Stereochemical Criteria For: Polypeptide and Protein
Stereochemical Criteria For: Polypeptide and Protein
Stereochemical Criteria For: Polypeptide and Protein
INTRODUCTION
The conformation of the backbone of a polypeptide or protein chain can be com-
pletely specified by giving the relative orientations of the two linked peptide groups
at each a-carbon atom. When the relative orientations of the peptide group are the
same at every a-carbon atom, then the chain takes up a regular helical folding. In
Part I (Ramakrishnan, 1964) methods were described of calculating the parameters
of such a helix, mainly the number of residues per turn, n, and the unit translation
of the residue along the helix, h, from a knowledge of the geometry of the peptide
group and the relative orientations of the linked peptide groups. However, not all
possible orientations will be stereochemically allowed, because of the short contacts
between the atoms of the adjacent residues. A study of this type has been made using
certain definite stereochemical criteria and the preliminary results corresponding to
the angle N-aC-C' (T) = 1000 have already been published (Sasisekharan, 1962;
909
Ramachandran, Ramakrishnan, and Sasisekharan, 1963a and b). This paper
describes the fuller details of the results for this value of the angle, 7, and also for
two other values of r, namely 105 and 1150. In addition, a complete survey of the
structures of di- and tripeptides, cyclic peptides, and polypeptides has also been
made to check the predicted ranges of allowed conformations. These results are
discussed in addition to a study of the conformations which occur in myoglobin.
It may be mentioned that although studies of this type have been reported so far
in the literature (Huggins, 1943; Bragg, Kendrew, and Perutz, 1950; Pauling, Corey,
and Branson, 1951; Low and Baybutt, 1952; Low and Grenville-Wells 1953;
Donohue, 1953; Lindley and Rollett, 1955; Shimanouchi and Mizushima, 1955;
Scheraga, 1960), they have not been definitive. Mizushima and Shimanouchi (1961)
have taken into account the restrictions or barriers due to the rotation about the
two single bonds meeting at the a-carbon atoms and have preferred nine conforma-
tions for the polypeptide chain. More recently, De Santis et al. (1965) have con-
sidered this problem from potential energy considerations, and Nemethy and
Scheraga (1965) have obtained interesting results regarding extended chains and
the formation of closed loops containing S-S bridges.
The notation used here for representing the relative orientation of the linked
peptide groups is the same as that described in Part I (Ramakrishnan, 1964). The
rotations of the two peptide groups are denoted by two dihedral angles (4, 4')
respectively, these being measured from an initial standard conformation 4 = 4' =
00, in which the planes of the two peptide groups lie in the plane N-aC-C` containing
the two axes of rotation, and the NH groups of the two residues are pointing towards
each other.'
DETERMINATION OF ALLOWED CONFORMATIONS
In order to determine the allowed conformations, the contact distances between the
atoms in the adjacent residues have to be examined using criteria for minimum van
der Waals contact distances. This is best done by first working out the positions of
lAt a recent conference of some of the representative workers in this field held in Bethesda,
it was decided to denote the two dihedral angles about the bonds N-Ca and C.-C' by 0
and 4' respectively, the sense of rotation being the same as that adopted here. The fully extended
chain, with N-H and C'=O trans with respect to one another, is to be taken as the standard
conformation with 0 = * = 0.
It is readily seen that the new 0 is the same as the old 0, but that 4' = 1800 + .' (and
o' = 180° + 4'). All the data reported here are thus readily converted into the (O, 4') coordi-
nates. The diagrams in Figs. 2, 3, and 6 have to be shifted up by 1800, or half the total length,
along the vertical direction. In particular, the right- and left-handed alpha helices will have (¢,
4') equal to (1330, 1230) and (2270, 2370). As before, a helix with (-p, -4') will be inverse
to one with (q, 4); i.e., it will be of opposite sense, but having the same number of turns
per unit.
This paper was finalized well before this meeting, and so the older conventions are adopted
here. However, it is proposed to use the new notation in the following papers in this series.
Throughout this study, the peptide group has been taken to be planar with NH
and CO groups in the trans configuration and having the dimensions given by Corey
and Pauling (1953).
