the helix with an –O–...O=C distance

of 3.1 Å.14 Two Aib residues probably prevent the distortion at around the Lac

moiety.

Not only destabilization, the ester group also stabilizes helical structure when

it works as a β-sheet breaker. The formation of sheet or helix for 1 and 3 can be

considered from two governing factors. One is the critical length to stabilize helices

in a solid state. The other is the repulsive force between an ester oxygen, –O–, and a

carbonyl oxygen, C=O. According to the conformational study of oligopeptides,

there is a critical size to fold helices in the solid states.79-88 Under the critical length,

they invariably exist in the sheet-form. For Leu and Ala based sequences, 10~14

residues are at least required to form a helical structure. In the case of

pentadecapeptides, far-IR spectra have detected the transformation from sheet to helix

promoted by shear stress.81 Therefore, the depsipeptides could take either

conformation depending on the chain length.

Anti-parallel β-sheet structure is expected to be very unstable due to the close

contact and the repulsive force between ester groups for the depsipeptides containing

a -(Leu-Leu-Lac)n- sequence. In fact, the X-ray crystal analyses of Boc-Leu-Lac-

OEt and Boc-(Leu-Leu-Lac)n-OEt (n = 1 and 2) have revealed the expelling

interaction between oxygen atoms for their β-sheet arrangements.89

As a result of two governing factors, chain-length and repulsion, helical

conformations are probably chosen for 1 and 3 by nature. Therefore we have

15

concluded that the ester connections can prevent β-sheet formation and thus promote

helix folding.

For the second question, a key to the answer is found in the repulsive

interaction between Leu3(C=O) and Lac7(–O–). To compensate the absence of [i,

i+4] hydrogen bond at the C=O of Leu3, there is a suitable NH at Leu6 closely

located to this C=O. Then there appears the other hydrogen bond by an [i, i+3]

interaction that forms a 310 helical segment between Leu3(C=O) and Leu6(NH).

Following the formation of the 310 helical segment, the readjustment of hydrogen

bonding pattern probably happens throughout the helix. This is the answer to the

second question. The α/310 conjugated conformation is thus the result of

rearrangement from an ideal α-helix by the expelling force between electronegative

oxygen atoms. Similar explanation is also applicable for the formation of 310 type

segments in 4.18 In this case, the repulsive interaction is observed between

Leu6(C=O) and Lac10(–O–). The associative interaction is also found between

Leu6(C=O) and Leu9(NH).

We have not yet clarified the reason why the depsipeptide 3 does not adopt a

α/310-conjugated helix as found in 1. At present we have estimated that the reason is

in the sequence uniformity of 3, which consists of a simple repetition, -Leu-Leu-Lac-

Leu-Leu-. To find out the mechanism of 310-helix formation, we are now continuing

the further study for various depsipeptide sequences.

To the third questions, an answer is found in the repulsive and attractive force

at the C=O of Leu3 as discussed above. This push-and-pull effect hinders folding

into a straight helix. Thus the overall structure of 1 is divided into two helices

centered at Lac7. These domains can be classified as a peptide (Boc1~Leu6) and a

depsipeptide (Lac7~Leu14) fragments. The conjugation of two different segments

16

appears to readjust 1 into the bent-helical conformation. The bent angle between

two helical domains is approximately 140˚. Bent conformation was also found in the

longer sequence, 4.18 In this structure, one [i, i+3] type interaction was found at the

junction of a peptide (Boc1~Leu9) and a depsipeptide (Lac10~Leu14) helices. This

310-helical segment located at the kink undoubtedly comes from the repulsive

interaction between oxygen atoms (Leu5 C=O and Lac9 –O–)18 as shown in Table V.

The structural distortion is expected for the engineered proteins, if an amino-

acid residue is replaced with a corresponding hydroxy-acid residue. For example,

the helix inducing effect by the depsipeptides could prevent aggregation of model

sequences of human amylin.32

α/310-conjugated helices are often observed in various enzymes and proteins

such as in a γ-class carbonic anhydrase,90 a neutrophil gelatinase,91 a ubiquitin-

conjugating enzyme Rad6,91 and a PII-homologue protein GlnK.93 In those cases,

the helices seem to be independent and have no strong interactions with other

domains. Therefore to stabilize the local segments by themselves, the helices

probably choose the α/310-conformation by forming both [i, i+4] and [i, i+3]

interactions and thus maximizing the number of hydrogen bonds in their structure.

