In the many publications and books authors write that the probe diameter is the most important factor for resolution in range of nanometers. We have probes with 10 nm diameter, it is possible to vizualize enzymes with such "big" probe?
It may also be helpful to use tapping/dynamic mode setting of the AFM, rather than contact mode.
The dimension of he probe is not the main parameter for AFM concerning protein samples. Of course the more small the better. However there are some other more important parameters:
1. Proteins have to be adsorbed firmly on the surface. Often AFM users use Mica. Mica is not reactive enough to adsorb the proteins. Try with simple glass plate (microscope plates). You can increase the adsorption by treating the glass plate with HCL or NaOH prior to deposition (just put a drop of HCL or NaOH on the plate clean with water and deposit protein..try different concentrations..there are no rules for things like that).
2. Try AFM in Water or Mother liquid if your AFM is adapted for that and search for an ionic strength that permits to the probe to stay far enough from the protein in order not to alterate mecanically its structure.
3. The AFM probe as well as the surface deforme the proteins. The best way to have a pertinent structural information would be to order the proteins on the surface and study the bidimensional ordered array; In this case the proteins are more rigid within the 2D ordered array. Also this method permits to nicely filter the AFM images by Fourrier filters
4. In any case AFM and proteins is a very very very difficult experimental adventure. Be patient, Try meny probes, try all possibilities ...tapping mode, contact, liquid everything...and don't deseperate. Just continue to try..You will have an nice image after ...god knows
Good Luck
For scanning biological samples like protein or DNA, the tapping mode is mostly preferred as the samples are very soft. Yes to get a good trace and retrace match is a matter of patience. So be patient and all the best
All above right - it really depends what you want to see...
You might want to dive into some old publications to learn some tricks... Perhaps even ask Prof. Radmacher for some non-published Diploma-Thesis:
Radmacher, M., M. Fritz and P. K. Hansma (1995). "Imaging soft samples with the atomic force microscope: gelatin in water and propanol." Biophys. J. 69(July): 264-270.
Radmacher, M., M. Fritz, J. P. Cleveland, D. R. Walters and P. K. Hansma (1994). "Imaging adhesion forces and elasticity of lysozyme adsorbed on mica by atomic force microscopy." Langmuir 10: 3809-3814.
However, when you want to dive into structural resolution, I doubt that AFM will help you a lot....
It is also better to do the scanning in liquid so that the topographical feature still retains. otherwise under air, the proteins donot retains its original shape
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