Biology Reference
In-Depth Information
3.2 Configurations versus Conformations; Covalent versus
Noncovalent Interactions (or Bonds)
It is important to distinguish between
conformations
and
configurations
on the one
hand, and between
noncovalent
and
covalent interactions
(or bonds) on the other.
Conflating these two sets of terms in chemistry is comparable to conflating
protons
and
neutrons
in particle physics and first (words -
>
sentences) and second (letters -
>
words) articulations in linguistics (Culler 1991). The conformation of a molecule
is a three-dimensional arrangement of atoms that can be altered without breaking or
forming covalent bonds, while the configuration of a molecule is a three-dimen-
sional arrangement of atoms in a molecule that cannot be changed unless at least
one of the covalent bonds in the molecules is broken. Covalent bonds are strong
taking 50-100 kcal/mol to break, since they are formed between two or more nuclei
through sharing of one or more pairs of valence electrons (i.e., the electrons residing
in the outermost electronic shell in an atom or a molecule). Noncovalent bonds are
relatively weak taking only 1-3 kcal/mol to break, because they do not require
sharing any electron pairs.
It is very common to hear experts in X-ray crystallography of biopolymers or in
the field of signal transductions say that the “phosphorylation of group X in protein
Y produced
conformation
changes.” Such statements, strictly speaking, are incor-
rect (Ji 1997a). The correct expression entails replacing
conformation
with
config-
uration
. To understand why, it is necessary to know how these two terms are
defined in physical organic chemistry (Fig.
3.5
).
Notice that all that is needed to convert a trans-conformer to a cis-conformer is to
rotate the carbon atoms around the carbon-carbon single bond relative to each other,
and no covalent bond needs be broken or formed in the process. Configurational
changes in contrast involve breaking or forming at least one covalent bond, and are
usually slow activation energy barriers being in the order of several dozen Kcal/
mole. Conformational changes are fast because they implicate the activation energy
barriers in the range of thermal energies, that is, about 1-3 kcal/mol. The biological
importance of distinguishing between
conformational
(also called noncovalent)
structures and
configurational
(or covalent) structures rests on the following facts:
1. All protein-protein, protein-nucleic acid, and RNA-DNA interactions are
completely determined by the three-dimensional shapes of proteins and nucleic
acids.
2. Molecular shapes carry molecular information (e.g., the molecular shape of
a transcription factor is recognized by and influences the structure and activity
of a regulatory segment of DNA).
3. There are two kinds of molecular shapes, to be denoted as Type I and Type II:
“Type I shapes” can be changed from one to another through conformational
(i.e., noncovalent) changes only.
“Type II shapes” can be changed from one to another through configuration
(i.e., covalent) changes only.
