Design of peptides with α,β-dehydro-residues: Syntheses, crystal structures and molecular conformations of two δPhe-Trp containing peptides

Article abstract of DOI:10.1016/S0022-2860(03)00173-X

The ΔPhe-Trp is a newly designed moiety that was found inducing a unique conformation in peptides. The peptides Boc-L-Val-ΔPhe-L-Trp-OCH₃ (I) and Boc-L-Leu-ΔPhe-L-Trp-OCH₃ (II) were synthesized by azlactone method in solution phase.

Full text of DOI:10.1016/S0022-2860(03)00173-X

Journal of Molecular Structure 654 (2003) 103–110
www.elsevier.com/locate/molstruc
Design of peptides with a,b-dehydro-residues: syntheses, crystal
structures and molecular conformations of two DPhe-Trp
containing peptides
*
R. Vijayaraghavan, J. Makker, P. Kumar, S. Dey, T.P. Singh
Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
Received 10 December 2002; revised 27 February 2003; accepted 27 February 2003
Abstract
The DPhe-Trp is a newly designed moiety that was found inducing a unique conformation in peptides. The peptides Boc-L-
Val-DPhe-L-Trp-OCH3 (I) and Boc-L-Leu-DPhe-L-Trp-OCH3 (II) were synthesized by azlactone method in solution phase.
The peptide (I) was crystallized from its solution in ethanol–water mixture in orthorhombic space group P212121 with
˚
˚
˚
a ¼ 10.663(3) A, b ¼ 11.204(3) A, c ¼ 26.516(10) A and peptide (II) was crystallized from its solution in acetone in a
˚
˚
˚
monoclinic space group P21 with a ¼ 9.354(1)A, b ¼ 11.218(4)A, c ¼ 15.633(1)A and b ¼ 101.83(1)8. The structures were
determined by direct methods. Peptide (I) was refined to an R value of 0.059 for 1554 observed reflections [I $ 2s (I)] and
peptide (II) was refined to an R value of 0.043 for 2920 observed reflections [I $ 2s (I)]. The structures of peptides (I) and (II)
were found to be identical. They formed an unusual type VIa b-turn conformation which is observed for the first time with a
DPhe residue at ði þ 2Þ position indicating a unique influence of DPhe-Trp moiety in inducing a reproducible new structure in
peptides.
q 2003 Elsevier Science B.V. All rights reserved.
Keywords: Peptide design; X-ray diffraction; DPhe-residue; DPhe-Trp moiety; Conformation; Crystal structure
1. Introduction
i.e. 260, 1408; 80, 08; 260, 2308 and their
enantiomers [2]. Furthermore, these values are
associated with a DPhe residue according to its
site of substitution in a peptide i.e. a DPhe residue
at ði þ 1Þ position adopts a conformation with f; c
value of 260, 1408, at ði þ 2Þ position 80, 08 and if
it is repeated twice or more in a peptide with a
sequence of atleast four amino acids, it adopted
a conformation with f; c values of 260, 2308.
Thus a set of rules to design peptides with
dehydro-residues has been reported [1]. In order
to extend the scope of these rules, we had earlier
reported the structure of Boc-Ile-DPhe-Trp-OCH3
a,b-Dehydro-residues have been found to be
strong inducers of specific conformations in pep-
tides. The introduction of dehydro-residues in the
peptide sequences has led to the design of a set of
rules that can be applied to generate required
structures of peptides [1]. It has been shown that
the DPhe residue adopts a conformation corre-
sponding to one of the three sets of torsion angles
*
Corresponding author. Tel.: þ91-11-659-3201; fax: þ91-11-
686-2663.
E-mail address: tps@aiims.aiims.ac.in (T.P. Singh).
