This work was supported by the Max Planck Society, the German Cancer Research Center, the University of T&#252;bingen, and the Bundesministerium f&#252;r Bildung und Forschung (grant no. 0312040).
We thank Eduard Hermann for helping us automate the analysis of the force curve data and Dr. Jakob Suckale for careful reading of this manuscript.

1. Preparation of Supported Lipid Bilayers (SLB)11,12,21
<ol>
	<li>Preparation of Lipid Mixture and Multilamellar Vesicle Suspensions
	<ol>
		<li>Prepare the following buffers beforehand.
		<ol>
			<li>Prepare PBS buffer at concentrations of 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HPO4, and 137 mM NaCl, pH 7.2.</li>
			<li>Prepare SLB (supported lipid bilayer) buffer at concentrations of 150 mM NaCl, 10 mM HEPES, pH 7.4.</li>
			<li>Prepare a solution of 1 M CaCl2.</li>
		</ol>
		</li>
		<li>Dissolve the following lipids in chloroform at a desired concentration: for example, di-oleoyl-phosphatidylcholine (DOPC) at 25 mg/ml, sphingomyelin (SM) at 25 mg/ml and cholesterol (Chol) at 10 mg/ml.</li>
		<li>Take 18.38 &#181;l of DOPC, 17.10 &#181;l of SM and 11.30 &#181;l of Chol to make a solution with 1 mg of total lipids in a 2:2:1 DOPC:SM:Chol molar ratio. Vary the volumes accordingly based on the concentrations of the lipids prepared in 1.1.2. However, maintain the molar ratio at 2:2:1 DOPC:SM:Chol, as changing the molar ratio will change the phase characteristics of the membrane25.</li>
		<li>Mix the solution completely by vortexing. Add a fluorescent lipidic dye at 0.05 mol % if one wishes to visualize the bilayer by a fluorescence microscope. 
		Note: The family of long-chain dialkylcarbocyanines, like DiD, DiI and DiO span a wide range of wavelengths and can be ideally used to label lipid membranes. Alternatively, fluorescently labeled lipids, like rhodamine-phosphatidylethanolamine or BODIPY-cholesterol can be used. In any case, the concentration of the dye should be optimized according to the microscopy setting, keeping in mind that high concentrations of the fluorophore bound to the lipid can change the lipid behavior19.</li>
		<li>Dry off the chloroform using N2 gas (or any available inert gas such as Ar and He).</li>
		<li>Further dry the lipid mixture under vacuum for at least 1 hr. 
		Note: If storing this lipid mixture, purge air with inert gas (N2, Ar or He) and store at -20 &#176;C. Aliquot excess lipids-in-chloroform into small brown vials. Dry them in a similar manner as the lipid mixture, displace air with inert gas (N2, Ar or He) and store at -20 &#176;C.</li>
		<li>Dissolve the dried lipids in PBS buffer to a concentration of 10 mg/ml.</li>
		<li>Vortex the mixture vigorously for about 20 sec to 1 min to get a cloudy suspension, containing multilamellar vesicles. Make sure that the there are no lipid films sticking to the sides of the vial.</li>
		<li>Distribute this suspension into 10 &#181;l aliquots (1 mg of lipid makes 10 aliquots).</li>
		<li>Store at -20 &#176;C until further use.</li>
	</ol>
	</li>
	<li>Preparation of Unilamellar Vesicles 
	Note: Various sizes of unilamellar vesicles can be prepared using the sonication method or the extrusion method. Sonication uses sound energy to agitate the mixture and separate the layers of the multilamellar suspension. This is indicated by clearing up of the hazy suspension. Extrusion forces the multilamellar vesicles to pass through a membrane filter with a definite pore size.
