A unique example of a core-modified bis-proline peptide self-assembling into an infinite hydrogen-bonded β-sheet ribbon: Crystal structure of Z-ProNH(CH2)2NHPro-Z

Article abstract of DOI:10.1039/b009532j

The crystal structure of Z-ProNH(CH₂)₂NHPro-Z exhibits an extended backbone, with occurrence of both a cis and a trans conformation preceding the two prolyl residues, that self-assembles into an infinite hydrogen-bonded β-sheet ribbo

Full text of DOI:10.1039/b009532j

A unique example of a core-modified bis-proline peptide self-assembling into
an infinite hydrogen-bonded b-sheet ribbon: crystal structure of
Z-ProNH(CH2)2NHPro-Z
Darshan Ranganathan,*a M. Gopi Kumar,a R. S. K. Kishorea and Isabella L. Karle*b
a Discovery Laboratory, Indian Institute of Chemical Technology, Hyderabad 500 007, India.
E-mail: ranganathan@iict.ap.nic.in
b Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5341, USA
Received (in Columbia, MO, USA) 6th November 2000, Accepted 5th December 2000
First published as an Advance Article on the web 23rd January 2001
The crystal structure of Z-ProNH(CH2)2NHPro-Z exhibits
an extended backbone, with occurrence of both a cis and a
trans conformation preceding the two prolyl residues, that
self-assembles into an infinite hydrogen-bonded b-sheet
ribbon.
a certain degree of conformational constraint in the protein or
peptide backbone causing bends or breaking helices,5 and
consequently proline-containing peptides are generally not
known to display extended structures. We describe herein a
unique example of a core-modified bis-proline peptide that is
preceded by both a cis as well as a trans amide bond in its
framework and self-assembles to form a hydrogen-bonded
infinite b-sheet ribbon in the solid state.
Proline, the only amino acid found in proteins with a secondary
amino group in a five-membered ring, is known to play an
important role in the folding of natural proteins.1 N-Acyl
prolines lacking amide NHs display energetically similar cis-
and trans-isomeric forms2 and both forms are known to occur in
proteins, for example, ribonuclease3 or in bioactive peptides
such as bradykinin.4 Being a cyclic amino acid, proline imposes
The 1,2-ethylenediamine spacer-linked bis-proline 1 [Fig.
1(a)] was prepared6 in a single step by coupling Z-proline with
1,2-diaminoethane using a direct azide coupling (diphenyl
phosphoryl azide) procedure. The bis-Pro peptide 1 was fully
characterized7,8 by spectral and analytical data.
Fig. 1 (a) Molecular formula of 1. (b) X-Ray structure of 1. The numbering is the same for each half except that the letter ‘s’ is added for atoms on one
side.
Fig. 2 (a) Flat ribbon formation by connecting the molecules by two types of hydrogen bonds, N(2)H····O(1) and N(2s)H····O(0). The molecules are repeated
by a vertical two-fold screw axis. (b) Schematic representation of the ribbon assembly of 1. (c) A side view of the ribbon. The dashed lines represent hydrogen
bonds. Both surfaces of the ribbon are largely hydrophobic by virtue of the extended placement of the benzyl moieties and prolyl rings.
DOI: 10.1039/b009532j
Chem. Commun., 2001, 273–274
This journal is © The Royal Society of Chemistry 2001
273

