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Conformational Preferences of Heterochiral Peptides.
Crystal Structures of Heterochiral Peptides Boc-(D) Val-
(D) Ala-Leu-Ala-OMe and Boc-Val-Ala-Leu-(D) Ala-OMe-
Enhanced Stability of β-sheet Through C-H…O Hydrogen
Bonds
G. Felcy. Fabiola a , Vivek Bobde b , L. Damodharan a , Vasantha Pattabhi a & S. Durani b
a Departrment of Crystallography and Biophysics , University of Madras , Chennai , 600 025 ,
India
b Department of Chemistry and Biotechnology , Indian Institute of Technology , Mumbai , 400
076 , India
Published online: 15 May 2012.
To cite this article: G. Felcy. Fabiola , Vivek Bobde , L. Damodharan , Vasantha Pattabhi & S. Durani (2001) Conformational
Preferences of Heterochiral Peptides. Crystal Structures of Heterochiral Peptides Boc-(D) Val-(D) Ala-Leu-Ala-OMe and Boc-
Val-Ala-Leu-(D) Ala-OMe-Enhanced Stability of β-sheet Through C-H…O Hydrogen Bonds, Journal of Biomolecular Structure and
Dynamics, 18:4, 579-594, DOI: 10.1080/07391102.2001.10506690
To link to this article: http://dx.doi.org/10.1080/07391102.2001.10506690
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Journal of Biomolecular Structure &
Dynamics, ISSN 0739-1102
Volume 18, Issue Number 4, (2001)
©Adenine Press (2001)
G. Felcy Fabiola1,
Vivek Bobde2,
L. Damodharan1,
Vasantha Pattabhi1*
and S. Durani2
Conformational Preferences of Heterochiral Peptides.
Crystal Structures of Heterochiral Peptides
Boc–(D) Val–(D) Ala–Leu–Ala–OMe and
Boc–Val–Ala–Leu–(D) Ala–OMe– Enhanced Stability
of β-sheet Through C-H...O Hydrogen Bonds
1Departrment of Crystallography
and Biophysics,
http://www.adeninepress.com
University of Madras,
Chennai – 600 025, India
2Department of Chemistry
and Biotechnology,
Abstract
The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-
(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P212121 with
a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)Å, V = 5884 (3) Å3, Z = 8, R = 0.086. VALa
crystallises in space group P21 with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) Å, β = 95.84
(8)°, V = 3040(4) Å3, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in
antiparallel β-sheet arrangement in both the structures. Several of the Cα hydrogens are in
hydrogen bonding contact with the carbonyl oxygen in the adjacent strand.
Indian Institute of Technology,
Mumbai – 400 076, India
An analysis of the observed conformational feature of D-chiral amino acid residues in
oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of
CSD has been carried out. This shows that all the residues except D-isoleucine prefer both
extended and αL conformation though the frequence of occurence may not be equal. In addi-
tion to this, D-leucine, valine, proline and phenylalanine have assumed αR conformations in
solid state. D-leucine has a strong preference for helical conformation in linear peptides
whereas they prefer an extended conformation in cyclic peptides.
Introduction
The L chiral nature of all asymmetric α-amino acids remains the fundamental con-
sideration in protein folding process, determining its structural as well as energetic
outcome. The underlying principles have, however, been difficult to decipher,
given the complexity of globular proteins. As a possible approach to this essential-
ly stereochemical problem, model peptides could be examined for effects of site
specific chiral inversions. Critical comparisons between diastereomers of identical
covalent structure but different chiralities at specific loci have the potential to illu-
minate peptide chain folding process for underlying stereochemical principles.
As functionally useful molecules, peptides with D and L chiral residues evoke con-
siderable interest. Chiral substitutions in bioactive peptides often produce diastere-
omers with remarkably modified pharmocological properties. Peptides of micro-
bial origin often feature multiple L and D residues, and many are useful antibiotic
drugs. There is therefore much interest to understand how the conformation of a
short peptide is affected when its residue chiralities are selectively inverted.
*Phone: 91 044 230 0122;
Fax: 91 044 235 2494;
E-mail: pvasantha@hotmail.com
Further, a systematic structural study of sequentially related oligopeptides is of
great significance for the elucidation of structure – function relationships of pep-
tides and in exploring possible conformations of polypeptide chains. Several
579