CONCLUSION

We have successfully prepared a single crystal of 1 by the segment

condensation between a peptide fragment, Boc-Leu-Leu-Ala-OH, and a depsipeptide

sequence, H-(Leu-Leu-Lac)3-Leu-Leu-OEt. From the crystallographic results, 1

adopts a α/310-conjugated helix with a kink at the junction of peptide and depsipeptide

segments, Leu3~Lac7. The bent structure is derived from the repulsive and the

17

attractive interactions at Leu3 C=O with Lac7 –O– and Leu6 HN, respectively.

Microcrystalline CD spectra were also useful to compare helical properties of 1

(α/310) and 3 (α).

CCDC 236273, 236274, and 236275 contain the supplementary crystallographic data

for 1, 3, and 4, respectively, in this paper. These data can be obtained free of charge

via www.ccdc.cam.ac.uk/data_request/cif, by emailing data_request@ccdc.cam.ac.uk,

or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road,

Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

This research was supported in part by a Grant-in-Aid for Scientific Research on

Priority Areas (HO, No. 15036212 and 16033211, Reaction Control of Dynamic

Complexes) from the Ministry of Education, Culture, Sports, Science and Technology

of Japan.

18

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23

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24

Table I Crystal and Diffraction Parameters of Boc-Leu-Leu-Ala-(Leu-Leu-

Lac)3-Leu-Leu-OEt (1)

Empirical Formula C79H141N11O20

Crystal Color, Habit colorless, needle

Crystal size (mm) 0.70 × 0.10 × 0.10

Formula Weight 1565.04

Crystal system, Space group Monoclinic, P21 (#4)

a (Å) 11.504(6)

b (Å) 20.43(1)

c (Å) 20.726(9)

β (deg) 97.54(1)

Volume (Å3) 4829.3(4)

Z 2

Density (g/cm3) (calcd) 1.076

F(000) 1704.00

µ (Cu-Kα), (cm-1) 6.30

temp, °C -100

2θmax deg 135.7

Measured reflections 39337

Unique reflections 8232 (Rint = 0.057)

R1 a 0.081

wR2 b 0.192

Goodness of fit 0.92

aR1 = (Σ||Fo| - |Fc||) / Σ|Fo|. bwR2 = (Σw||Fo|2 - |Fc|2|2) / Σw(Fo2)2)1/2.

25

Table II Torsion angles (deg.) for Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-

OEt (1)

Angles

Residues φ ψ ω χ χ 1 2

Boc(1) -173.3(8)b

Leu(2) -58(1)c -41(1) -173.4(7) 174.9(8) 62(1)

-174.4(8)

Leu(3) -71(1) -24(1) 171.5(8) -59(1) -57(1)

-179.7(7)

Ala(4) -80(1) -33(1) -179.7(7)

Leu(5) -67(1) -39(1) 178.3(8) -67(1) -71(1)

168.7(9)

Leu(6) -49(1) -41(1)d -177.5(7)e -71(1) -71(1)

162.4(9)

Lac(7) -84.1(9)f -44(1)g -171.4(7)

Leu(8) -76(1) -38(1) 175.9(8) -64(1) -62(1)

171.9(9)

Leu(9) -59(1) -33(1)h -178.2(7)i -65(1) -64(1)

174(1)

Lac(10) -80.9(9)j -37(1)k -179.7(6)

Leu(11) -66(1) -41(1) -179.4(8) 179.7(7) 56(1)

176.9(9)

Leu(12) -59(1) -27(1)l -177.2(7)m -71(1) -72(1)

166.4(9)

Lac(13) -88.2(9)n -18(1)o -176.2(8)

26

Leu(14) -93(1) -35(1) -179.5(9) -68(1) -68(1)

169(1)

Leu(15) -143.2(2) -19.4(2)p -179.2(6)q -73(1) 74(1)

-174(1)

a The torsion angles for rotation about bonds of the peptide backbone (φ, ψ, and ω)

and about bonds of the amino acid side chains (χ1, χ2) are described in Ref. 3.

b O(1)-C’(1)-N(2)-Cα(2). c C’(1)-N(2)-Cα(2)-C’(2). d N(6)-Cα(6)-C’(6)-O(7). e

Cα(6)-C’(6)-O(7)-Cα(7). f C’(6)-O(7)-Cα(7)-C’(7). g O(7)-Cα(7)-C’(7)-N(8). h

N(9)-Cα(9)-C’(9)-O(10). i Cα(9)-C’(9)-O(10)-Cα(10). j C’(9)-O(10)-Cα(10)-

C’(10). k O(10)-Cα(10)-C’(10)-N(11). l N(12)-Cα(12)-C’(12)-O(13). m Cα(12)-

C’(12)-O(13)-Cα(13). n C’(12)-O(13)-Cα(13)-C’(13). o O(13)-Cα(13)-C’(13)-

N(14). p N(15)-Cα(15)-C’(15)-O(16). q Cα(15)-C’(15)-O(16)-C1(16).