0022-2860/03/$ - see front matter q 2003 Elsevier Science B.V. All rights reserved.
doi:10.1016/S0022-2860(03)00173-X

104
R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
[2]. This peptide with f; c torsion angles:
w1 ¼ 90.8(8)8, c1 ¼ 2151.6(6)8, w2 ¼ 89.0(8)8 and
c2 ¼ 15.9(9)8 was found in an uncommon confor-
mation. A large number of structures with DPhe at
ði þ 2Þ position have indicated that a DPhe at ði þ
2Þ position induces a common type II b-turn
conformation with torsion angles centred around
w1 < 2 608, c1 < 1408, w22 < 808 and c2 < 08. In
order to establish the reproducibility of formation
of the uncommon conformation in peptides with
DPhe-Trp moiety as indicated by Boc-L-Ile-DPhe-
L-Trp-OCH3 [2], we have synthesized two peptides
(I) Boc-L-Val-DPhe-L-Trp-OCH3 and (II) Boc-L-
Leu-DPhe-L-Trp-OCH3 by varying the residue at
ði þ 1Þ position and keeping the DPhe-Trp-OCH3
moiety unaltered. The detailed syntheses, crystal
structures and molecular conformations of peptides
(I) and (II) are reported here.
2. Experimental
In order to synthesize the peptides Boc-L-Val-
DPhe-L-Trp-OCH3(I) and Boc-L-Leu-DPhe-L-Trp-
OCH3 (II) the following steps were used:
Table 1
The details of crystal data intensity data collection and refinement
Peptide (I)
Peptide (II)
2.1. Synthesis of Boc-Val-(b-OH)-Phe-OH (1)
Molecular
formula
C31H38N4O6
562.66
C32H40N4O6
576.69
To a precooled solution (10 8C) of Boc-L-Val-OH
(3 g, 13.8 mmol) in dry tetrahydrofuran (THF)
(10 ml), N-methylmorpholine (NMM) (1.51 ml,
13.8 mmol) and isobutylchloroformate (IBCF)
(1.79 ml, 13.8 mmol) were added. After 15 min of
stirring a solution of DL-(b-OH)-Phe-OH (3.0 g,
16.5 mmol) in 1N NaOH (16.5 ml) was added to it
and the mixture was stirred at 0 8C. The resulting oily
compound had the yield ¼ 4.6 g (68%), Rf ¼ 0.45
(CHCl3: MeOH: 9:1).
Molecular
weight
Crystal system
Space
Orthorhombic Monoclinic
P212121
P21
group
˚
a (A)
˚
b/A
10.663(3)
9.354(1)
11.218(4)
15.633(1)
101.83(1)
2
11.204(3)
˚
c (A)
26.516(10)
b (8)
Z
–
4
(molecules/unit cell)
dc (gcm23
)
1.17
1.19
Fð000Þ
1200
Cu Ka
616
Radiation
Cu Ka
2.2. Boc-L-Val-DPhe azlactone (2)
˚
˚
(l ¼ 1.5418 A) (l ¼ 1.5418 A)
Total no. of
2302
3424
Compound (1) (4.6 g, 12.1 mmol) was reacted with
anhydrous sodium acetate (1.0 g, 12.1 mmol) and
freshly distilled acetic anhydride (10 ml) for 96 h at
room temperature. The yield was: 3.5 g (74%),
Rf ¼ 0.97 (CHCl3: MeOH:: 9:1).
independent
reflections
No of observed
reflections ðI $ 2sðIÞÞ
1554
2920
Crystal dimensions (mm3) 1.5 £ 0.2 £ 0.1 1.6 £ 0.4 £ 0.3
mr
Instrument used
0.66
0.67
Enraf-Nonius
CAD4
Enraf-Nonius
CAD4
2.3. Boc-L-Val-DPhe-L-Trp-OCH3 (I)
Mode of data
v 2 2u
v 2 2u
collection
Maximum 2u (8)
R
110
140
To a solution of compound (2) (1.0 g, 3.0 mmol) in
dichloromethane (DCM), Trp-OCH3.HCl (0.91 g.
3.6 mmol) neutralized by adding triethylamine
(TEA) (0.5 ml, 3.6 mmol) and the solution was
stirred for 200 h at room temperature. The yield of
peptide (I) was: 0.98 g (72%), Rf ¼ 0.58 (CHCl3:
MeOH:: 9:1).