If x, y, z and x', y', z' are the coordinates of an atom before and after rotation,
the relations connecting these are given by (Whittaker, 1952)
xi = (a2 + b2 _ c2-d2)x + 2(bc-ad)y + 2(bd + ac)z
y' = 2(bc + ad)x + (a2 - b2 + c2 - d2)y + 2(cd- ab)z (la)
z' = 2(bd - ac)x + 2(cd + ab)y + (a2 - b2 _ c2 + d2)z
where
a = cos (w/2), b = L sin (c/2), c = M sin (w/2), d = N sin (w/2) (lb)
m being the angle of rotation and L, M, N, the direction cosines of the axis of
rotation with respect to the chosen system of coordinates. The sign of a) is taken
TABLE II
MINIMUM CONTACT DISTANCES ASSUMED
Contact Normally allowed Outer limit
A A
C ...c 3.20 3.00
C' ... C' 2.95 2.90
C ...0 2.80 2.70
C N 2.90 2.80
C ...H 2.40 2.20
O ...- O2.70 2.60
O *--.N 2.70 2.60
O *--.H 2.40 2.20
N---.N 2.70 2.60
N ... H 2.40 2.20
H *--.H 2.00 1.90
18C
_U I
10'~~~~~~~~~0 36
n e0
ong
50O
¢? ~~~FIGuRz 2a
O DI -AND TRIPEPTIDES - NON.GLYCYL
* DI-AND TRIPEPTIDES- GLYCYL
CYCLOHEXAGLYCYL HEMIHYDRATE
O FERRICHROME- A OINO*OLYCYL
G a-HELIX RIGHT-HANDED 3
~ ~_f aw~~
L _ __ J
__ oc-HELIX LEFT -
^ POLY-GLY- PRO-HYPRO
HANDEDJ'"3)
I*ft
me ~ O COLLAGEN
o SILK
W-FORM OF POLY-p-BENZYL-L-ASPARTATE
RIBBON STRUCTURE - 2 27- HELIX
®) (-HELIX (5117)
it-HELI X (4-416)
) 27-HELIX
30io1HELIX
4-314-HELIX
P-C- PUCKERED CHAIN
a V ANOTHER POSSIBLE TRIPLE HELIX
a
180i -I
a
a
T 'I
I I
I I
-
I i .
0O 180- 36so
FIGURE 2b
0 180 360
FIGURE 2c
FiouRE 2 The normally allowed ( ) and the outer limit (----) regions of
(0, 0') for (a) r = 1050, (b) r = 1100, (c) r = 1150. The conformations of known
simple peptides, polypeptides, and proteins are also marked in Fig. 2b.
residues (i.e. where there is no 8-carbon atom), the contract distances between the
hydrogen atoms attached to the a-carbon atom and the various backbone atoms
were evaluated for r = 110 and 1150. The two hydrogen atoms were fixed at
tetrahedral directions to N1-C2 and C2-C2' and at a distance of l.OA from C2.
It was found that both for X = 110 and 1150, for all values of p and q', there were
no short contacts between the hydrogen atoms attached to the a-carbon atom and
the backbone atoms. As a result, the permitted ranges of c& and 4' are larger for
glycyl residues than for non-g1ycyl residues. The permitted ranges are given in the
second half (b) of Table III. The regions of allowed conformations for glycyl
residues when all the contact distances were taken into account are shown in Figs.
3a and b, where shaded regions are those allowed by only the outer limits, but not
the normally allowed contact distances.
It may be mentioned that for glycyl residues the contact distances between any
two atoms of the backbone in the adjacent residues for any conformation (4, 4') is
the same as for the inverse conformation (-cp, -4') [as can be seen from the rela-
tions (1), where, if x', y', and z' are the coordinates of a backbone atom for 4
(or 4') then the coordinates of the same atom for -4 (or -4') are x', y', and -z].
The results shown in Figs. 2 and 3 will be useful in investigating the conformation
at an a-carbon atom when the two dihedral angles 4, and 4' are known. For poly-
peptide and protein chains, the parameters that are obtainable from x-ray diffrac-
tion studies are the number of residues per turn, n, and the unit translation, h,
(Ramachandran, 1960) along the axis of the helix. Hence, the stereochemically
allowed combinations of n and h were evaluated using the detailed results of the
calculations described in Part I (Ramakrishnan, 1964) and are represented graphi-
cally in Figs. 4a, b, and c for the three values of T. In these figures also, the regions
of (n, h) allowed by the normally allowed contact distances are shown by continuous
line boundaries, while those allowed by outer limit values are shown by broken lines.