tetrapeptides have been synthesised with D-residues at different positions. The aim
is to study systematically the change in the conformation of short peptides in the
presence of D-residues.
580
Fabiola et al.
The crystal structures of Boc–(D) Val–(D) Ala–Leu–Ala–OMe (hereafter referred
as vaLA) and Boc–Val–Ala–Leu–(D) Ala–OMe (referred as VALa) were taken as
a continuing series of investigations of a number of linear peptides. In this line of
investigation, crystal structures of
i. Boc–(D) Val–Ala–Leu–Ala–OMe (vALA)
ii. Boc–Val–(D) Ala–Leu–Ala–OMe (VaLA)
[1]
[2]
have already been determined by our group. The packing motifs observed in the
crystal structures of short acyclic peptides have resulted in either parallel or
antiparallel β-sheet conformation. It was therefore of interest to attempt to crys-
tallise the peptides vaLA and VALa.
Experimental Procedures
The crystal data for vaLA and VALa are given in Table I. The structures of vaLA
and VALa were obtained by direct method using SHELXS-97 (3) and SHELXS-86
(4) respectively. Repeated attempts to solve vaLA structure using SHELXS-86
failed. However, the structure was solved using SHELXL-97 in automatic mode.
Because of the large number of parameters involved in the refinement, the two
independent molecules were refined in separate blocks. Each of these blocks were
refined in alternate cycles by “blocked full matrix” least-square refinement. Bond
length and angle constraints were applied to the terminal groups such as Boc, Leu
etc. During the course of refinement, the atoms C4A in Molecule A and C8′ in
Molecule B of vaLA and C1A, N2, C2A and N4 in Molecule A and C6A, C6B,
C7A and C7D2 in Molecule B of VALa showed high non-positive definite temper-
ature factors. Hence they were included in subsequent refinement with isotropic
temperature factors. The refinement was terminated when the maximum shift in
any parameter was less than 0.1σ. The final R-factor was 0.08 (RW = 0.2217) for
1031 observed reflections, with I ≥ 2 σ(I) 0.128 for vaLA and (RW = 0.3148) for
1162 observed reflections, with I ≥ 2 σ(I) for VALa.
Results and Discussion
The tetra peptides vaLA and VALa crystallize with two molecules in an asymmet-
ric unit. The two molecules in the asymmetric unit are designated as A and B.
The torsional angles for vaLA and VALa are listed in Tables II and IV. The hydro-
gen bond parameters for vaLA and VALa are given in Tables III and V. The posi-
tional parameters of non-hydrogen atoms and the observed bond lengths, bond
angles of vaLA and VALa are deposited in CSD (CODE: 153721 & 154115).
The observed geometry of the Boc moiety in the two molecules is very similar to
what has been reported earlier (6). The conformation of the Boc group characterised
by two torsion angles ω0 [C1A -N1 –C6 –O5] and θ0 [N1 –C6 –O5 –C4] is trans-
trans in both vaLA and VALa. The torsion angles in both molecules [C1 - C4 - O5 -
C6 = -178(2)°, -180(2)°; C2 - C4 - O5 - C6 = -52(3)°, -64(3)° and C3 - C4 - O5 - C6
= 66(3)°, 58(3)° in vaLA and C1 - C4 - O5 - C6 = -63(3)°, -60(3)°; C2 - C4 - O5 -
C6 = 60(3)°, 63(3)° and C3 - C4 - O5 - C6 = 178(3)°, -179(3)° in VALa] indicate that
the Boc methyl group is in energetically favourable staggered conformation with
respect to the C6-O5 bond. The bond angle O7 –C6 –O5 [129(2)° and 126(2)° in
Molecule A and B respectively in vaLA and 125(2)° and 122(3)° in Molecule A and
B respectively in VALa] is significantly higher than the values observed for ester
groups (7). This may be due to the steric hindrance between the tertiary butyl group