0.059
0.059
Unit
0.043
0.049
Rw
W
ðs2ðFÞþ
1.0963/
)
0:000768F2
weight
1.61
S (goodness
of fit)
1.50
T (8K)
293
293

R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
105
Table 2a
characteristics peaks were observed: d 8.4 (s, 1H, NH
DPhe); d 7.5 (d, 1H, NH Trp); d 7.0–7.4 (m, 12H, DPhe
Ar, Olefinic and indole); d 6.7 (d, 1H, NH Urethane); d
5.0(q,1H,CaVal);d4.04(q,1H,CaTrp);d3.7(s,3H, –
OCH3); d 3.4 (m, 2H, CbTrp); d 2.1 (m, 1H, CbVal); d
Atomic coordinates ( £ 104) and equivalent isotropic thermal
parameters ( £ 103) of the peptide (I) (estimated standard deviations
are given in parentheses)
2
Ueq (A )
˚
Atoms
x
y
z
C0
21677(9)
5316(8)
6041(9)
4016(8)
3682(3)
4102(4)
3788(4)
3581(4)
3201(2)
3134(4)
3454(3)
2657(3)
2502(3)
1962(4)
1938(4)
1569(3)
2554(3)
2528(2)
2635(2)
2721(3)
3185(4)
3689(3)
3793(4)
4103(4)
4276(4)
4581(5)
4671(4)
2282(4)
2298(2)
1844(3)
1398(4)
1445(4)
1526(3)
1974(4)
1898(3)
1150(4)
1406(4)
636(4)
59(3)
91(4)
112(6)
91(4)
55(2)
57(3)
103(3)
50(2)
47(3)
66(4)
103(5)
87(4)
40(3)
57(2)
45(2)
46(3)
50(3)
55(3)
68(4)
79(4)
85(4)
99(5)
99(5)
52(3)
66(2)
53(2)
63(3)
65(4)
49(3)
53(3)
60(3)
64(4)
55(3)
78(4)
101(5)
96(6)
81(4)
80(5)
96(3)
110(4)
163(9)
Table 2b
C01
C02
C03
O0
C00
O00
21129(10)
21591(5)
23012(8)
21059(6)
157(9)
Atomic coordinates ( £ 104) and equivalent isotropic thermal
parameters ( £ 103) for peptide (II) (estimated standard deviations
are given in parentheses)
5663(11)
5594(5)
5407(8)
5102(8)
5609(6)
5534(7)
5043(8)
3741(8)
5783(9)
6726(7)
7653(5)
6611(6)
7650(7)
8040(7)
7593(8)
6554(8)
8272(9)
6223(10)
7885(12)
6865(12)
8255(8)
9260(5)
7653(6)
8001(8)
7870(8)
6605(8)
6006(9)
4866(6)
5799(7)
4720(8)
5860(11)
3745(9)
3830(6)
4890(8)
7236(11)
6383(7)
7645(7)
6955(7)
2
eq (A )
˚
Atoms
x
y
z
U
879(7)
N1
C1a
480(6)
C0
0891(5)
1696(9)
6449(0)
7627(8)
0460(3)
0490(4)
456(1)
728(2)
823(2)
641(1)
477(8)
361(1)
484(8)
374(9)
314(1)
360(1)
436(1)
758(2)
715(2)
312(9)
533(9)
316(8)
335(1)
393(1)
428(1)
492(1)
563(1)
717(2)
563(1)
645(2)
377(1)
506(1)
367(9)
402(1)
455(1)
408(1)
438(1)
603(1)
817(3)
863(3)
741(2)
557(1)
408(1)
501(1)
456(1)
582(1)
654(1)
453(3)
1772(7)
1918(1)
1452(11)
1253(10)
2444(8)
1897(6)
3681(6)
4425(8)
4706(8)
4407(9)
3724(9)
4809(11)
3505(11)
4573(14)
3905(13)
4954(8)
5423(6)
4908(7)
5558(10)
6966(9)
