Lecture 3 – Introduction to

Molecular
Symmetry
Biological Systems tend to be
Symmetric
At various levels:
 organism shape:
 e.g., bilateral, spiral, radial
symmetry.
 shape of molecular
structures:
 e.g., α-helix (polypeptides),
B-helix (DNA).
 even though monomers are
asymmetric (chiral).
Here, we focus on
symmetry in biological
macromolecules.
 the types of symmetry.
 developing a mathematical
description.
Why Model Symmetry?
A model provides a compact, simplified
description of a complex structure.
 which retains important details in minimal form.
Simplifies many problems in Physical
Biochemistry:
 structural prediction:
 e.g.: helices describe the most likely local secondary
structures (key to protein folding).
 help predict the likely outcomes of monomer
variations.
 structural determination:
 helps interpret results from X-ray diffraction, electron
diffraction, etc.
 image reconstruction:
Defining Symmetry
‘Symmetry’ refers to:
 a correspondence in system properties on opposite
sides of a dividing line or median plane.
 shape, composition, or relative position of parts.

A Symmetric object will be reducible to a set of

copies of an elementary object…
 each approximately identical.
 this unique, elementary object is called a motif, m.
 The choice of motif depends upon the structure.
 e.g., starfish has 5 ‘identical’ arms…each is a motif.
 Symmetry implies an orderly arrangement of the
copies to make the whole object.
 starfish = 5 arms, arranged by rotation about a point.
 then…object = ‘motif details’ + ‘arrangement details’.
The Symmetry Operator
A model of symmetry:
 models the structure of the overall object, in terms of
the arrangement of the motif copies.
 Copies arranged about a point, line, or plane of
symmetry.
Operator Model: m repeatedly copied about
the axis of symmetry…
 by applying a symmetry operator, O on m to give a
related motif (copy), m’ :
O (m) = m’.
 In general, application of O may result in:
 a translated, reflected, or rotated copy of m
(biopolymers).

Point Symmetry

The simplest type of symmetry is point

symmetry:
 motifs are arranged about a point.
 then O(m) implements a rotation and/or a reflection.
 the complete set of motifs generated by O is called
a point group.
There are two types of point symmetry:
 mirror symmetry – motifs related by reflection.
 rotational symmetry – motifs related by rotation.
The Types of Point Symmetry
Mirror Symmetry –
 relates two motifs on opposite
sides of a line or plane.
 e.g.: the Human Body.
 motif = ½ body.
 two halves related by reflection.
Rotational Symmetry –
 relates motifs distributed about
a point or axis.
 Radial symmetry about a point:
 motifs related by rotation.
 e.g.: diatoms.
 Screw symmetry about an axis:
 motifs also translated down the
axis.
 e.g.: spiral seashell.
Conventions

We will discuss each type of symmetry in some

detail.
 but first, some conventions:
Each atom in our molecule is placed at
a unique set of coordinates, (x,y,z).
 we adopt a right-handed, Cartesian
coordinate system.
xxy=z
 positive rotations: right-hand rule.
 Any rotation is multi-valued...
 e.g., +90o is also –270o, +450o, etc…
 Convention: Rotations are single-valued and right-
handed.
 rotation described by the (smallest) positive value of the
The Symmetry Operator, O
Application of symmetry operator, O to motif,
m, generates a second motif, m’.
 the coordinates of corresponding points in m (x,y,z)
and m’ (x’,y’,z’) are related by the transformation
equations:
a1x + b1y + c1 z = x’
a2x + b2y + c2 z = y’
a3x + b3y + c3 z = z’
 or, in matrix form:

 this model correponds to O(m) = m’ …

Mirror Symmetry
Left and right hands are related by mirror
symmetry.
 about a plane passing through the center of the body.
Consider the ‘structure’ formed by 2 facing
hands:
 1 on either side of the xz plane…
 let m = right hand.
m’ = left hand.
 corresponding pts in m and m’
related by the mirror operator,
Mirror Symmetry (cont.)
The mirror operator, i :
 expresses the mathematical relationship between any
pair of motifs that are exact mirror images…
 about an appropriately defined plane of symmetry.
 includes the stereoisomers of chiral monomers:
 L- and D- forms of the amino acid residues.

