J. theor. Biol.

(1976) 60,481-486

Preferred Backbone Conformations of Amino Acid Residues

for Solvent Interactiont

The preferred conformation of an amino acid residue in a polypeptide or

protein molecule is determined by a variety of factors such as steric and
polar interactions (including hydrogen bonding) and solvent-solute inter-
actions (including hydrophobic bonding) and the study of the various
observed conformational states of amino acid residues in protein crystals
has been a subject of intensive investigation in the past few years. Hard-
sphere and potential energy studies (Bamachandran & Sasisekharan, 1968;
Scheraga, 1968; Ponnuswamy & Sasisekharan, 1971; Ponnuswamy, Warme
& Scheraga, 1973 ; Lewis, Momany & Scheraga, 1973) on a variety of model
systems have established the importance of short-range interactions in
dictating the preferred conformations of an aminoacid residue. Excellent
agreements between the theoretically predicted local low energy backbone
conformations for dipeptide models and those actually observed for the
respective amino acid residues in the protein crystals support this view.
However, there are quite a number of observations that occur at confor-
mational regions which are energetically not favoured (Burgess, Ponneswamy
& Scheraga, 1974). For example, the large number of conformations observed
around the CR-bridge region 4 N -90” and JI N 0” (see Fig. 1 for locating
the right- and left-handed u-helical conformations (crR and cc‘), right- and
left-handed bridge conformations (rR and lL), and extended (B) structure
conformation on the &JI plot. The convention followed is that of IUPAC-
IUB Commission (1970) and Burgess et al. (1974)) do not conform to the
predictions of classical (Ponnuswamy & Sasisekharan, 1971) and quantum
mechanical calculations (Pullman & Pullman, 1974) based on short-range
interactions. These conformations obviously indicate that forces originating
from longer ranges than a dipeptide and (or) additional stabilization from
solvent-solute interactions play a decisive role under specific conformational
situations. Attempts to incorporate longer-range interactions (Ponnuswamy,
Warme & Scheraga, 1973) and solute-solvent interactions (Venkatachalam
& Krimm, 1973 ; Forsythe & Hopfinger, 1973 ; Perricaudet & Pullman,
1973) have been reported and these methods are yet to be developed for

7 Contribution No. 411 from the Centre of Advanced Study in Physics, University of
Madras, Gtidy Campus, Madmw5OW25, Tamil Nadu, India.
481
482 P. K. PONNUSWAMY AND P. MANAVALAN

180, \,
\t I

\ I
\
i
I
I

I
-120 :
II
I\
-180
-180
L -120 -60

FIG. 1. Xamachandran (4, IJI) plot showing the locations of the right- and left-handed
a-helical (aR and aL) conformations, the right- and left-handed (<a and CL) bridge confor-
mations and the extended (8) structure conformation. Potential energy (nonbonded i-
electrostatic) contours of 3 kcal/mol above the global minima at (-NY, 90”) for alanyl
and at (T go”, * 90”) for glycyl dipeptide units are marked. - alanyl; - - - -, glycyl.
CRregion is less stable by about 2.75 kcal/mol than the &region. ’

interpreting data from protein molecules in general. We have made some

extensive studies on conformational states of amino acid residues using a
model in which solvent accessibility to the C=O and N-H groups in the
backbone of dipeptides and oligopeptides of different types to determine
the probable backbone conformations which are preferred for solvent
interaction. In the course of such a study we found some interesting obser-
vations regarding the (,-bridge region. Here we give a resume of the results
of our study.
We followed the method proposed by Lee & Richards (1971) to calculate
the accessibility of a solvent molecule to an atom or group of atoms in a
molecule. An atom (group) in the solute molecule is said to be accessible
to a solvent molecule if the solvent molecule can be brought into van der
Waals contact with it. The molecule is represented by a set of interlocking
 LETTERS TO THE EDITOR 483
spheres of appropriate van der Waals radii assigned to each atom and the
solvent molecule of known size is rolled along the envelope of the van der
Waals surface for the molecule at planes conveniently sectioned. The acces-
sible surface area of an atom of radius r is the area on the surface of a sphere
of radius R = r+ rsolvcnton each point of which the centre of the solvent
molecule can be placed in contact with this atom without penetrating any
other atoms of the molecule. This area A and the accessibility S are calculated
using the formulae A = c (R/JR2-2:). D.L1 and S = 100A/4nRZ, where
Li is the length of the arc computed on a given section i, Zi the perpendicular
distance from the centre of the sphere to the section i and D is the spacing
between the sections. The number S represents the total static accessibility
for an atom in the solute molecule which in turn reflects the possible extent
of solvent interaction with that atom.
We have taken up for investigation, glycyl, alanyl and seryl dipeptides
of the form CH,-CO,,,-N,,,H-CHR-CO,,,-N,,,H-CH, and the
H,O molecule as solvent. The bond lengths and bond angles were taken
from Momany, McGuire & Scheraga (1975) and the van der Waals radii
were the same as those used by Lee & Richards (1971), except for OH of
seryl side chain for which the value was taken to be I.52 A. The accessibility
values were computed by varying the conformational angles 4(N-C? and
(Cm-C’) at 20” interval and are represented in the (6-$ plane.
The accessibility maps constructed suggest that the N and 0 atoms of
the backbone could interact with solvent molecules selective!y in the most
commonly observed structural regions aR, aL, /I, <s and CL (Fig. 1). Con-
sidering the accessibility values of individual atoms, N, in glycyl dipeptide
has higher values in the bridge regions, CRand CL and in the b-region (near
polyglycine-II conformation) whereas in the alanyl case, aL region is more
preferred for solvent interaction. The accessibility of 0, is higher for CR
(also CL for glycyl case) and /?-structure regions in both glycyl and alanyl
dipeptides; Nz has higher accessibility in the /l-region and O2 in CRand CL
regions. Considering the total accessibility of polar atoms in these two
dipeptides, extended conformational region is preferred over any other
region for solvent accessibility which implies that in this conformational
region the C=O and N-H groups are completely exposed outside. However,
given due considerations to the fact that the accessibilities of N and 0 atoms
will be drastically reduced in the regular a-helical and &structure confor-
mations (Lee & Richards, 1971) as these atoms take part in intra- and
inter-chain hydrogen bonding when the dipeptide unit forms part of a chain
segment, the only region preferred for solvent accessibility is the CR-bridge
region for alanyl dipeptide and both CRand CL regions for glycine. The sum
of the accessibilities of polar atoms N,, O1 and O2 is maximum in CRregion
 484 P. K. PONNUSWAMY AND P. MANAVALAN

