AFM experiment

The avidin-biotin complex, known for its extremely high affinity (Green, 1975), has been studied experimentally more extensively than most other protein-ligand systems. The adhesion forces between avidin and biotin have been measured directly by AFM experiments (Florin et al., 1994 Moy et al., 1994b Moy et al., 1994a). SMD simulations were performed on the entire tetramer of avidin with four biotins bound to investigate the microscopic detail of nnbinding of biotin from avidin (Izrailev et al., 1997). 

The SMD simulations were based on an NMR structure of the Ig domain 127 of the cardiac titin I-band (Improta et ah, 1996). The Ig domains consist of two /9-sheets packed against each other, with each sheet containing four strands, as shown in Fig. 8b. After 127 was solvated and equilibrated, SMD simulations were carried out by fixing one terminus of the domain and applying a force to the other in the direction from the fixed terminus to the other terminus. Simulations were performed as described by Eq. (1) with V = 0.5 A/ps and if = 10 ksT/A 414 pN/A. The force-extension profile from the SMD trajectory showed a single force peak as presented in Fig. 8a. This feature agrees well with the sawtooth-shaped force profile exhibited in AFM experiments. 

This result reflects the Kramers relation (Gardiner, 1985). A millisecond time of unbinding, i.e.. Tact 1 ms, corresponds in this case to a rupture force of 155 pN. For such a force the potential barrier AU is not abolished completely in fact, a residual barrier of 9 kcal/mol is left for the ligand to overcome. The AFM experiments with an unbinding time of 1 ms are apparently functioning in the thermally activated regime. 

The rupture force measured in AFM experiments is given, therefore, by the average slope of the energy profile minus a correction related to the effects of thermal fluctuations. Equation (11) demonstrates that the rupture force measured in AFM experiments grows linearly with the activation energy of the system (Chilcotti et ah, 1995). A comparison of (10) and (11) shows that the unbinding induced by stiff springs in SMD simulations, and that induced by AFM differ drastically, and that the forces measured by both techniques cannot be readily related. 

That simulation study [49] aimed at a microscopic interpretation of single molecule atomic force microscope (AFM) experiments [50], in which unbinding forces between individual protein-ligand complexes have been m( asured... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

However, one significant difference between the AFM experiment and its simulations cannot be avoided at present Whereas the AFM experiment... 

The dependence of friction on sliding velocity is more complicated. Apparent stick-slip motions between SAM covered mica surfaces were observed at the low velocity region, which would disappear when the sliding velocity excesses a certain threshold [35]. In AFM experiments when the tip scanned over the monolayers at low speeds, friction force was reported to increase with the logarithm of the velocity, which is similar to that observed when the tip scans on smooth substrates. This is interpreted in terms of thermal activation that results in depinning of interfacial atoms in case that the potential barrier becomes small [36]. 

Fig. 19—Force curve in a AFM experiment as the probe travels along the surface of NaCI crystal (from Ref. [14]).

The objective of this book is to highlight the important strides being made toward a molecular understanding of the processes that occur at surfaces through the unique information provided by the proximal scanning probe family of techniques this principally involves scanning tunneling microscopy (STM) but some atomic force microscopy (AFM) experiments are also included. 

It is difficult to evaluate the shape of such dendritic particles experimentally. However, some insight can be gained by atomic force microscopy (AFM) and transmission electron microscopy experiments (TEM). AFM experiments can give information about the overall size of the dendrimers, as shown by De Schryver [43], by spincoating very dilute solutions of dendrimers like 30 on mica, then visualizing single dendrimers. Their height measured in this manner corresponds very well to the diameters calculated by molecular mechanics simulations. First results from TEM measurements also confirm the expected dimensions [44]. Unfortunately, due to resolution limits, up to now direct visual information could not be obtained about the shape of the dendrimers. 

Importantly, the AFM experiments set a lower limit of 350 pN for the unraveling of individual nucleosomes. We will come back to the significance of these results later. 

Figure 2.21. Schematic representation of colloid probe-PDMS droplet interaction during the AFM experiment. Solid line depicts the undeformed profile of the PDMS droplet and the rigid colloid probe. Dashed line shows the deformed profile of the PDMS droplet.

Fig. 5 Evolution of the forces during an AFM experiment. Note that the original position of the cantilever is shown in blue...

An increase of the invasiveness of AFM experiments allows the probing of the moleciflar parameters of, and molecular interactions associated with, the DNA molecule rather than merely its imaging. As mentioned before, other... 

An enormous amount of work, part of which has been recently reviewed [28,29], has been reported regarding the immobilisation of DNA molecules in high concentration layers, mostly referring to hard surfaces (e.g., glass or mica) and mainly for practical devices and AFM experiments. However, the rapid development of, and increasing demand for, DNA-based microdevices both push for lower cost, easily processable materials, and towards disposable devices. As polymers seem to be the logical choice, the resulting DNA layers will almost certainly be amorphous. 

The van der Waals force occurring in STM and AFM is much smaller than the van der Waals force between a neutral hydrogen atom and a proton. Actually, in STM and AFM experiments on conducting materials, the atoms near the gap are nearly neutral, which is similar to the situation of a pair of neutral hydrogen atoms rather than a proton with a neutral hydrogen atom. The van der Waals force between a pair of neutral hydrogen atoms is also a well-studied problem. The exact result at large distances is (Landau and Lifshitz, 1977) ... 

For Ag(lOO) crystals, a similar electrochemical behavior was observed with quasi-reversible adsorption/desorption of Cd and surface alloying, faster than for Ag(lll) [286]. Electrochemical and AFM experiments have shown that the alloying process consisted of two steps a very fast reaction occurring within a few atomic layers, and a much slower one, represented by a solid-state diffusion process [244]. 

Vidu et al. [424] have studied the kinetics of thin alloy film formation and growth during Cd electrodeposition on Au(lOO) and Ag(lOO) within the Cd UPD range from —0.3 to —0.45 V. Electrochemical and AFM experiments in 1 mM CdS04 and 0.05 M H2SO4 solutions have revealed that the overall alloying process comprises two processes the first occurring relatively fast within a few atomic layers (D 10 , and the second much slower... 

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