	<ol>
		<li>Sonication Method
		<ol>
			<li>Take the 10 &#181;l of multilamellar lipid suspensions and add 150 &#181;l of SLB buffer.</li>
			<li>Transfer the mixture into small (2 ml) capped glass vials and seal with Parafilm.</li>
			<li>Sonicate the mixture at room temperature in a bath sonicator for 10 min or until it becomes clear to yield small unilamellar vesicles (SUVs, below 50 nm in diameter).</li>
		</ol>
		</li>
		<li>Extrusion Method
		<ol>
			<li>Take the 10 &#181;l of multilamellar lipid suspensions and add 150 &#181;l of SLB buffer.</li>
			<li>Transfer the suspension into a cryogenic tube.</li>
			<li>Freeze the lipid suspension by submerging the cryogenic tube for a few seconds in liquid nitrogen.</li>
			<li>Thaw the lipid suspension by submerging the cryogenic tube in a water bath at room temperature or 37 &#176;C for a few minutes. Repeat the freeze-thaw steps at least 10 times.</li>
			<li>In order to extrude the lipid suspension, use a polycarbonate membrane with 200 nm pore size (other pore sizes are available like, 100 nm or 400 nm) and a commercial extrusion device26. 
			Note: Currently, there are two extruder devices commercially available: a manual extruder is available for small volumes (200 &#181;l to a few ml). In this case, the sample is extruded through the membrane by manually pushing the suspension back and forth between two syringes. Depending on the manufacturer, lipid aliquots would need to be combined to reach minimum volume of the set up. For bigger volumes (up to 50 ml) more sophisticated devices are used in which the suspension is forced through the polycarbonate membrane by using compressed gas. Set-up and extrusion conditions can change according to the model. Refer to the instructions from the manufacturer before use. This protocol refers to the manual extruder for small volumes.</li>
			<li>Equilibrate the extruder in water by passing water through the extruder. Immerse the membrane in water.</li>
			<li>Place the membrane between the two pistons, assemble the device and equilibrate in buffer, by passing the buffer through the extruder, from one syringe to the other.&#160;This step allows additionally testing the leakiness of the system. If it leaks, disassemble and reassemble it again changing the membrane.</li>
			<li>Take the lipid suspension using one syringe of the extruder (&#39;dirty side&#39;).</li>
			<li>Attach the syringe containing the lipid suspension on one chamber and the empty syringe on the opposing chamber.</li>
			<li>Push the syringe on one end. Pass the solution through the membrane and into the opposing syringe. This is the 1st pass.</li>
			<li>Pass it through the membrane for a total of 31 times such that the solution ends up on the opposing syringe (&#39;clean side&#39;). 
			Note: Check the membrane after extruding. If it was broken, then extrusion process was not successful and needs to be repeated.</li>
			<li>Empty the syringe into a small tube. Large unilamellar vesicles (LUVs) are stable for 1-2 days if kept at 4 &#176;C.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Preparation of Mica and Coverslips
	<ol>
		<li>Wash coverslips first in water and then in ethanol. Air dry.</li>
		<li>Take mica discs and peel off the outer layer using adhesive tape.</li>
		<li>Attach the mica disc onto the coverslip. Transparent optical glues are optimal so that one can check the bilayers with a fluorescence microscope.</li>
		<li>Attach plastic cylinders (2.5 cm outer diameter, 2 cm inner diameter, and 0.5 cm height) using optical glue/grease. Make sure that everything is sealed and that there are no leaks. Use grease when wanting to re-use the cylinders as they can be easily detached from the coverslip and washed. The dimensions of the plastic cylinders depend on the size of the AFM cantilever holder and should be adjusted accordingly.</li>
	</ol>
	</li>
	<li>Deposition of Unilamellar Vesicles on Solid Support
	<ol>
		<li>Pipet the whole liposome solution directly onto the mica. Add more SLB buffer to reach a volume of 300 &#181;l.</li>
		<li>Add 0.9 &#181;l of 1 M calcium chloride solution to reach a final concentration of 3 mM Ca2+.</li>
		<li>Incubate at 37 &#176;C for 2 min and then at 65 &#176;C for at least 10 min. Always cover the bilayers with buffer. Contact with air and air bubbles will destroy it. During incubation, add more buffer if necessary, especially if incubating at higher temperatures. 