7392(8)
7402(8)
7825(7)
7829(9)
8080(8)
8050(9)
8538(10)
8749(8)
8508(11)
5010(9)
4386(8)
5417(9)
5061(6)
C1b
Cg11
Cg12
C10
C01
C02
C03
O0
C00
O00
20509(6)
1839(7)
0411(3)
1389(4)
2696(3)
0719(4)
1587(4)
0587(5)
20453(5)
0347(7)
21375(6)
2568(4)
2087(3)
3954(3)
4896(4)
5893(4)
6365(4)
5879(5)
6395(6)
7882(6)
7388(5)
7391(7)
4763(4)
5273(3)
4083(4)
3966(5)
5424(5)
5935(4)
5741(4)
5162(6)
5169(7)
5721(8)
6287(7)
6316(5)
6830(5)
6600(5)
2764(6)
2273(4)
2357(5)
1228(11)
6438(11)
5413(8)
6242(6)
6176(7)
6280(6)
5991(6)
5858(6)
5679(7)
6700(8)
7854(8)
6346(9)
4764(6)
3793(6)
4928(6)
3926(6)
3530(7)
3978(7)
5044(7)
5387(8)
3669(9)
3303(8)
4719(9)
3304(6)
2296(6)
3912(6)
3498(7)
3597(7)
4862(7)
5595(7)
5428(9)
6418(12)
7528(11)
7691(8)
6732(7)
6659(7)
5549(7)
4216(8)
5118(7)
3689(7)
4314(15)
20207(3)
0292(4)
1282(2)
2038(3)
2127(2)
2710(2)
3587(2)
4240(3)
4314(3)
4558(4)
4985(4)
3658(3)
3391(2)
4099(2)
4335(3)
3899(3)
3124(3)
2696(3)
1966(3)
2070(4)
2801(3)
1646(4)
5154(3)
5340(2)
5691(2)
6556(3)
7221(3)
7395(3)
8100(3)
8850(4)
9401(5)
9226(6)
8501(6)
7950(4)
7207(3)
6883(4)
6827(3)
6486(2)
7507(2)
7841(6)
O10
N2
C2a
C2b
C2g
N1
C1a
C1b
C1g
Cd22
Cd21
Ce22
Ce21
C2h
C20
Cd11
Cd12
C10
O10
N2
C2a
C2b
C2g
O20
N3
C3a
C3b
C3g
Cd21
Ce21
Ce22
Cd22
C2h
C20
Cd31
Ne31
Cd32
Ce32
Ce33
Cj32
C3v
Cj33
C30
O20
N3
1145(5)
654(5)
C3a
C3b
C3g
380(4)
969(4)
Cd31
Ce33
Cj33
C3h
Cj32
Ce32
Ne31
Cd32
C30
O30
1032(3)
530(3)
O4
C4
96(4)
2.4. H-NMR Spectra of Boc-L-Val-DPhe-L-Trp-OCH3
(I)
O30
Inordertoconfirmthesynthesisofthepeptide(I)1H-
NMRspectraofthepeptidewasobtainedinCDCl3 with
400 MHz Bruker DRX 400 instrument. The following
O4
C4

106
R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
Fig. 1. Boc-Val-DPhe-Trp-OCH3 (a) and Boc-Ile-DPhe-Trp-OCH3 (b)
1.5 (s, 9H, Boc); d 0.95 (d, 3H, Cg1Val); d 0.82 (d, 3H,
Cg2Val); d 0.82 (d, 3H, Cg2Val). The assignments of
peaks as described above clearly indicated the correct
synthesis of the required peptide.
stirred at 0 8C. The yield was 2.5 g (63%), Rf ¼ 0.42
(CHCl3: MeOH:: 9:1).
2.6. Boc-L-Leu-DPhe Azlactone (4)
Compound (3) (2.5 g, 6.3 mmol) was reacted with
anhydrous sodium acetate (0.52 g, 6.3 mmol) and
freshly distilled acetic anhydride (10 ml) for 96 h at
room temperature. The yield was 1.90 g (80%),
Rf ¼ 0. (CHCl3: MeOH:: 9:1).