Table I
581
Crystal data for vaLA and VALa.
vaLA
23 H42 N4 O7
486.6
0.4 x 0.2 x 0.15
Needle
VALa
23 H42 N4 O7
486.6
Conformational Preferences
of Heterochiral Peptides
Molecular Formula
Molecular Weight
Crystal size (mm)
Crystal shape
Crystallising Solvent
Space group
C
C
0.4 x 0.2 x 0.1
Needle
Methanol/Water
P 212121
Methanol/Water
P 21
Cell parameters
a(Å)
9.401 (1)
17.253 (1)
36.276 (1)
-
9.683 (1)
17.355 (4)
18.187 (3)
95.84 (8)
b(Å)
c(Å)
β(°)
V(Å3)
5883.8 (7)
3040.4 (9)
Z
Molecules/Asymmetric unit
F (000)
8
2
2112
4
2
1056
Radiation
CuKα
120°
CuKα
120 °
2θmax
Scan-type
ω/2θ
3264
1031
ω /2θ
2907
1162
Independent reflections
Observed reflection (1 > 2σ (1))
Final R (%)
0.08
0.2217
1.724
0.24
0.128
0.3148
1.493
0.5
Final Rw (%)
Goodness of Fit
ρ
ρ
max (e Å-3)
(e Å-3)
-0.25
-0.41
min
Table II
Torsional angles (°) in vaLA.
Residue
side chain torsions
φ
ψ
ω
Molecule A
Val
Ala
Leu
Ala
131 (3)
149 (2)
-116 (2)
-86 (3)
-162 (2)
-146 (2)
137 (2)
165 (2)
-172 (2)
-168 (2)
-179 (2)
173 (2)
(-76 (2), 155 (2))
-59 (2) (-179 (2), -57 (2))
Molecule B
Val
Ala
Leu
Ala
114 (2)
147 (2)
-104 (2)
52 (4)
-156 (2)
-139 (2)
126 (2)
-138 (3)
-173 (2)
-166 (2)
178 (2)
-168 (4)
(56 (3), -76 (3))
180 (2) (67 (3), –180 (3))
Table III
Hydrogen bonds in vaLA.
D...A (Å) H...A (Å)
D
A
D-H...A (°)
141 (2)
C1A
N2
3.35 (3)
2.89 (2)
2.53 (3)
2.14 (2)
O6′
146 (2)
O6′
C3A
N4
C5A
O16
O16
O2′
3.49 (2)
3.06 (2)
3.55 (3)
2.67 (2)
2.23 (2)
2.77 (3)
141 (2)
162 (2)
137 (2)
N6
2.83 (2)
2.09 (2)
144 (2)
O2′
N8
C2A
O7
2.76 (2)
3.28 (2)
1.92 (2)
2.44 (2)
166 (2)
144 (2)
O5′1
O5′1
O7′1
O7′1
O172
O3′3
O1′3
O1′3
N3
N1
2.95 (2)
3.02 (2)
3.61 (3)
3.50 (3)
2.98 (2)
3.46 (2)
2.85 (2)
2.11 (2)
2.20 (2)
2.68 (3)
2.76 (3)
2.13 (2)
2.62 (2)
2.01 (2)
164 (2)
159 (2)
164 (3)
135 (2)
174 (2)
144 (2)
165 (2)
C1G1
C4B
N5
C6A
N7
1
2
3
x+1, y, z; x+1/2, -y+1/2, -z; x-1, y, z.