		&#8203;Note: Incubation temperatures vary according to the lipid mixtures and phases required. Incubation time of at least 10 min is needed to form supported bilayers, but it could be longer, depending on the temperature and composition.</li>
		<li>Wash the bilayer with hot (65 &#176;C) SLB buffer 15-20 times to remove calcium and unfused vesicles. Take extra care during the washing steps to keep the bilayer under buffer and gently pipet the washing solution to avoid destroying the bilayer.</li>
		<li>Cool supported bilayers to room temperature before AFM measurements. This is needed to form the different phases of the membrane as well as minimize thermal drift in the instrument.</li>
	</ol>
	</li>
</ol>
2. Atomic Force Microscopy Measurements11,12
<ol>
	<li>Imaging 
	Note: Perform atomic force microscopy imaging in contact mode or tapping mode. Image supported bilayers in solution; do not allow solution to evaporate completely as this will destroy the bilayers. As one would be working with buffer, please observe safety precautions in making sure that any AFM part is protected from liquid spills.
	<ol>
		<li>Select a soft cantilever (below 0.2 N/m spring constant is advised) and mount it to the AFM. The choice of cantilever stiffness is more critical for force spectroscopy (and this will be discussed later).</li>
		<li>Mount the sample on the AFM stage and make sure that all vibration-isolation modules are turned on. Wait for at least 15 min to equilibrate and reduce thermal drift of the system. Depending on the AFM set-up, tuning and imaging specifications may vary. Consult the manufacturer&#8217;s handbook.</li>
		<li>Approach the sample with the AFM tip until contact.</li>
		<li>Since lipid bilayers are usually 4 nm in height, use the Z-range of the instrument that will give the highest z-resolution (for example 1.5 &#181;m).</li>
		<li>Select a region to image. To get an overview of the lipid bilayer, a 50 &#181;m x 50 &#181;m or 25 &#181;m x 25 &#181;m region will be a good starting point to image. If smaller features appear, one can image in smaller areas (10 &#181;m x 10 &#181;m, or 2 &#181;m x 2 &#181;m). The choice of the imaging area also depends on the working range of the piezoelectric scanner. Please consult the instrument manual for this.</li>
		<li>As bilayers are very fragile, adjust the set point of the AFM tip during imaging to keep the force at minimum and correct for thermal drift, while maintaining contact with the sample. In contact mode, minimize the set point. In tapping mode, maximize the set point.</li>
		<li>Process images by fitting each scan line to polynomial leveling functions. Perform line removal for scans that lose contact with the membrane using the proprietary software of the AFM manufacturing company.</li>
	</ol>
	</li>
	<li>Force Spectroscopy
	<ol>
		<li>Calibrate the cantilever following the instructions according to manufacturer&#8217;s protocol. Calibration allows the conversion of the electrical signal of the photodiodes to force (Figure 1B).
		<ol>
			<li>Calibrate the tip&#8217;s sensitivity to measure deflection as z-piezo movement (in units of length) instead of electrical signal in volts. 