The origins in these figures correspond to n = ± 2, and h = 0 A. The positive and
Ia
I~~~~~~~~~~~~~~~~~3
.i.
low 34 aO
_-
FIoUR 3b
FIOURE 3 Allowed regions of (0, 4") for (a) r = 110', (b) r = 1150, for glycyl
residues. The shaded regions represent conformations which are allowed only by the
outer limit contact distances. The glycyl conformations observed in simple peptides are
also marked in Fig. 3a: 0 = Di- and Tripeptides; 0 = Cyclic peptides; 5 =
Polyglycine II.
Amino Acids. The two values 01', 42' for the various known crystal
structures of amino acids are given in Table V along with the values of the angle
N-aC-C (T). In general, 4' lies between + 30° and 1800 + 300, exceptions being
L-arginine HCl (Mazumdar, 1964), DL-aspartic acid (Dawson, 1953), L-glutamic
acid (Hirokawa, 1955), L-tyrosine HCl and L-tyrosine HBr (Srinivasan, 1959a
and b).
Di- and Tripeptides. In this case, for the N-terminal residues, c is the
only relevant parameter, since the positions of the hydrogen atoms attached to No
are not usually available. For the C-terminal residues, there is one value of t and
two values of 4/ corresponding to the two oxygen atoms of the C( group. For the
other residues (middle), there is one value of 4 and one value of 0'. These are
shown in Fig. 5, where the a-carbon atom under consideration is C1. The results are
given in Table VI along with the value of the angle N-aC-C' (T).
Considering the N-terminal residues, for which only k' is relevant, the observed
values ofqb'liewl
\ :,5 s \ ~ ~0-SILK
~
andnon-bl
case ofglyyl
- -
<,
3ariwlwhhtnoeei
,,
A
/~~~~~~
"
.40
\ X
°
XL - LEFT4HANDED QXHELIX
dR- RIGHT-HANDED OC- HELIX
T -GAMMA HELIX
2 -27- HELIX
-R - RIBBON- STRUCTURE
~~~~~3-3 *010 HELIX
\ ~~~~~~4 _4 314 -HELIX
Jr -A[-HELIX
3W - C4J -HELIX
FIGUREPC
taloergoinTbI
reidues.In adition,# in
A/_POLY-GLY-PRO-HYPRO
~A -COLLAGEN
a
PUCKERED CAN
allowed
vleof4'lewlwihnthe
ntecsregion. fnngyy mentionediiner itablesIbthiinth
oe
that six out of nine conformations listed in Table VI lie well within the normaly
allowed region and two more lie within the outer limit but outside the normally
allowed region. The one conformation that lies outside the allowed region is that
of the cysteine residue of the compound glutathione. But the value of r in this case
is 1150 and so the conformation comes into the allowed region corresponding to
7 = 1150 (Fig. 2c). In addition, the value of p' in many cases lies close to 1500,
which agrees well with the trend observed in amino acids.
*In the structures of L-arginine HBr, L-arginine HCl, H20, and L-arginine HC1, there are two mole-
cules per asymmetric unit.
References: (1) Donohue (1951); (2) Karle and Karle (1964); (3) Work done in Madras, Mazumdar
(1964); (4) Kartha and De Vries (1961); (5) Dr. B. Dawson, private communication; (6) Work done in
N-TERMINAL RESIDUE
Ho 0
CO% NoX C
i
_
-2
110 c.
00
C-TERMINAL RESIDUE
11 OIH
, CO NZ"'CI_.C'NI -,C
"'
Considering the glycyl residues, almost all of them lie within the allowed region.
Also in the case of C-terminal glycyl residues of the compounds Cys-Gly NaI and
Gly-Phe-Gly and in the case of middle and C-terminal residues in Gly-Gly-Gly
copper chloride, the observed conformations are such that they are allowed only
for glycyl residues.