Table IV
Torsional angles (°) in VALa.
582
Residue
side chain torsions
φ
ψ
ω
Fabiola et al.
Molecule A
Val
Ala
Leu
Ala
-129 (3)
-115 (2)
-133 (2)
147 (3)
161 (2)
129 (2)
120 (2)
-72 (4)
166 (2)
-178 (2)
180 (2)
-173 (4)
(61 (3), -57 (3))
-75 (3) (156 (2), 71 (3))
Molecule B
Val
Ala
Leu
Ala
-72 (3)
-147 (2)
-137 (2)
124 (3)
-19 (4)
138 (2)
125 (2)
-168 (3)
179 (2)
176 (2)
(66 (4), -62 (3))
178 (2) -171 (2) (-176 (3), 60 (4))
-173 (3)
Table V
Hydrogen bonds in VALa.
D
A
D...A (Å) H...A (Å) D-H...A (°)
C1A
3.31 (3)
3.00 (3)
3.43 (3)
2.76 (3)
3.29 (3)
2.97 (2)
3.52 (4)
3.13 (3)
2.98 (2)
3.56 (3)
2.92 (2)
3.48 (3)
3.14 (2)
3.51 (4)
2.61 (3)
2.15 (3)
2.58 (3)
1.91 (3)
2.41 (3)
2.15 (2)
2.70 (4)
2.26 (3)
2.14 (2)
2.71 (3)
2.07 (2)
2.62 (3)
2.34 (2)
2.65 (4)
128 (2)
169 (2)
145 (2)
170 (2)
149 (3)
159 (2)
143 (3)
172 (2)
166 (2)
146 (2)
167 (2)
146 (2)
154 (2)
149 (3)
O7′
O7′
O5′
O5′
O2′
O2′
O8 a
O8 a
O6a
O6a
O1b
O1b
O3b
O8c
N2
C3A
N4
C6A
N7
C1G1
N1
N3
C2A
N8
C7A
N6
C18
c
a
b
x-1, y, z; x+1, y, z; x, y, z-1.
Table VI
Torsional angles (°) of related structures.
vALA1
VaLA2
vaLA VALa
A
B
A
B
Val
φ
139 (3)
114 (2)
-129 (3)
-161 (2)
-72 (3)
-19 (4)
148 (3)
-123 (2)
110 (2)
-162 (2)
-156 (2)
-149 (3)
ψ
Ala
φ
149 (2)
147 (2)
-115 (2)
129 (2)
-147 (2)
138 (2)
-146 (3)
149 (3)
133 (2)
-146 (2)
-139 (2)
-126 (2)
ψ
Leu
φ
-116 (2)
137 (2)
-104 (2)
126 (2)
-133 (2)
120 (2)
-137 (2)
125 (3)
-116 (3)
125 (3)
-120 (2)
104 (2)
ψ
Ala
φ
-86 (3)
165 (2)
52 (4)
147 (3)
110 (6)
124 (3)
-111 (2)
138 (6)
53 (2)
33 (2)
-138 (3)
-168 (3)
ψ
1
2
Bobde et. al. 1995.
Nagarajan et. al. 1997
and atom O7. The stereochemical reasoning for the observed conformation of the
Boc group has been discussed in detail by Benedetti et al., (6).
All the peptide units are trans with significant deviations from planarity for the sec-
ond residue in molecule A and B (∆ω = 12° and 14°) in vaLA and for the first
residue in molecule A (∆ω = 14°) in VALa. Similar large distortions from planari-
ty in peptide bonds have been observed earlier (8,9,10,11). Such distortions are
usually accompanied by hydrogen bonding interactions involving the amide func-