Suitable crystals for X-ray diffraction were obtained from a
mixture of ethyl acetate and hexane. The crystal structure of 1
showed a backbone extended in two sections with a sharp bend
at Pro(1s) [Fig. 1(b)]. Interestingly, the two halves of the
molecule are not symmetric. On one side of the molecule the Z-
The present results demonstrate that appropriate core inserts
can modify the conformational behavior of proline residues in a
peptide.
This work was financially supported by the Department of
Science and Technology, New Delhi, National Institute of
Health (GM-30902), USA, and the Office of Naval Research.
Helpful advice from Professor S. Ranganathan is acknowl-
edged. D. R. is an honorary faculty member of Jawaharlal Nehru
Center for Advanced Scientific Research.
L
-Pro (1) amide bond C0A–N1 has the cis conformation, whereas
on the other side the Z- -Pro (1s) amide bond C0As–N1s has the
L
trans conformation. A similar occurrence of a cis amide bond
preceding a Pro residue had been noted in 1974 for the Boc-Pro
(1) amide bond in Boc-(
-Pro)4-OBzl.9
L
The hydrogen-bonding pattern [Fig.2(a)] in the crystal lattice
showed the formation of an infinite ribbon assembly around a
two-fold screw axis (space group P21). There are only two
independent hydrogen bonds, N(2)H···O(1) and N(2s)H···O(0)
that connect the molecules into ribbons. Fig. 2(b) shows the
schematic picture of the ribbon assembly. A side view of the
ribbon in Fig. 2(c) shows a relatively flat structure. The
protruding phenyl and pyrrolidine rings on either side impart a
hydrophobic surface to the ribbon. Table 1 presents the
hydrogen bond parameters and torsional angles in 1. In solution-
state conformational studies of 1, while 1H NMR (variable
temperature measurements) has shown agreement with the
solid-state structure in exhibiting high dd/dT values ( > 4 ppb
K21) indicating the absence of any intramolecular hydrogen
bonding, the FTIR spectrum in chloroform solution at 297 K
showed two bands in the NH stretch region. The band at ca.
3430 cm21 is assigned to the non hydrogen-bonded NH and the
concentration independent, major band at ca. 3340 cm21 is
attributed to an internally hydrogen-bonded NH, possibly, in a
seven-membered ring.
Notes and References
1 For reviews on protein folding, see: T. E. Creighton, Proc. Natl. Acad.
Sci. USA, 1988, 85, 5082; G. T. Montelione and H. A. Scheraga, Acc.
Chem. Res., 1989, 22, 70; J. King, Chem. Eng. News, 1989, 67, 32; R. L.
Baldwin, Trends Biochem. Sci., 1989, 14, 291; L. M. Gierasch and J.
King, Protein Folding; Deciphering the Second Half of the Genetic
Code, AAAS Pub., Washington D.C., 1990; T. E. Creighton, Biochem.
J., 1990, 270, 1; R. Jaenicke, Biochemistry, 1991, 30, 3147; C. M.
Dobson, A. Sali and M. Karplus, Angew. Chem., Int. Ed., 1998, 37,
868.
2 W. S. Blair and B. L. Semler, Curr. Opin. Cell. Biol., 1991, 3, 1039 and
references therein.
3 P. N. Lewis, F. A. Momany and H. A. Scheraga, Biochim. Biophys.
Acta, 1973, 303, 211.
4 R. E. London, J. M. Stewart, R. Williams, J. R. Cann and N. A.
Matwiyoff, J. Am. Chem. Soc., 1979, 101, 2455.
5 J. L. Crawford, W. N. Lipscomb and C. G. Schollman, Proc. Natl. Acad.
Sci., USA, 1973, 70, 538; P. Y. Chou and G. D. Fasman, Biochemistry,
1974, 13, 222; C. M. Venkatachalam, Biopolymers, 1969, 6, 1425.
6 The NaZ protected proline azide, generated in situ, directly from Z-Pro
(5 mmol) and diphenylphosphoryl azide (DPPA, 5 mmol) in dry
CH2Cl2–DMF (5 mL, 3:2) was admixed with 1,2-diaminoethane (2.5
mmol) and the reaction mixture was left stirred for 8 h at 0 °C and 12 h
at room temp., the solvents evaporated in vacuo, residue mixed with
water (ca. 50mL), extracted with ethyl acetate (2 3 50 mL), organic
extract washed with aq. bicarbonate solution and dried (anhyd. MgSO4).
The residue, after solvent removal in vacuo, was purified on a short
column of silica gel using ethyl acetate–hexane as eluents.
7 Selected data for 1. Yield 80%; mp 158–160 °C; dH (200 MHz CDCl3)
1.80–2.31 (m, 8H), 3.05–3.71 (m, 8H), 4.20 (m, 2H), 5.15 (m, 4H),
6.6–7.0 (br, 2H), 7.35 (br s, 10H); FAB-MS (m/z) 523 (MH)+, 545
(M+Na+).
Table 1 Structural characteristics of 1
(a) Intermolecular hydrogen bonds (Å) and angles (°)
N2…O1a
H2…O1a
N2…O1NC
2.899
2.10
153
N2s…O0b
H2s…O0b
N2s…O0NC
2.877
2.09
152
(b) Selected torsional angles (°)c
C2C1O00C0A
+83 C2sC1sO00sC0As
179 C1sO00sC0AsN1s
+12 O00sC0AsN1sC1as wos 2171
290 C0AsN1sC1asC1As
27 N1sC1asC1AsN2s
+155
yos 2176
C1O00C0AN1
O00C0AN1C1a
C0AN1C1aC1A
N1C1aC1AN2
C1aC1AN2C1m
C1AN2C1mC1ms
N2C1mC1msN2s
yo
wo
f1
f1s
y1s 212
282
8 Crystal data for 1: C28H34N4O6, space group P21, a = 9.992(2), b =
y1
10.251(2), c = 13.325(3), b = 90.25(2)°, V = 1364.9(5) Å3, Dc
=
w1 2173 C1asC1AsN2sC1ms w1s
+92 C1AsN2sC1msC1m
2175
177
1.272 g cm23, Cu-Ka radation, l
refinement on F, R 0.0578 for 1652 data [F > 3.0s(F)]. Data
= 1.54178 Å. Least-squares
299
=
collection at 293 °C. CCDC 182/1884.
9 T. Matsuzaki, Acta Crystallogr., Sect. B, 1974, 30, 1029.
10 IUPAC-IUB Commission on Biochemical Nomenclature, Biochem-
istry, 1970, 9, 3471.
a Symmetry equivalent 2x, 20.5 + y, 1 2 z. b Symmetry equivalent 2x,
+0.5 + y, 1 2 z. c Conventions for labels in ref. 10.
274
Chem. Commun., 2001, 273–274