2.5. Synthesis of Boc-L-Leu-(b-OH)-Phe-OH (3)
To a precooled solution (10 8C) of Boc-L-Leu-OH
(2 g, 8.6 mmol) in dry tetrahydrofuran (THF) (10 ml),
N-methylmorpholine (NMM) (1.51 ml, 13.8 mmol)
and isobutylchloroformate (IBCF) (0.95 ml,
0.6 mmol) were added. After 15 min of stirring a
solution of DL-(b-OH)-Phe-OH (1.87 g, 10.3 mmol)
in 1N NaOH (10.3 ml) was added and the mixture was
2.7. Boc-L-Leu-DPhe-L-Trp-OCH3 (II)
To a solution of compound (4) (1.15 g, 3.1 mmol)
in dichloromethane (DCM), Trp-OCH3.HCl (0.94 g.

R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
107
Table 3
DRX 400 instrument. The observed proton peaks
were assigned as follows: d 7.0–7.6 (m, 11H, Ar
DPhe, indole); d 7.0 (s, 1H, DPhe olefinic); d 8.4 (bs,
1H, NH, DPhe); d 6.9 (bd, 1H, NH Trp); d 5.0 (q, 1H,
CaTrp); d 4.9 (bd, NH Urethane); d 4.2 (q, Ca Leu); d
3.6 (s, 3H, –OMe); d 3.4 (d, 2H, CbTrp); d 1.4 (s, 9H,
t-Bu); d 1.2 (m, 4H, Cb and Cg Leu); d 0.9 (d, 6H,
CdLeu). The unambiguous assignments of peaks
confirmed the right sequence of the peptide (II).
Torsion angles (8) with estimated standard deviations in parenth-
eses)
Peptide (I)
Peptide (II)
u0
v0
C0–O0–C00 –N1
O0–C00 –N1–Ca1
C00 –N1–Ca1 –C10
N1–Ca1 –C10 –N2
N1–Ca1 –Cb1 –Cg1
N1–Ca1 –Cb1 –Cg11
N1–Ca1 –Cb1 –Cg12
Ca1 –Cb1 –Cg1 –Cd11
Ca1 –Cb1 –Cg1 –Cd12
Ca1 –C10 –N2–Ca2
C10 –N2–Ca2 –C20
N2–Ca2 –C20 –N3
N2–Ca2 –Cb2 –Cg2
Ca2 –Cb2 –Cg2 –Cd22
Ca2 –Cb2 –Cg2 –Cd21
Ca2 –C20 –N3–Ca3
C20 –N3–Ca3 –C30
N3–Ca3 –C30 –O4
N3–Ca3 –Cb3 –Cg3
C30 –Ca3 –Cb3 –Cg3
Ca3 –Cb3 –Cg3 –Cd31
Ca3 –Cb3 –Cg3 –Cd32
173.7(7)
176.1(7)
289.9(9)
152.0(6)
–
179.6(4)
178.3(4)
262.9(6)
135.9(5)
261.8(6)
–
f1
C1
x1
x11;1
x11;2
x21;1
x21;2
v1
264.7(9)
59.2(9)
–
2.9. Structure determination
–
257.5(7)
179.0(5)
169.2(5)
283.8(6)
216.9(7)
3.0(10)
–
2176.4(7)
288.3(9)
213.0(10)
1.0(11)
The peptide Boc-Val-DPhe-Trp-OCH3 (I) was
crystallized from its saturated solution in ethanol–
water mixture while the peptide Boc-Leu-DPhe-Trp-
OCH3 (II) gave diffractable crystals from its saturated
solution in acetone. The detailed crystal data are given
in Table 1. The structures were determined by direct
methods using the program SHELX 86 [3]. The
coordinates of non-hydrogen atoms were refined
anisotropically using the program SHELX 76 [4].