tion. In the present case, the distortion is presumably correlated to the formation of
intermolecular hydrogen bond involving the amide nitrogen and carbonyl oxygen.
583
Conformational Preferences
of Heterochiral Peptides
vaLA
The molecular structure of individual tetrapeptide molecule is shown in Figure 1,
while its stereo view is shown in Figure 2. The two independent molecules in vaLA
are in an ‘extended form’ forming antiparallel β-sheets. The (φ,ψ) values (Table II)
of D-Val1 and D-Ala2 are slightly higher than that reported for antiparallel β-sheet
(135°, -135° for a D residue) (12). The (φ,ψ) values of Leu3 are closer to those
reported for a parallel β-sheet. (13). The (D) Val1 – (D) Ala2 – (L) Leu3 segment
forms a segment with the hydrophobic residues at the convex surface, resembling
the situation in gramacidin (14).
Figure 1: Perspective view of molecule vaLA.
Side Chain Conformation
The Val and Leu side chains have different conformations in the two molecules. A
Val side chain can assume one of three conformations, (g+ t), (g- g+), (t g-). An
Figure 2: Stereo view of the molecule vaLA.

analysis of the side chain conformation in proteins (15) showed that the conforma-
tion (t g-) is overwhelmingly predominant among the three. (g- g+) has a consider-
able chance to occur, especially if the residue has an extended form as in the
antiparallel β-sheet (16). In molecule A, CG1 is trans against N with respect to CA
– CB bond and CG2 is –gauche (t g-), while in B, CG1 is –gauche and CG2 is
gauche (g- g+). Such a case in which two independent molecules in a crystal have
essentially the same main chain conformation, but different side chain conforma-
tions, has also been found in crystals of valine (17).
584
Fabiola et al.
The side chain conformation (χ1, χ21, χ22) of the leucine residue in the two molecules
A and B are (g- t g-) and (t g+ t) respectively. The χ1 distribution for the leucyl side
chain in oligopeptides (18) shows that χ1 around g- is most favoured, around t is next
-
favoured and around g+ is least favoured. The (g- t g ) conformation for leucine is the
most widely observed conformation in short as well as long peptides (16,19,20).
Crystal Packing
A stereo view of the packing of the molecules in the unit cell is shown in Figure 3.
vaLA contains two independent molecules with antiparallel β-sheet hydrogen
bonding motifs and the individual molecules in the asymmetric unit pack in a head-
to-tail arrangement in which the carboxyl terminal of one molecule comes close to
the amino terminal of the next molecule. The molecules in the crystal are packed
in antiparallel head–to–tail fashion with their long dimension extending along c-
axis by a number of N-H...O hydrogen bonds. Each one of them makes the
Figure 3: Stereo view of the packing of vaLA mole-
cules down the b-axis.

head–to–tail hydrogen bonding interactions with their translationally related mol-
ecules along the crystallographic a-direction. The molecular packing generates a
channel extending throughout the crystal parallel to the a-axis.
585
Conformational Preferences
of Heterochiral Peptides
VALa
The molecular structure of individual tetrapeptide molecule is shown in Figure 4,
while its stereo view is shown in Figure 5. The two independent molecules in vaLA
are in an “extended form” forming antiparallel β-sheets. All the (φ,ψ) angles seem
to approximate the antiparallel β-sheet values (-135°, 135°), with the notable
exception that Val in one of the molecules is in αR conformation, more particular-
ly in 310 type conformation (21) for which the standard torsional angles are φ = -
60° and ψ = -30°. One of the strands is thus fully extended while the other one is
bent near its N-terminal, obviously due to intermolecular packing.
Side Chain Conformation
It can be seen from Table IV that leucine side chain in molecule A adopts (g- t g+) and (t
g+ t) in molecule B. Valine side chain in both the molecules adopts (g+, g-) conformation.
The (t g-) conformation for valine is the most widely observed conformation in
short as well as long peptides (16,19,20). However (g+ g-) conformation observed
for valine has also been noticed in the crystal structures of oligopeptides (16,19).
Figure 4: Perspective view of molecule VALa.
Figure 5: Stereo view of the molecule VALa.