Pseudo-symmetry
 Another instance of mirror symmetry: the Human
body.
 where each half is a motif.
 however, the symmetry is only approximate.
 e.g.: the heart is not in the center, but displaced.
 Approximate symmetry is called pseudo-symmetry.
Rotational Symmetry
Symmetry about a point or axis is rotational
symmetry.
 no inversion of a motif.
 instead: reorientation in space, about the center of
mass (axis).
Consider the ‘structure’ formed by 2 right hands:
 placed in the 1st and 3rd quadrants…
 let m = hand in the 1st quadrant.
m’ = hand in the 3rd quadrant.
 corresponding pts in m and m’
related by a rotation operator,


2-fold Rotational Symmetry
Two applications of c causes a full 360o
rotation.
 mathematically, c2 = I, the identity matrix.
c is thus identified as C2 :
 the 2-fold rotation operator.
 said to produce a 2-fold rotation.
 and our object’s symmetry axis
 the z-axis…
 is called a 2-fold rotational axis
of symmetry.
 as denoted by the symbol at the origin.
C2 symmetry is also called Dyad symmetry.

 and the axis the dyad axis.

n-fold Rotational Symmetry
An object with n motifs, related by rotation, Θ
=360o/n about an axis of symmetry…
 is said to have n-fold rotational, or Cn symmetry.
The general operator for rotation
about the z axis by Θ is:

 for Θ = 180o, c reduces to C2.

 For Θ= 360o/n, c = Cn, the n-fold rotational symmetry
operator.
 note: C1 applies to non-symmetric (i.e., chiral)
n-fold Rotational Symmetry
(cont.)
Some examples of n-fold rotational symmetry:

 each symmetry axis denoted by an n-sided figure.

n
 note: in each case, O = I, the identity matrix…
 n x Θ-sized rotations visit all motifs, and return us back
Higher Symmetry
Symmetry operators does not neet be
restricted:
 to n-fold rotations, or rotations about the same axis
or point.
 Multiple symmetry elements may be combined to
produce ‘higher’ symmetries.
In Biopolymers, such multiple sets relate
identical subunits,
 organized at the level of quaternary structure.
 examples discussed next lecture.
Common symmetry groups in biopolymers:
 Cn – rotational symmetry about a point, or axis.
 D – dihedral symmetry.
 T – tetragonal symmetry.
 O – octahedral symmetry.
Dihedral Symmetry
The most elementary ‘higher’ symmetry is
Dihedral.
 n-fold Dihedral symmetry (Dn) combines:
 n-fold rotational symmetry about one axis;
 n C2 axes, each perpendicular to the n-fold axis.
 total number of motifs = 2n.
 Example:
 D4 symmetry combines 1 C4 and 4 C2 axes (each
degenerate):

 (*) Note the alternate view:

m-hedral Symmetry

Point groups that combine multiple rotational

axes describe m-hedral symmetry.
 m = the number of faces on the solid shape.
 m also indicates the total # of C3 axes.
 Axes may pass through faces or corners…
 N = the number of repeating motifs = 3m.
 3 motifs/face or 3 motifs/corner…

Objects with m-hedral symmetry will also exhibit

point symmetries for n < m.
 N must be divisible by n for Cn axes to be present.
 if Cn axes present… N = n x m,
 determines number of Cn symmetry axes (m = N/n).
 C3 symmetry always present;
m-hedral Symmetry
m=4: Tetrahedral symmetry (T).
 12 motifs = (3/face)(4 faces)

 C2 and C3 symmetry:
 4 C3 axes; 6 C2 axes.

m=8: Octahedral symmetry (O).

 Octahedron (or cube).
 24 motifs… C2, C3, and C4 symmetry.
 3/face and 3/corner, respectively.
 6 C4 axes; 8 C3 axes; 12 C2 axes.

m=20: Icosahedral symmetry (I).

 60 motifs = (3/face)(20 faces)

 C2, C3, and C5 symmetry.

 C6 not present...
Screw Symmetry
For radial symmetry:
 motifs periodically arranged about a point or axis.
 360o rotation returns us to the starting position.
 e.g.: for Cn , we require that On = I.

If (only) requirement 2 is broken…

 i.e., 360o rotation also causes a translation P,
 down the axis of symmetry.
 Then: the object has Screw symmetry.
Example of Screw Symmetry
The spiral staircase:
 Has steps symmetric about the z-axis.
 This sounds like point symmetry…
 But, a 360o rotation also causes a
translation (movement) down the z-
axis.
 This translation, P is called the pitch.
 This is generally called Screw
symmetry.
 May also have a scaling of motifs.
 Examples: spiral seashell, a screw

The staircase is actually a special

case:
 symmetry only at discrete points about
the axis.
n-fold Screw Symmetry
For an object with n-fold screw symmetry:
 n equal rotations of Θ = 360o/n generate:
 1 turn of the helix.
 a translation, P down the axis (assume, z-axis).
 corresponding points related by:

(x’,y’,z’) = Cn (x,y,z) + T ;

 Cn is the corresponding point group.

 T = translation operator, (0, 0, P/n).

Screw symmetry can be either:

 right-handed:
 Tz > 0 for CW (+) rotation.
 left-handed:
 Tz < 0 for CCW (-) rotation.
Conclusion
In this Lecture, we have discussed:
 The use of Symmetry in simplifying the description of
macromolecular structure;
 Various types of simple Symmetry.

In the next Lecture, we begin our discussion of

biopolymer structure:
 With a description of the typical folded structures of
proteins and polypeptides.