The positions of hydrogen atoms were obtained from
difference Fourier maps and were included in the final
cycles of refinements using isotropic thermal par-
ameters of the non-hydrogen atoms to which they
f2
C2
x21
x22;2
x22;1
v2
2.0(11)
2176.2(5)
5.3(1)
2177.0(11)
2168.9(8)
2167.6(9)
169.7(9)
63.0(11)
257.0(10)
97.0(10)
281.0(10)
2174.2(5)
2163.0(5)
164.8(5)
64.6(6)
f3
T
C
3
x3
1
x
3
256.0(7)
97.2(7)
2;1
3
x
2;2
x
278.8(8)
3
3.7 mmol) neutralized by adding triethylamine (TEA)
(0.5 ml, 3.7 mmol) and the solution was stirred
for 200 h at room temperature. The yield of
peptide (II) was 0.95 g (72%) Rf ¼ 0.58 (CHCl3:
MeOH:: 9:1).
were attached. During the refinement the function
minimized was
P
wðlFobsl 2 lFcallÞ where the
weights were w ¼ 1:0 for peptide (I) and w ¼
1:0963=ðs2ðFÞ þ 0:000768lFl2Þ for peptide (II). The
final R factors for observed reflections 1554 in (I) and
2920 in (II) were 0.059 and 0.043, respectively. The
atomic scattering factors used in these calculations
were those of Cromer and Mann [5] for non-hydrogen
atoms and of Stewart, Davidson and Simpson [6] for
hydrogen atoms. The atomic coordinates for peptides
(I) and (II) are listed in Tables 2a and 2b, respectively.
The solvent molecules were not observed in these
2.8. H-NMR Spectra of Boc-L-Leu-DPhe-L-Trp-
OCH3
In order to ascertain the correctness of the
1
sequence of the peptide a H-NMR spectra of the
peptide was observed in CDCl3 with 400 MHz Bruker
Table 4
The f; c torsion angles (8) in sequences containing DPhe-Trp element: (I) Boc-L-Val-DPhe-L-Trp-OCH3 (II) Boc-L-Leu-DPhe-L-Trp-OCH3
and (III) Boc-L-Ile-DPhe-L-Trp-OCH3
Peptides
f1
c1
f2
c2
f3
c3
Ref
(I)
289.9(9)
262.9(6)
290.8
152.0(6)
135.9(5)
151.6(6)
288.3(9)
283.8(6)
289.0(8)
213.0(10)
216.9(7)
215.5(5)
2167.6(9)
2163.0(5)
2167.7(7)
169.7(9)
164.8(5)
166.0(7)
Present study
Present study
2
(II)
(III)

108
R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
Fig. 2.
Table 5a
Hydrogen bonds for peptide (I) and peptide (II) with estimated standard deviations in parentheses
˚
Lengths (A)
˚
Angle (A) /N–H· · ·O
Type
H bond
Symmetry
Peptide (I)
Intermolecular
N2 2 H2· · ·O02
Ne31 2 He3l· · ·O01
N3 2 H3· · ·O03
2.830(9)
2.944(9)
2.648(10)
170.9(7)
159.8(8)
107.4(7)
2x þ 1; y 2 1=2-z þ 1=2
2x þ 1; y 2 1=2; 2z þ 1=2
x; y; z
Intermolecular
Intramolecular (intra-residue)
Peptide (II)
Intermolecular
N3 2 H2· · ·O02
Ne31 2 He3l· · ·O01
N3 2 H3· · ·O03
2.844(9)
2.832(9)
2.665(7)
169.7(4)
166.1(6)
106.3(4)
2x þ 1; y 2 1=2; 2z þ 1=2
2x þ 1; y 2 1=2; 2z þ 1=2
x; y; z
Intermolecular
Intramolecular (intra-residue)

R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
109
Table 5b
˚
The van der Waals interactions with distances #3.5 (A) between pairs of symmetry related atoms for peptides (I) and (II)
˚
Distances (A)
˚
Distances (A)
van der Waals pairs in peptide I
van der Waals pairs in peptide II
C
03· · ·Cg2 (3)
3.544(16)
3.415(12)
3.375(9)
C02· · ·Cz32 (1)
O0· · ·Ch2 (3)
O00 · · ·Cb2 (4)
N1· · ·Ch2 (3)
Ca1· · ·O20 (4)
Cb2· · ·Ne3l (2)