586
Fabiola et al.
Figure 6: Stereo view of the packing of VALa mol-
ecules.
Crystal Packing
A stereo view of the packing of the molecules in the unit cell is shown in Figures 6.
The molecules are packed in antiparallel head –to –tail fashion with their long dimen-
sion extending along c-axis by a number of N-H...O hydrogen bonds. The molecular
packing generates a channel extending throughout the crystal parallel to the a-axis.
The most remarkable observation is that a contiguous Cα - H...O hydrogen bonds
are found to be operative in both the structures though some of the distances are a
bit long, the hydrogen bond angle is supportive of hydrogen bond formation(22).
Possibly the Cα-H...O interactions are facilitated by the specific crystal conforma-
tions adopted by vaLA and VALa. A similar contiguous Cα - H...O bond has been
reported in the peptide structure VaLA adopting β-sheet (2).
A comparison between the backbone torsion angles for the molecules vaLA, VALa
(present study), VaLA (2) and vALA (1) clearly indicates their similar conforma-
tion in crystals (Table VI). In conformity with the non-observation of any specific
backbone folds in the solution state (2), all the short heterochiral peptides studied
by us are found to be essentially extended β-strand structures in crystalline state
irrespective of the position or type of the D residue.
Conformational Analysis of D-Chiral Residues in Oligopeptides
Structural and conformational studies on peptides are fundamental to an under-
standing of the principles governing folding of protein chains. Theoretical and
experimental studies over the past few decades have shown that protein structures
can be reduced to a few elements or motifs which are arranged in different ways in
different proteins. Each of the motifs can be further understood in terms of the con-
formational possibilities of the amino acids.
An analysis of the observed conformational feature of D-chiral amino acid residues
in both linear and cyclic oligopeptides, using coordinates of 123 crystal structures
selected from the 1998 release of CSD is presented.
The analysis is generally restricted to a discussion of the conformational features

of the backbone of the peptide chains. It may be noted that a tripeptide, consisting
of two linked peptide units, is perhaps the smallest fragment of a peptide chain in
which the effects of immediately neighbouring residues on the conformational
preferences of a given residue can be investigated.
587
Conformational Preferences
of Heterochiral Peptides
In peptides with n > 5, n being the number of residues in the peptide sequence, the
number of possible conformations are large and contact distance criteria can only
give the allowed conformations but cannot predict which are the likely ones to occur.
Table VII gives the CSD codes and the number of various D-amino acid residues in each
peptide sequence. The data do not include D-Trp, Asn, Gln, Lys and Arg since no entries
are found for these residues. Also the data for the amino acid residues D-Met, Ser, Thr,
Tyr and Glu is small and not enough to draw any conclusions. Hence, the discussion on
the above mentioned amino acid residues has not been included.
The Ramachandran diagrams for the D and L-chiral residues in both cyclic and lin-
ear oligo peptides are shown in Figure 7(a-e). As expected L-proline and D-proline
show a cluster of points in the extended as well as helical regions(23). The con-
spicuous and interesting aspect of this figure (Figure 7a) is that the clustering of
points around ψ = 0° and 180°. In contrast the number of conformations around ψ
= 0° and 180° is less for D-proline. It is very clear from the graph that D-proline
residues in both cyclic and linear peptides have conformational freedom whereas
L-proline residues are more restricted.
Table VII
Number of various D-amino acid residues in peptide sequences with their CSD codes.
CSD code
ALAMET10
ALPRAL10
BALGLH
A
V
L
I
P
M
F
S
T
C
Y
H
E
1
1
1
4
1
BEHTEN
2
BEMKIN
2
2
BIHTUH10
BIPVUR10
BIXPAZ10
BOCAPR
2
1
2
BOLWEE
BONROL
1
1
BONROL10
BOPPOL10
BXCPGL
1
2
1
1
2
CACNOJ10
CAHWEX
CAPHOQ
1
1
4
CDGLLL10
CDILIH10
CEWCIQ10
CGPGAP10
CGPSAQ
4
2
1
1
1

