Biomolecular Recognition: Analysis of DFS Data - Dynamic Force Spectroscopy and Biomolecular Recognition - page 166

polymers with the study of Ralstonia pickettii T1 poly[(R)-3-hydroxybutyrate]
(P(3HB)) depolymerase with P(3HB) and poly(L-lactic acid) (PLLA) (Matsumoto
et al. 2008).
Regarding entire cells or viruses, DFS obtained promising results such as the
study of LFA-1 expressed on Jurka T cells and intercellular adhesion molecule-1
and -2 (ICAM-1 and ICAM-2) (Wojcikiewicz et al. 2006); human rhinovirus 2
(HRV2) with very low-density lipoprotein receptor (VLDLR)1-8 (Rankl et al. 2008);
transferring with HeLa cells (Yersin et al. 2008); heregulin 1 (HRG) with cells

expressing growth factor receptors (HER2 and HER3) (Shi et al. 2009); junctional
adhesion molecules (JAM) with murin L929 cells expressing JAM-A (Vedula et al.
2008). DFS has also been attempted on cell-cell interactions such as the study of
E-cadherin expressed on the surface of live human parental breast cancer cells and
cells reexpresseing a-catenin (Bajpai et al. 2009).
Finally, DFS has been useful not only in the study of unfolding and extraction
of consensus sequence for TM protein segments (WALP), with a N-terminal Cys
residue, from gel-phase DPPC and DSPC bilayers (Contera et al. 2005); unfolding
membrane proteins such as the Na+/H+ antiporter NhaA (Kedrov et al. 2008), bovine
rhodopsin and bacteriorhodopsin (Sapra et al. 2008); myomesin the most prominent
structural component of the sarcomeric M-band (Bertoncini et al. 2005); but also in
the study of nonbonded rupture such as in the interaction between a silicon nitride
tip and 1-nonanethiol self-assembled monolayer on gold (Ptak et al. 2009).
What is the strength of AFM over other techniques for measuring kinetics
parameters? Undoubtedly, the advantage of AFM is the possibility to measure bio-
logical system with apparent ultra-high affinities in solution that would take weeks or
years with classical techniques such as surface plasmon resonance. The avidin-biotin
complex, which is widely used in biotechnology, epitomizes the need for alternative
techniques due to its femtomolar affinity (Green, 1963). Such affinity is due to the
tetrameric quaternary structure of avidin, that is, with the presence of four binding
sites toward biotin. The importance of multiple bonds will be emphasized later in
this chapter. The first study of avidin-biotin complex using AFM was made in 1994
(Florin et al. 1994) and about 20 reports followed on this system or its bacterial
equivalent of streptavidin-biotin complex (Teulon et al. 2011). Avidin-biotin sys-
tems have been studied using at least 10 different experimental setups that explained
the current lack of consensus in the results (Walton et al. 2008) although a reconcil-
ing hypothesis has been recently proposed (Teulon et al. 2011). Avidin-biotin system
has also been chosen for performing molecular simulations (Zhou et al. 2006; Wal-
ton et al. 2008), for measuring the energy landscape roughness (Rico & Moy, 2007),
or to test concepts related to multiple-bond systems (Guo et al. 2008). It should be
emphasized that DFS can be performed with other techniques different from AFM
such as the biomembrane force probe with micropipettes (Merkel et al. 1999), opti-
cal tweezers (Arya et al. 2005; Andersson et al. 2006; Bjornham et al. 2009), or the
laminar flux chamber (Robert et al. 2007).
Why write a chapter on DFS data analysis? The first thing that comes to mind
is probably the lack of details in publications. Due to the restriction in page length, it

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