Biomolecular Recognition: The Current Challenge - Dynamic Force Spectroscopy and Biomolecular Recognition - page 27

and electronic charges. These charges are expected to generate attractive or repulsive
interactions between approaching protein surfaces. A prominent example is provided
by hydrogen bonds. As a consequence of the. high electronegativity of atoms such
as oxygen or nitrogen, the electronic cloud involved in a bond such as O-H or N-H is
asymmetric, resulting in a net negative charge on oxygen or nitrogen and a net pos-
itive charge on the proton H. As a consequence, an atom with a net negative charge
such as oxygen, will be attracted by H atoms bearing a net positive charge. While this
simple mechanism may be considered as the basis of the hydrogen bond, it must be
emphasized that this is only an approximation, and a quantum mechanical approach
is required to achieve a more accurate description of this interaction. A notable con-
sequence is that the hydrogen bond is dependent on the orientation of interaction
molecules, not only on the distance between positive and negative sites, and there
is still an interest in quantitative modeling of this interaction [37]. Hydrogen bonds
such as O-H-O play a major role in protein or nucleic acid organization. Also, they
are thought to account for the highly particular structure of water [58]. The H 2 O
molecule may be viewed as a tetrahedron with two positive and two negative charges
on the four vertices, which may allow extensive clustering of these molecules. This
extensive hydrogen bonding capacity of water is responsible for its high boiling point
and dielectric constant.
As a consequence, protein-protein association often results in the replacement of
protein-solvent hydrogen bonds with protein-protein hydrogen bonds, which makes
it difficult to predict the total contribution of hydrogen bonds to biomolecule inter-
actions. While the energy of a typical hydrogen bond may be on the order of about 8
k B T , the contribution of an hydrogen bond to a protein-protein interaction may not
be higher than k B T [43].

1.5.1.3 Different Timescale: Electrodynamic Interactions
In addition to the aforementioned rather static view of electrical forces between fixed
charges in a biological environment, other interactions are dependent on different
timescales and deserve a separate treatment. The basis is the presence of a dipole
of moment p that may be permanent or induced by the presence of a surrounding

electric field E according to Equation 1.9

p = α E (1.9)

where αis called the polarizability. Further, the interaction energy between a dipole
and an electric field is simply the scalar product . − p E , and the electric field gener-

ated at point r (starting from the dipole) is

) r 3 E =( 1 / 4πε grad ( p . r / ) (1.10)

These equations are the basis of two interactions:
The so-called Keesom interaction term represents the interaction between
two freely rotating dipoles p 1 and p 2 . Following Boltzmann's law, the relative