588
CSD code
CIBWUF
CLPGDH
COYJIJ10
CTILIH10
CTPROL10
CTVHVH
CTVHVH01
CVPVHD
CYBGPP
CYCAPP
CYDGPA
CYPAPR10
DABVIL
A
V
L
I
P
M
F
S
T
C
Y
H
E
1
Fabiola et al.
1
1
1
2
3
3
2
2
2
1
2
1
1
2
DASXIE
2
DETWUU
DIFNAH
2
1
2
2
DUPKEE
DUYTIA
1
DVLTLV10
FEYZEO
1
1
1
FIVSAE
FUDWIK
GAJDUQ
GAJFAY
1
2
CSD code
GESKIY
A
V
L
I
P
M
F
S
T
C
Y
H
E
2
2
GESKUE
GGAAGG
GICHOP
GLDLPA
GLTHRE
GLYDLA
GLYTRE02
HADFAT
HAFLAB
HAFKUU
HEBHUR
HEBLIJ
2
1
1
1
1
1
2
1
1
2
2
HESFUG
6

589
CSD code
HICJUY
A
V
L
1
2
2
I
P
M
F
1
1
S
T
C
Y
H
E
Conformational Preferences
of Heterochiral Peptides
HTENTX10
HIHYAY
JAGFOM
JIYHII
1
2
1
1
JOZZUT
1
2
1
1
JUJHUR
JUKMIL
JUVJAL10
KIVDIC
1
2
2
2
2
KVYSIG
CSD code
LENKIY
A
V
L
I
P
M
F
S
T
C
Y
H
E
2
LICSOF
2
1
2
1
2
2
LINCOA
MLEUGY
NAFGIN
NAHTEV
PAGLAL
PANTOM
PAPGAP
PAPRVA
PEDDAD
PEDDEH
PEZNAJ
1
2
2
1
1
1
1
2
1
1
1
1
PHLEGL10
PVPALM
PVPALM10
PIJPAZ
1
1
1
1
1
ROQMUF
SIFFUI
1
2
SOBVOU
SOWGOA
TAHGUE
TERCOI
3
1
2
1
TIMDOI
1
1
1
1
TIMDUO

590
CSD code
TOFMIK
TRDMPP02
TRDMPP10
TSQRRR10
VELSEK
A
V
L
I
P
M
F
S
T
C
Y
H
E
1
Fabiola et al.
1
1
3
1
VEVHAF
VOKBIG
VOKBOM
VOKKAH
VOPVUU
VOYZOY
VUGMEP
VUPPIF
1
1
3
1
1
1
1
3
1
WASVER
WEPVUI
WEXPOE
WEXPUK
WIPVEZ
2
2
1
1
2
2
1
1
WIPXUO
WIPYAV
YECDUF
YIJDIE
1
4
2
4
YILMUB
YOMLEO
ZADREB
ZADRIF
3
1
1
2
Figure 7b shows that D-alanine residues in linear as well as cyclic peptides occur
in the Dβ and αL conformational regions. In cyclic peptides, the distribution shows
a sort of continuum from the Dβ to αL region in addition to a few Lβ conformations.
However, most of the conformations fall in the β-sheet region. The potential ener-
gy calculations have showed that the minimium energy in poly-L-alanine corre-
spond to three regions αR, αL and a broad minimum around collagen. The optimal
conformation for poly-L- alanine is near αR and the less preferred conformation is
near αL. αR is more stable than αL by a difference of the order of 2 kcal/mole. As
we are dealing with D-residues, the situation is reversed.
D-Asp residues occur in the αL region whereas the L-Asp residues occur in the Lβ
extended region as suggested by Eswar & Ramakrishnan (24) as seen from Figure 7b.
D-valine residues in both cyclic and linear peptides occur mostly in the Dβ and αL
conformational regions as predicted by contact distance criteria (Figure 7c).
However a strong sheet favouring prefernce for L-valine residues in proteins has
been predicted by Chou & Fasman (25).