Cg2· · ·Cz32 (2)
Ch2· · ·O0 (5)
Ch2· · ·N1 (5)
O20 · · ·Ca1 (2)
Cb3· · ·O00 (2)
Cz32· · ·C20 (6)
Cz32· · ·Cg2 (4)
Ne31· · ·Cb2 (4)
3.547(8)
3.446(7)
3.186(7)
3.512(6)
3.468(5)
3.481(6)
3.482(6)
3.446(7)
3.512(6)
3.468(5)
3.186(7)
3.472(8)
3.482(6)
3.481(6)
O00 · · ·Cb3 (2)
Ca1· · ·O20 (2)
Cb2· · ·Ne3l (1)
Cg2· · ·C03 (3)
Cg2· · ·Cz32 (1)
Cd22· · ·Cz32 (1)
O20 · · ·Ca1 (1)
Cb1· · ·O00 (1)
Ne31· · ·Cb2 (2)
Cz32· · ·Cg2 (2)
Cz32· · ·Cd22 (2)
3.419(11)
3.544(17)
3.439 (14)
3.458(14)
3.375(9)
3.415(12)
3.419(11)
3.438(14)
3.458(14)
Peptide I: (1) 2x þ 1; y þ 1=2; 2z þ 1=2; (2) 2x þ 1; y 2 1=2; 2z þ 1=2; (3) x þ 1; y; z: Peptide II: (1) x 2 1; y; z 2 1; (2) 2x þ 1; y 2 1=2;
2z þ 1; (3) x 2 1; y; z; (4) 2x þ 1; y þ 1=2; 2z þ 1 (5) x þ 1; y; z; (6) x þ 1; y; z þ 11:
structures and hence the interactions of peptides with
solvent molecules were not determined.
3.2. Conformation of the peptides
The torsion angles that define the conformations of
the two peptides are listed in Table 3. The backbone
torsion angles: w1 ¼ 289.9(9)8, c1 ¼ 152.0(6)8,
w2 ¼ 288.3(9)8, c2 ¼ 213.0(10)8, w3 ¼ 2167.6(9)8,
cT2 ¼ 169.7(9)8 in peptide (I) and w1 ¼ 262.9(6)8,
c1 ¼ 135.9(5)8, w2 ¼ 283.8(6)8, c2 ¼ 216.9(7)8,
w3 ¼ 2163.0(5)8, cT2 ¼ 164.8(5)8 in peptide (II) are
identical and clearly indicate the formation of an
unusual type VIa b-turn conformation [7]. This has
been observed for the first time with a DPhe residue.
The structure of a peptide Boc-L-Ile-DPhe-L-Trp-
OCH3 reported earlier also showed the formation of a
similar conformation (Table 4). Although, three
peptides listed in Table 4 have different residues at
ði þ 1Þ position yet they adopt identical confor-
mations. The common moiety in all of them is
DPhe-Trp. Thus it can be termed as the inducer of the
observed similar conformations in these peptides.
Therefore, an unusual type VIa b-turn conformation
can be generated by substituting a DPhe at ði þ 2Þ and
Trp at ði þ 3Þ positions. This is a new rule for peptide
design with DPhe residue.
3. Results and discussion
The stereoviews of peptides (I) and (II) are shown
in Fig. 1a and b, respectively. The conformations of
both peptides are similar. These structures are
characterized by an unusual type VIa b-turn confor-
mation which is observed for the first time with a
DPhe residue at ði þ 2Þ position indicating the
significance of a new element DPhe-Trp in these
peptides.
3.1. Molecular dimensions
The CyC double bond of DPhe in the two peptides
has the trans configuration of the phenyl group with
respect to the carbonyl group. The CyC bond lengths
˚
˚
of 1.34(1) A in peptide (I) and 1.33(7) A in peptide
(II) correspond to the typical value for a styrenic
double bond conjugated with an aromatic ring. The
values of bond angles Ca2 –C2b–C2g in DPhe of the two
peptides are 132(2) and 131(5)8, respectively. The
large deviations of these angles from 1208 of a
trigonal arrangement are notable features caused by
steric constraints in a flattened DPhe residue and have
been observed invariably [1].