			Note: AFM detects changes in the deflection of the cantilever using a laser reflected at the back of the cantilever. The laser reaches a photodiode that can spatially detect the position of the laser spot. A change in the deflection of the cantilever as it bends upon contact with the sample is detected by this photodiode as &#8220;vertical deflection&#8221;, and this is in the units of voltage. Since the cantilever is moved by the z-piezo, the vertical deflection is related to the movement in the z-piezo. The ratio between vertical deflection and z-movement is called sensitivity and converts voltage to distance.</li>
			<li>Calculate the cantilever spring constant using the thermal noise frequency method, usually incorporated in the AFM software. In this method, plot the amplitude of vibration from noise with respect to frequency of oscillation, creating a power spectral density plot. This plot will show a peak around the resonance frequency. The frequency where the amplitude is the greatest is the resonance frequency. Fit a Lorentzian function around the peak to automatically calculate the spring constant by the software. Some useful resources for the theory of the thermal noise method are given in references27-30.</li>
		</ol>
		</li>
		<li>After imaging an area of the bilayer, select a 5 &#181;m x 5 &#181;m region in the bilayer to perform force spectroscopy.</li>
		<li>Set up the AFM so that it takes force curves in a 16 x 16 grid of that region. This results in 256 force curves per region. The space between two neighboring points should be enough to avoid that the membrane area being probed by one point would coincide with the next point. This is dependent on the tip radius. A 100 nm distance between two points would be ideal. Divide the 5 &#181;m x 5 &#181;m region into 16 x 16 grid. Depending on the size of the phase, one can select a smaller or bigger region, and then adjust the grid size accordingly.</li>
		<li>Set z-piezo displacement to 400 nm. This determines the maximum range of movement of the z-piezo. It should be big enough to make sure that the cantilever has fully retracted away from the sample in between measurements.</li>
		<li>Set approach speed to 800 nm/sec and retract speed to 200 nm/sec. Use an approach speed between 400 to 6,000 nm/sec depending on the bilayer composition and lipid phase to be studied6,16.</li>
		<li>After setting up all the parameters, acquire force curves, by pressing the &#8220;run&#8221; button of the AFM software.</li>
		<li>Save force curves as force vs. height curves (a measure of z-piezo movement). This does not take into account the bending of the cantilever when in contact with the sample. During the data processing step, the AFM software allows correction for cantilever bending to get force vs. tip-sample separation curves (Figure 1C), which will give proper values for bilayer thickness. The correction values are usually incorporated in the calibration, which is saved with each force curve. Calculate tip-sample separation by subtracting the vertical deflection from the piezo movement at a given point. 
		Note: The peak in the approach force curve (the force value goes down even if the cantilever movement is still on the approach cycle) is the breakthrough force of the membrane, while the difference between the position of this peak and the position of the point where the force begins to rise up again provides the thickness of the membrane.</li>
		<li>Acquire at least 500 force curves for each condition to get good statistics. Plot a histogram of the values using programs like Origin or MatLab, and fit the histograms to a Gaussian distribution to get the peak and width of the distribution.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Binnig, G., Quate, C. F., Gerber, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+Force+Microscope.">Atomic Force Microscope.</a> Phys. Rev. Lett. 56, 930-933 (1986).</li><li>Hansma, P. K., Elings, V. B., Marti, O., Bracker, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scanning+Tunneling+Microscopy+and+Atomic+Force+Microscopy:+Application+to+Biology+and+Technology.">Scanning Tunneling Microscopy and Atomic Force Microscopy: Application to Biology and Technology.</a> Science. 242, 209-216 (1988).