Cyclic Peptides. Recently, the crystal structures of two cyclic hexapeptides,
cyclohexaglycyl hemihydrate (Karle and Karle, 1963), and Ferrichrome A (Zalkin,
Foster, and Templeton, 1964) have been reported. Of these, the former contains
four molecules per asymmetric unit and offers twenty four glycyl conformations for
investigation. The latter hexapeptide (Ferrichrome A) with the sequence Gly-Ser-Ser-
Orn-Orn-Orn (Orn standing for omithine) gives six conformations, one glycyl and
five non-glycyl. The parameters (S, 0') for these two hexapeptides are given in
Madras; (7) Hine (1962); (8) Oughton and Harrison (1959); (9) Peterson et al. (1960); (10) Hirokawa
(1955); (11) Dawson (1953); (12) Wright (1958); (13) Cochran and Penfold (1952); (14) Freeman
et al. (1964b); (15) Marsh (1958); (16) Itaka (1960); (17) Itaka (1961); (18) Harding and Cole (1963);
(19) Kretsinger and Cotton (1963); (20) Donohue and Caron (1964); (21) Donohue and Trueblood
(1952); (22) Trommel and Bijvoet (1954); (23) Subramanian (1965); (24) Wright and Marsh (1962);
(25) Mathieson (1952); (26) Mathieson (1953); (27) Mathieson and Welsh (1952); (28) Shoemaker
et al. (1953); (29) Shoemaker et al. (1951); (30) Work done in Madras; (31) Srinivasan (1959a);
(32) Srinivasan (1959b); (33) Parthasarathy (1962); (34) Work done in Madras; (35) Work done in
Madras.
*(1) Donohue and Marsh (1962); (2) Hughes and Moore (1949); (3) Pasternak et al. (1954); (4) Smith
and Wiebenga (1953); (5) Pasternak (1956); (6) Yakel and Hughes (1954); (7) Dyer (1951); (8) Wright
(1958); (9) Fridrichsons and Mathieson (1962); (10) Work done in Madras; (11) Work done in
Madras; (12) Freeman et al. (1964a); (13) Marsh and Glusker (1961); (14) Leung and Marsh (1958).
*(1) Bamford et al. (1956); (2) Pauling and Corey (1951); (3) Donohue (1953); (4) Low and Grenville-
Wells (1953); (5) Crick and Rich (1955); (6) Sasisekharan (1959a); (7) Cowan and McGavin (1955);
(8) Sasisekharan (1959b); (9) Bradbury et al. (1962); (10) Ramachandran (1963); (11) Marsh et al.
(1955); (12) Pauling and Corey (1953).
a-helix. Both the right-handed a-helix (1320, -57°) and the left-handed
a-helix (-132°, 570) lie within the outer limit regions only. However, slight
perturbations such as changing the value of r would bring the right-handed helix
into the normally allowed region but the left-hand a-helix is always outside the
normal limits although it is just allowed by the outer limits. Also the right-handed
a-helix can accommodate L-proline towards an end, since f' 1200, while the
left-handed a-helix cannot. Even in the former case, because the planes of the
peptide groups are nearly vertical, short contacts arise between the imino carbon
atom, C, and the atoms of the backbone of the residue on top of it, if it is in the
middle. It has been found that the two a-helical portions adjoining the proline ring
must be inclined by at least 350 in order that these short contacts may be relieved.
Even in this case, there arise two short contacts C2' . . . C1' = 2.61 A and
C2 ... 01 = 2.45 A between atoms in the adjacent residues and these can be
relieved only by distorting the planarity of the peptide group.
y-helix. The conformation of the right-handed y-helix (-96°, 780) lies
well outside the allowed region and hence is not likely to be observed.
this distance forms part of a possible intrachain hydrogen bond with N2 .01 =
2.72 A and H2N201 = 28'30', this is really not a short contact.
2.27-helix (ribbon structure). This structure proposed by Donohue (1953)
has the conformation (1020, 590) and this also apparently lies outside the allowed
region. As in the previous case, the short contact 01 H2 (1.88 A) forms part
..
CONCLUDING REMARKS
Thus the conformations observed in simple and cyclic peptides are seen to confirm
the predictions of the theory, thereby proving the validity of the stereochemical
criteria assumed in this study.
Finally, the results obtained in our study agree well with those obtained by
others from considerations of potential energy. Thus, Mizushima and Shimanouchi
(1961), from a study of the internal rotation of simple molecules have preferred
nine orientations. In our notation, these correspond to 4) = 0, 120, and 2400,
)' = 60, 180, and 3000. These are given in Table IX, along with the values of the
unit twist t and the unit translation h. An examination of these in the light of the
present study shows that all except d, e, and i lie within the allowed region. Even
among these conformations, i becomes allowed because of the formation of a hydro-
gen bond of the type N2-H2 ... 01, which offsets the short contact, thus leaving the
conformation d and e alone to be really disallowed.