3.3. Molecular packing and hydrogen bonding
The molecular packing in the crystals of peptides
(I) and (II) are illustrated in Fig. 2a and b,

110
R. Vijayaraghavan et al. / Journal of Molecular Structure 654 (2003) 103–110
respectively. As seen from Table 5a, the molecules in
the two structures are linked by intermolecular
hydrogen bonds involving NH of DPhe and its
carbonyl oxygen of a symmetry related molecule.
The other intermolecular hydrogen bond involves Ne1
of Trp residue as a donor and carbonyl oxygen of a
symmetry related Val residue in peptide (I) and
symmetry related Leu residue in peptide (II) as
acceptors. The packing of the molecules in these
peptides are further stabilized by van der Waals
forces (Table 5b) involving hydrophobic groups
(Fig. 2a and b).
residue at ði þ 3Þ position induces an unusual
type VIa b-turn conformation. This is a new
design rule with a DPhe at ði þ 2Þ position and
is a valuable addition to the already existing
design rules with dehydro-residues that can be
exploited to provide specific structures for useful
applications.
Acknowledgements
The authors thank Council of Scientific and
Industrial Research (CSIR), New Delhi for financial
support.
4. Conclusions
The peptide design rules with a DPhe residue at
ði þ 2Þ position are summarized below:
References
[1] T.P. Singh, P. Kaur, Prog. Biophys. Mol. Biol. 66 (1996)
141.
1. The DPhe residue has been found to adopt one out
of the three conformations belonging to the
following three sets of f; c torsion angles, 260,
1408; 80, 08 and 60, 2308 or their enantiomers [1].
2. A peptide with a DPhe residue at ði þ 2Þ position
prefers a type II b-turn conformation [1].
3. A peptide with a DPhe residue at ði þ 2Þ
position and a branched b-carbon residue (Val) at
ði þ 3Þ position adopts a distorted b-turn II
conformation [8].
[2] R. Vijayaraghavan, P. Kumar, S. Dey, T.P. Singh, J. Pep. Res.
52 (1998) 89.
[3] G.M. Shedrick, SHELX 86, A Program for the Determination of
Crystal Structures, Anorganisch-Chemisches Institut der Uni-
¨ ¨
versitat, Gottingen, Germany, 1986
[4] G.M. Shedrick, SHELX 76, A Program for the Determination of
Crystal Structures, Anorganisch-Chemisches Institut der Uni-
¨ ¨
versitat, Gottingen, Germany, 1976
[5] D.T. Cromer, J.B. Mann, Acta Crystallogr. A24 (1968) 321.
[6] R.F. Stewart, E.R. Davidson, W.T. Simpson, J. Chem. Phys. 42
(1965) 3175.
4. A peptide having a DPhe residue at ði þ 2Þ
position with branched b-carbon residues on its
both sides, adopts a characteristic unfolded S-
shaped conformation with the values of f; c
torsion angles in which their signs change
alternately [9,10].
[7] J.S. Richardson, Adv. Protein Chem. 34 (1981) 167.
[8] (a) T.P. Singh, M. Haridas, V.S. Chauhan, A. Kumar, D.
Viterbo, Biopolymers 26 (1987) 816. (b) T.P. Singh, M.
Haridas, V.S. Chauhan, A. Kumar, D. Viterbo, Biopolymers 27
(1987) 1333.
[9] S.N. Mitra, S. Dey, S. Bhatia, T.P. Singh, Int. J. Biol. Marcol.
19 (1996) 103.
5. As observed in the present case, a peptide with
a DPhe residue at ði þ 2Þ position and a Trp
[10] S. Dey, S.N. Mitra, T.P. Singh, Int. J. Peptide Protein Res. 48
(1996) 123.