</li><li>Gaczynska, M., Osmulski, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AFM+of+biological+complexes:+What+can+we+learn.">AFM of biological complexes: What can we learn.</a> Curr, Opin. Colloid In. 13, 351-367 (2008).</li><li>Goksu, E. I., Vanegas, J. M., Blanchette, C. D., Lin, W. -. C., Longo, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AFM+for+structure+and+dynamics+of+biomembranes.">AFM for structure and dynamics of biomembranes.</a> BBA-Biomembranes. 1788, 254-266 (2009).</li><li>Muller, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AFM:+A+Nanotool+in+Membrane+Biology.">AFM: A Nanotool in Membrane Biology.</a> Biochemistry-US. 47, 7986-7998 (2008).</li><li>Redondo-Morata, L., Giannotti, M. I., Sanz, F., Bar&#243;, A. M., Reifenberger, R. G., Sanz, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Atomic Force Microscopy in Liquid: Biological Applications. , (2012).</li><li>Castellana, E. T., Cremer, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solid+supported+lipid+bilayers:+From+biophysical+studies+to+sensor+design.">Solid supported lipid bilayers: From biophysical studies to sensor design.</a> Surf. Sci. Rep. 61, 429-444 (2006).</li><li>Frederix, P. L. T. M., Bosshart, P. D., Engel, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+Force+Microscopy+of+Biological+Membranes.">Atomic Force Microscopy of Biological Membranes.</a> Biophys. J. 96, 329-338 (2009).</li><li>Mennicke, U., Salditt, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+Solid-Supported+Lipid+Bilayers+by+Spin-Coating.">Preparation of Solid-Supported Lipid Bilayers by Spin-Coating.</a> Langmuir. 18, 8172-8177 (2002).</li><li>Raviakine, I., Brisson, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Formation+of+Supported+Phospholipid+Bilayers+from+Unilamellar+Vesicles+Investigated+by+Atomic+Force+Microscopy.">Formation of Supported Phospholipid Bilayers from Unilamellar Vesicles Investigated by Atomic Force Microscopy.</a> Langmuir. 16, 1806-1815 (2000).</li><li>Chiantia, S., Ries, J., Kahya, N., Schwille, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combined+AFM+and+Two-Focus+SFCS+Study+of+Raft-Exhibiting+Model+Membranes.+.">Combined AFM and Two-Focus SFCS Study of Raft-Exhibiting Model Membranes. .</a> ChemPhysChem. 7, 2409-2418 (2006).</li><li>Unsay, J., Cosentino, K., Subburaj, Y., Garcia-Saez, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cardiolipin+effects+on+membrane+structure+and+dynamics.">Cardiolipin effects on membrane structure and dynamics.</a> Langmuir. 29, 15878-15887 (2013).</li><li>Dom&#232;nech, &. #. 2. 1. 0. ;., Sanz, F., Montero, M. T., Hern&#225;ndez-Borrell, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermodynamic+and+structural+study+of+the+main+phospholipid+components+comprising+the+mitochondrial+inner+membrane.">Thermodynamic and structural study of the main phospholipid components comprising the mitochondrial inner membrane.</a> BBA-Biomembranes. 1758, 213-221 (2006).</li><li>Dom&#232;nech, &. #. 2. 1. 0. ;., Morros, A., Caba&#241;as, M. E., Teresa Montero, M., Hern&#225;ndez-Borrell, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Supported+planar+bilayers+from+hexagonal+phases.">Supported planar bilayers from hexagonal phases.</a> BBA-Biomembranes. 1768, 100-106 (2007).</li><li>Garcia-Saez, A. J., Chiantia, S., Schwille, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+line+tension+on+the+lateral+organization+of+lipid+membranes.">Effect of line tension on the lateral organization of lipid membranes.</a> J Biol Chem. 282, 33537-33544 (2007).</li><li>Alessandrini, A., Seeger, H. M., Caramaschi, T., Facci, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+Force+Spectroscopy+on+Supported+Lipid+Bilayers:+Effect+of+Temperature+and+Sample+Preparation.">Dynamic Force Spectroscopy on Supported Lipid Bilayers: Effect of Temperature and Sample Preparation.</a> Biophys. J. 103, 38-47 (2012).</li><li>Butt, H. -. J., Franz, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rupture+of+molecular+thin+films+observed+in+atomic+force+microscopy+I.+Theory.">Rupture of molecular thin films observed in atomic force microscopy I. Theory.</a> Physical Review E. 66, 031601 (2002).</li><li>Garcia-Manyes, S., Oncins, G., Sanz, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+Temperature+on+the+Nanomechanics+of+Lipid+Bilayers+Studied+by+Force+Spectroscopy.">Effect of Temperature on the Nanomechanics of Lipid Bilayers Studied by Force Spectroscopy.