Recently, De Santis et al. (1963) have attempted a study of the stability of
helical conformations of linear polypeptide chains from potential energy considera-
tions. Although there is a broad similarity between their potential energy contours
and the boundaries of our diagrams, there are some differences, for example a deep
potential mini'mum corresponding to about (1200, 300°) and another one at about
(1600, 600). Neither of these are particularly populated in Fig. 2b, showing that
for a single pair of residues these are not specially favored. The potential energy
data that are fed in such studies may have to be further revised.
APPENDIX
While evaluating the contact distances for non-glycyl residues, only the pl-carbon atom
of the side chain was taken into account. It has been possible to extend the study to
working out the effect of the y-carbon atom on the conformation of the two residues.
This was made possible since it has been found in Madras, from an analysis of the
observed orientation of the side chains in the structures of various amino acids and
peptides, that there are three preferred positions for the y-carbon atom.
The position of C, may be represented by a parameter + which measures the rotation
of C, about the C6-C, bond from a standard initial conformation (& = 00) in which
the atom C, lies in the plane N-Ca-Cp and with atoms N and C, being in the cis configura-
tion with respect to the C.-Cp bond. Viewing from Cp to C., & is taken to be positive for
an counterclockwise rotation. With this convention, the three positions of C, are found
to lie close to values of 60, 180, and 3000 for b, and these are indicated by indices 1, 2,
and 3 respectively.
The contact distances between the y-carbon atom in these three positions and the back-
bone atoms were calculated in the range of (4), 4') allowed by the ,8-carbon atom (given
in Table III) for r = 1100. The alterations in the outer limit boundaries thus worked
out are shown in Fig. 6, where the shifts in the boundary due to the y-carbon atom in the
three positions are shown by arrows.
In all the three cases, there are some additional restrictions in the allowed ranges of
either 4 or 4', or both, as can be seen from Fig. 6. For the first position of C, (v = 600),
there are restrictions on both 4 and 4', while for the second position (& = 1800), the
restrictions are on 4' only and for the third position (& = 3000), on 4 only.
Fig. 6 also contains the conformations of the right-handed and left-handed a-helices
marked in it. It is interesting to note that for the first position C, (g = 600) the con-
3BC
OP ISO*18 36d
FIouRB 6 The shifts in the boundaries (indicated by .) of the allowed regions
(outer limit) taking into account the restrictions due to 'y-carbon atom in the three
positions: C, alone; ---- with C, in position 1; .... .... C, in position 2;
and -.-.-.-. C, in position 3. The conformations of the right- and left-handed a-
helices are also marked.
formation of the right-handed a-helix lies just on the boundary of the outer limit region,
while the conformation of the left-handed a-helix goes outside the outer limit. In the
other two cases, both are only within the outer limits and there is no obvious case for
either the right-handed or the left-handed a-helix to be more likely. In the analysis made
on amino acid side group conformations (Lakshminarayanan, unpublished), both
L-glutamic acid and L-glutamic acid HCI have the y-carbon atom in position 1, which
may explain why poly-L-glutamic acid has a hight-handed helix. However, the three
positions are found to occur fairly evenly distributed in different amino acids, and this
explanation will not hold good for the very common occurrence of the right-handed alpha
helix in preference to the left-handed one in various polypeptides.
Our thanks are due to Dr. V. Sasisekharan for the discussions which we had with him. One of
the authors (C.R.) wishes to thank the Ministry of Scientific Research and Cultural Affairs
and The Council of Scientific and Industrial Research, India, for financial support. The other
author (G.N.R.) is grateful to the United States National Science Foundation for a Senior
Visiting Fellowship, which enabled him to spend a year in the University of Michigan. We are
very grateful to Professor J. L. Oncley for his interest in these studies.
Part I of this article appeared in Proc. Indian Acad. Sc., 1964, A59, 327.
Received for publication, July 19, 1965.
REFERENCES
BAMFORD, C. H., ELLIOTr, A., and HANBY, W. E., 1956, Synthetic Polypeptides, New York,
Academic Press, 260.
BRADBURY, E. M., BROWN, L., DowNiE, A. R., ELLIOTT, A., FRASER, R. D. B., and HANBY,
W. E., 1962, J. Mol. Biol., 5, 230.