27

Table III Comparison of NH---O= geometries (Å, deg.) for Boc-Leu-Leu-Ala-

(Leu-Leu-Lac)3-Leu-Leu-OEt (1)

acceptor

C=O or

–O–

donor

NH

O- - -N H- - -O N–H- -O N–H- -O Type

O12 C=O

(Boc1)

N41

(Ala4)

3.15(1) 2.46 129.8 129.8 i+3

N51

(Leu5)

3.062(9) 2.20 150.9 151.1 i+4

O21 C=O

(Leu2)

N51

(Leu5)

3.15(1) 2.60 117.7 117.9 i+3

N61

(Leu6)

3.019(9) 2.10 161.7 161.6 i+4

O31 C=O

(Leu3)

no pairs

found

O41 C=O

(Ala4)

N81

(Leu8)

2.897(9) 2.04 149.6 150.1 i+4

O51 C=O

(Leu5)

N81

(Leu8)

3.312(9) 2.83 112.2 112.2 i+3

N91

(Leu9)

2.95(1) 2.04 159.7 158.7 i+4

O61 C=O

(Leu6)

no pairs

found

O71 –O–

(Lac7)

N81

(Leu8)

2.830(9) 2.49 101.2 101.4 ester--amide

28

O72 C=O

(Lac7)

N111

(Leu11)

2.924(9) 2.11 143.3 144.0 i+4

O81 C=O

(Leu8)

N111

(Leu11)

3.30(2) 2.80 113.7 113.9 i+3

N121

(Leu12)

2.930(9) 1.99 169.9 169.4 i+4

O91 C=O

(Leu9)

no pairs

found

O101 –O–

(Lac10)

N111

(Leu11)

2.801(9) 2.47 100.5 100.0 ester--amide

O102 C=O

(Lac10)

N141

(Leu14)

3.131(9) 2.46 127.5 126.8 i+4

O111 C=O

(Leu11)

N141

(Leu14)

3.05(1) 2.27 138.8 138.2 i+3

N151

(Leu15)

2.95(1) 2.04 159.8 159.6 i+4

O121 C=O

(Leu12)

no pairs

found

O131 –O–

(Leu13)

N141

(Leu14)

2.70(1) 2.30 45.6 104.0 ester--amide

O132 C=O

(Leu13)

no pairs

found

O141 C=O

(Leu14)

no pairs

found

O151 C=O no pairs

29

(Leu15) found

O161 –O–

(OEt16)

N151

(Leu15)

2.74(1) 2.45 97.9 97.6 ester--amide

* Hydrogen atoms were placed at idealized positions with N–H = 0.95 Å.

30

Table IV Intermolecular hydrogen bonds (Å, deg.) for Boc-Leu-Leu-Ala-

(Leu-Leu-Lac)3-Leu-Leu-OEt (1).

Acceptor (type)

-O-

Donor

NH

O- - -N H- - -O N–H- -O Codea

O132 (main chain) N21 2.88(1) 1.96 160.7 (i)

O141 (main chain) N21 3.32(1) 3.17 90.8 (i)

O141 (main chain) N31 2.87(1) 1.98 156.6 (i)

* Hydrogen bonds were picked up within 3.5Å.

* Hydrogen atoms were placed at idealized positions with N–H = 0.95 Å.

a Symmetrical operators: (i) 1+x, +y, 1+z.

31

Table V Intramolecular O- - -O atomic distances (Å, deg.) for Boc-Leu-Leu-

Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (1), Boc-(Leu-Leu-Lac)3-Leu-Leu-OEt (3),

Boc-(Leu-Leu-Ala)2-(Leu-Leu-Lac)3-OEt (4).

