Biomedical Engineering Reference
In-Depth Information
6.2.3 DFS
AND
C
OMPUTATIONAL
M
ETHODS
Both the design of DFS experiments and the corresponding data analysis can take
large advantage of computational methods and in particular of docking and steered
molecular dynamics (see also Chapter 1). To achieve effective and functional immo-
bilization of the biomolecules to the substrates, the knowledge of the interaction sites
between the two partners would be crucial to maximize the interaction probability
by avoiding the involvement of the complex binding sites in the anchoring proce-
dures (Bonanni et al., 2005; Bizzarri et al., 2007). If the molecular structure of the
complex is not known, computational docking can be applied to predict the most
probable arrangement of the complex starting from the 3D structures of the indi-
vidual partners (Jones and Thornton, 1996). Briefly, the surfaces of each partner are
probed by looking for all the possible binding modes that are then ranked according
to a score function taking into account geometric, electrostatic, energy criteria, and
so on (Camacho and Vajda, 2002). The predicted structure of the complex can also
be used to evaluate the probability that the two partners may form a complex upon
their immobilization on the surfaces, resulting in some help to estimate the unbind-
ing frequency (Bizzarri et al., 2009). Notably, the predicted structure of the complex
could be also extremely useful to analyze the unbinding process in connection with
the structural properties at the complex interface (i.e., the H-bond network, the salt
bridges, or the charge distribution).
DFS experiments can also be combined with steered molecular dynamics, a com-
putational tool suitably developed from molecular dynamics simulation, to predict
the unbinding dynamics of biomolecules under the application of an external force
(Rief and Grubm uller, 2002). More specifically, the dynamics of the system can be
followed at atomic resolution while one or both the biomolecular partners, bound to
a spring, are pulled at a constant velocity to induce their unbinding. Although the
pulling speed of the simulations (m/s range) is generally orders of magnitude higher
than that used in DFS (
μ
/s range), steered molecular dynamics has been demon-
strated to provide information on the sequence of the unbinding steps, thus helping to
elucidate the molecular mechanisms regulating the unbinding processes (Grubm uller
et al., 1996; Izrailev et al., 1997; Bayas et al., 2003).
6.3 DFS STUDIES OF BIOMOLECULAR COMPLEXES
The selected DFS studies of biomolecular complexes have been grouped into five
subsections, each one of them having been focused on a specific class of biologi-
cal systems. In each section, the most important aspects of the experimental setup
(immobilization procedure, cantilever spring constant, and loading rate range) and
the main results (unbinding force, dissociation rate, and energy barrier width) for a
collection of DFS studies have been summarized in five tables. Some of the investi-
gations reported in these tables are discussed into details with some emphasis on the
relevance of the DFS approach for the biological functions in which the systems are
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