591
Conformational Preferences
of Heterochiral Peptides
Figure 7a: Ramachandran diagram for
a) L-proline and D-proilne.
b) D-proline in cyclic and linear peptides shown sep-
arately.
Figure 7b: Ramachandran diagram for
a) D-alanine in cyclic and linear peptides.
b) L-Asp and D-Asp residues.
Figure 7c: Ramachandran diagram for
a) D-valine in cyclic and linear peptides.
b) D-leucine in cyclic and linear peptides.

592
Fabiola et al.
Figure 7d: Ramachandran diagram for
a) D-Phe in cyclic and linear peptides.
b) D-Cys and D-Ile residues.
Figure 7e: Ramachandran diagram for
a) D-Glu, D-Met and D-Ser in linear peptides.
b) D-Thr and D-Tyr residues.
The Ramachandran diagram for D-leucine residues in oligopeptides is shown in
Figure 7c. D-Leu residues in cyclic peptides occur in the Dβ region whereas they
occur mostly in the αL region in linear peptides. L-leucine is reported to have a
strong helical preference in proteins (25). D-Phe residues occur mostly in the Dβ
conformational region in cyclic peptides whereas they occur mostly in αR confor-
mational region in linear peptides (Figure 7d). D-Ile occurs in the Dβ conformation-
al region and D-Cys occur both in the αL and Dβ region in cyclic peptides. Observed
conformations for D-Glu, D-Met, D-Thr, D-Ser and D-Tyr are given in Figure 7e.
Table VIII gives the summary of the conformational preferences of the D-amino
acids obtained from database analysis. This shows that all the residues except D-
isoleucine prefer both extended and αL conformation though the frequenc of
occurence may not be equal. In addition to this, D-leucine, valine, proline and
phenylalanine have assumed αR conformations in solid state. D-leucine has a
strong preference for helical conformation in linear peptides whereas they prefer an
extended conformation in cyclic peptides.

Table VIII
593
Summary of the conformational preferences of D-amino acids.
β
β
Conformational Preferences
of Heterochiral Peptides
α
/B
α
/ B
Residue
Alanine
D
L
L
R
Cyclic
Linear
H(20)
H(8)
M(7)
M(5)
L(5)
-
-
L(1)
Valine
Cyclic
Linear
H(15)
H(8)
M(5)
M(4)
-
-
-
L(1)
Leucine
Cyclic
Linear
H(13)
L(3)
L(2)
H(5)
L(2)
L(2)
-
L(1)
Proline
Cyclic
Linear
H(10)
H(6)
L(4)
L(2)
M(6)
M(3)
L(1)
L(2)
Phenylalanine
Cyclic
H(8)
M(2)
L(1)
L(1)
-
-
Linear
M(2)
H(5)
Cysteine
Cyclic
H(8)
M(5)
-
-
Isoleucine
Cyclic
H(8)
-
-
L(8)
-
-
-
Aspartic acid
H(3)
Number of structures in each regions is given in parantheses B→ Bridge region, H → Hish (50-
100)%, M → Moderate (20-50)%, L → Low (5-20)%.
Conclusion
All the heterochiral peptides with D-chiral residue at different positions in a short
sequence containing hydrophobic residues like valine, alanine and leucine prefer an
extended β-strand structure, irrespective of the position of the D-residue. The most
remarkable observation is that contiguous Cα -H...O hydrogen bonds are found to
be operative in both the structures.
The use of conformationally constrained D-chiral amino acid residues in generat-
ing modules of defined secondary structures has been illustrated. Though the
results obtained so far have demonstrated the design of synthetic peptides with
desired structures, further studies on longer peptides may reveal great surprises. D-
chiral residues in conjunction with non-standard amino acids seem to be a preferred
strategy for the design of novel peptide structures.
Acknowledgement
The Department of Science and Technology is acknowledged for the financial assis-
tance. GFF gratefully acknowledges CSIR for the Senior Research Fellowship.

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594
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Date Received: October 20, 2000
Communicated by the Editor Manju Bansal