Compound ester –O–

ester or

amide O=C

O- - -O O- - -O=C type

1 O71

(Lac7)

O31

(Leu3)

4.071(9) 123.1(6) i+4

O41

(Ala4)

3.40(1) 104.4(6) i+3

O101

(Lac10)

O61

(Leu6)

4.19(1) 114.4(2) i+4

O72

(Lac7)

3.508(9) 99.1(6) i+3

O131

(Lac13)

O91

(Leu9)

3.63(1) 128.0(8) i+4

O102

(Lac10)

3.150(9) 110.2(6) i+3

2 a O41

(Lac4)

O11

(Boc1)

3.29(2) 117(1) i+3

O71

(Lac7)

O31

(Leu3)

3.47(3) 131(1) i+4

O42

(Lac4)

3.17(2) 103(1) i+3

O101 O61 3.24(3) 141(1) i+4

32

(Lac10) (Leu6)

O72

(Lac7)

3.40(3) 102(1) i+3

5 b O71

(Lac7)

O31

(Leu3)

3.80(2) 146(2) i+4

O41

(Ala4)

3.24(2) 107(2) i+3

O101

(Lac10)

O61

(Leu6)

3.87(2) 108(2) i+4

O72

(Lac7)

3.30(2) 100(2) i+3

O131

(Lac13)

Extended

chain end

* Inter-atomic distances were picked up from the helical segments, not from the chain

ends, such as -OEt.

a Residue numbering scheme for 3: Boc1-Leu2-Leu3-Lac4-Leu5-Leu6-Lac7-Leu8-Leu9-

Lac10-Leu11-Leu12-OEt13.

b Residue numbering scheme for 4: Boc1-Leu2-Leu3-Ala4-Leu5-Leu6-Ala7-Leu8-Leu9-

Lac10-Leu11-Leu12-Lac13-Leu14-Leu15-Lac16-OEt17.

33

34

Figure Captions

Figure 1. Stereo drawing of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (1).

Displacement spheres are drawn at the 20% probability level. Hydrogen atoms

except NHs are omitted for clarity.

Figure 2. A packing view of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (1).

Intermolecular hydrogen bonds are indicated as dotted lines ( |||||||| ).

Figure 3. Solution CD spectra of (a) Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-

OEt (1) and (b) Boc-(Leu-Leu-Lac)3-Leu-Leu-OEt (3). [peptide] = 1 mg / 1 mL at

293 K in n-BuOH (- - - - - - -), TFE (__ __ __) and MeOH (__________).

Figure 4. Microcrystalline CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-

Leu-OEt (1) (__ __ __) and Boc-(Leu-Leu-Lac)3-Leu-Leu-OEt (3) (__________) using

nujol mulls (1 mg / 1 mL) at 293 K.

Figure 5. Helix bending at the junction of peptide and depsipetide segments,

Leu3~Lac7, observed for Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt (1). α-

and 310-Helical interactions are indicated as thin (- - - -) and bold ( |||||||| ) dotted lines,

respectively.

Figure 6. Straight helical structure observed for Boc-(Leu-Leu-Lac)3-Leu-Leu-OEt

(3). α-Helical interactions are indicated as dotted lines (- - - -).

Straight α-HelixBoc1-Leu2-Leu3-Lac4-Leu5-Leu6-Lac7-Leu8-Leu9-

Lac10 Extended Chain End-Lac10-Leu11-Leu12-OEt13

Lac4

Leu9

Boc1

OEt16

Lac7

9

2

34

5

6

7

12

13

10

11

8

1

Figure 6. Oku et al.

Peptide HelixBoc1-Leu2-Leu3-Ala4-Leu5-Leu6-

Depsipeptide Helix-Lac7-(Leu-Leu-Lac)3-Leu14-Lac7

Helix End Capping-Leu15-OEt16

9

2

3

4

56

7 8

10

11

12

13Leu14

Boc1

OEt16

Leu3

1

Lac10

Leu6

Leu5

Leu8

14

1516

Figure 5. Oku et al.

~140 deg.

Figure 4. Oku et al.

0Ellipticity(mdeg)

190 200 210 220 230 240Wavelength (nm)

193

211

219 223

Figure 3. Oku et al.

0

190 200 210 220 230 240Wavelength (nm)

222

215195

203

[θ]R x 10-3

(deg.cm-2.dmol-1)

0[θ]R x 10-3

(deg.cm-2.dmol-1)

10

10

-10

-20

-10

-20

194

199198

190

192 202

(a)

(b)

Figure 2. Oku et al.

a

b co

Figure 1. Oku et al.

Boc1

Leu2

Leu3Ala4

Leu5Leu6

Lac7

Leu8

Leu9

Lac10

Leu11 Leu12

Lac13OEt16

Leu15Leu14