Bioorganic Chemistry
9
reality, the contribution of a salt bridge to
the stability of a complex is on the order of
0to3kca
lmo
l
1
.Thesourceo
fth
isd
i
f
-
ference lies in the presence of water. In all
associative processes, it is imperative not
only to examine the energy being released
by bringing two groups together but also
the energy required to remove the species
fromcon
tac
tw
i
ththeso
lven
t(
i
.e
.wa
ter
)
.
Inthecaseofthesaltbridge
,thisrequires
taking into account the desolvation of the
amino group and carboxyl group as the
salt bridge forms. This desolvation is an
energetically expensive process because al-
though water has no net charge, it still has
a strong attraction to charged groups be-
cause of its dipole moment (i.e. separation
of charge within the molecule) (Fig. 6). In
addition to this effect, water decreases all
electrostatic interactions through a general
shielding effect.
An example of salt bridges in action may
be found in the structure of the restriction
endonuclease
ECO
RV
bound
to
an
oligomeric double-stranded DNA. Along
the contact surface of the nuclease and the
polynucleotide, there are seven positively
charged groups (arginines, lysines, and
histidines)
within
salt
bridge–forming
range of the anionic phosphate backbone
of DNA, while no negatively charged
groups (aspartic and glutamic acids) are
in similar positions. These nonspeci±c salt
bridges ensure that the nuclease will bind
to DNA in general, while other speci±c
hydrogen bonding
interactions
give
it
speci±city for its unique cleavage site.
2.2.2
Hydrogen Bonding
Hydrogen bonding is also an electrostatic
interaction, although the participants are
not necessarily formally charged. Exam-
ples of hydrogen bonds are shown in Fig. 7.
The de±ning characteristics are (1) a hy-
drogen atom attached to an electronegative
atom such as nitrogen or oxygen (this is
the hydrogen bond donor) and (2) a lone
electron pair on a nitrogen or oxygen (this
is the hydrogen bond acceptor). The hy-
drogen has a partial positive charge due
to the electron-withdrawing nature of the
atom to which it is attached, and this in-
teracts with the negatively charged lone
pair on the hydrogen bond acceptor in
an essentially coulombic attraction. Hy-
drogen bonds also contribute on the order
of 0 to 3 kcal mol
1
to molecular associ-
ations, although there can be variation in
this number.
X
H
Y
dd
X and Y are electronegative atoms such as O and N
O
N
H
R
O
N
O
OR
H
NN
O
O
N
N
H
N
H
H
N
N
Fig. 7
Hydrogen bond formation in (left) protein beta sheets and
(rights) nucleotide base pairing.
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