for both glycyl and analyl dipeptides. In this conformational region, i.e.
around 4 N -90” and $ N 0”, the above said three atoms point outwards
without any interference from neighbouring atoms, thus having maximum
potentiality for solvent interaction. As this conformation results in a hinge
[such a hinge is also produced at locations where an isolated residue adopts
a-helical (4, $) values] the likelihood of hydrogen bonds of the type observed
in u-helical and B-structure is very remote. Also as the chain extends on both
sides, the N, atom, having comparatively low accessibility value in this
region, could take part in hydrogen bonding with the C==O group of the
second neighbour peptide unit (Fig. 2) resulting in the p-bend type I (type II

(a) (b)
FIG. 2. Skeleton of j+bends. (a) type I and {b) type II. The shaded dipeptide segments
are in &(a) and CL(b) conformations. CL is stable only for the glycyl case.

bend results when q5 N 90”, which is possible only for the glycyl case;
Venkatachalam, 1968), thus further stabilizing this conformation. This
situation however does not affect the accessibility potentialities of N,, 0,
and O2 atoms. Therefore, it is not surprising to observe a number of amino
acid residues in the [a region, which is favoured both for solvent interaction
and intra-chain hydrogen bonding.
In Fig. 3, the sum of the accessibilities of atoms N,, 0, and O2 is plotted
in the $-tj plane for the glycyl and alanyl dipeptides. Iso-accessibility curves
have been drawn with respect to the highest accessibility value marked
 LETTERS TO THE EDITOR 485

FIG. 3. Solvent accessibility maps for glycyl (a) and alanyl (b) dipeptides. Sum of the
accessibilities for the atoms N1, 01 and 02 have been plotted. Iso-accessibility curves
have been drawn with respect to the maximum value marked as X. (S = 91 for gly and
85 for ala). Observed conformations of glycyl and non-glycyl residues occurring in /kurns
on the surface of seven proteins (lysozyme, ribonuclmS, cl-chymotrypsin, myoglobin,
carboxypeptidase-A, horse ferricytochrome-C and staphylococcal nuclease; see Burgess
et al. (1974) for references to these structures) within regions / =f!W f 40” and
w = 0” & 40” have been plotted.

as X. [Note that the region in which X is marked in the analyl map is ener-
getically completely disallowed (see Fig. l).] The observed +$ values of
glycyl and non-glycyl amino acid residues in seven proteins in the [ regions
are plotted in the respective glycyl and alanyl maps. The residues plotted on
these maps are the I+ 1 and 1+2nd residues in the /?-turns (having
4 ~T90”f40° and e N 0” f 40”) that occur on the surface regions in
these proteins (Ku&, 1972). As these residues, being on the surface of
protein molecules, could be interacting with aqueous solution, the agreement
between the predicted preferred conformational region for solvent interaction
and the observed conformations of the surface residues is very good.
It is interesting to note that N and 0 atoms of the backbone themselves
prefer this I& region for solvent association. The curiosity is that 43 out of
54 non-glycyl residues that occur in the CR region [Fig. 3(b)] have polar
atoms in their sidechains. The polar atoms in the side chain then simply
further stabilizes this conformational region by interacting with the solvent
molecules. Accessibility calculations on seryl dipeptide supports this view.
The Oy atom has the highest accessibility around x1 N -60” and this con-
figuration does not reduce the accessibilities of backbone atoms 0,, N,
486 P. K. PONNUSWAMY AND P. MANAVALAN

and 0, in the cK region. Interestingly the conformation of maximum acce ssi-

bility in seryl dipeptide shifts to 4 =- 90’ and $ N -20’ around which
location the observed conformations cluster in the CR-region.
It should be mentioned here that a higher accessibility value for a polar
atom does not mean a stronger hydrogen bond (which depends mostly on
the proper directional approach of donor and acceptor groups) with the
solvent molecule but it simply suggests the probability of association with
solvent molecules at that region is high. The method used here is crude
and could be compared to the earlier hard-sphere model in deducing the
allowed and disallowed regions ignoring their relative stabilities.

One of us (P.M.) thanks the University Grants Commission for financial

assistance.

Centre of Advarxed Study in Physics, P. I<. PONNUSWAhlY

University of Madras, Guindy Campus, P. MANAVALAN
Madras - 600025, India

(Received 7 August 1975, and k revised form 26 October 1975)

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