</a> Biophys. J. 89, 4261-4274 (2005).</li><li>Chiantia, S., Kahya, N., Schwille, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Raft+domain+reorganization+driven+by+short-+and+long-chain+ceramide:+a+combined+AFM+and+FCS+study.">Raft domain reorganization driven by short- and long-chain ceramide: a combined AFM and FCS study.</a> Langmuir. 23, 7659-7665 (2007).</li><li>Canale, C., Jacono, M., Diaspro, A., Dante, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Force+spectroscopy+as+a+tool+to+investigate+the+properties+of+supported+lipid+membranes.">Force spectroscopy as a tool to investigate the properties of supported lipid membranes.</a> Microsc. Res. Techniq. 73, 965-972 (2010).</li><li>Garc&#237;a-S&#225;ez, A. J., Chiantia, S., Salgado, J., Schwille, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pore+Formation+by+a+Bax-Derived+Peptide:+Effect+on+the+Line+Tension+of+the+Membrane+Probed+by+AFM.">Pore Formation by a Bax-Derived Peptide: Effect on the Line Tension of the Membrane Probed by AFM.</a> Biophys. J. 93, 103-112 (2007).</li><li>Moreno Flores, S., Toca-Herrera, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+new+future+of+scanning+probe+microscopy:+Combining+atomic+force+microscopy+with+other+surface-sensitive+techniques,+optical+microscopy+and+fluorescence+techniques.">The new future of scanning probe microscopy: Combining atomic force microscopy with other surface-sensitive techniques, optical microscopy and fluorescence techniques.</a> Nanoscale. 1, 40-49 (2009).</li><li>Simons, K., Vaz, W. L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Model+Systems,+Lipid+Rafts,+and+Cell+Membranes1.">Model Systems, Lipid Rafts, and Cell Membranes1.</a> Annu. Rev. Bioph. Biom. 33, 269-295 (2004).</li><li>Pike, L. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rafts+defined:+a+report+on+the+Keystone+symposium+on+lipid+rafts+and+cell+function.">Rafts defined: a report on the Keystone symposium on lipid rafts and cell function.</a> The Journal of Lipid Research. 47, 1597-1598 (2006).</li><li>Kahya, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+Lipid+Mobility+of+Raft-exhibiting+Model+Membranes+by+Fluorescence+Correlation+Spectroscopy.">Probing Lipid Mobility of Raft-exhibiting Model Membranes by Fluorescence Correlation Spectroscopy.</a> J. Biol. Chem. 278, 28109-28115 (2003).</li><li>Akbarzadeh, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Liposome:+classification,+preparation+and+applications.">Liposome: classification, preparation and applications.</a> Nanoscale Research Letters. 8, 102 (2013).</li><li>Butt, H. -. J., Jaschke, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calculation+of+thermal+noise+in+atomic+force+microscopy.">Calculation of thermal noise in atomic force microscopy.</a> Nanotechnology. 6, 1-7 (1995).</li><li>Chon, J. W. M., Mulvaney, P., Sader, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Experimental+validation+of+theoretical+models+for+the+frequency+response+of+atomic+force+microscope+cantilever+beams+immersed+in+fluids.">Experimental validation of theoretical models for the frequency response of atomic force microscope cantilever beams immersed in fluids.</a> Journal of Applied Physics. 87, 3973 (2000).</li><li>Sader, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frequency+response+of+cantilever+beams+immersed+in+viscous+fluids+with+applications+to+the+atomic+force+microscope.">Frequency response of cantilever beams immersed in viscous fluids with applications to the atomic force microscope.</a> Journal of Applied Physics. 84, 64 (1998).</li><li>Sader, J. E., Pacifico, J., Green, C. P., Mulvaney, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=General+scaling+law+for+stiffness+measurement+of+small+bodies+with+applications+to+the+atomic+force+microscope.">General scaling law for stiffness measurement of small bodies with applications to the atomic force microscope.</a> Journal of Applied Physics. 97, 12490310 (2005).</li><li>Canale, C., Torre, B., Ricci, D., Braga, P. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recognizing+and+avoiding+artifacts+in+atomic+force+microscopy+imaging.">Recognizing and avoiding artifacts in atomic force microscopy imaging.</a> Methods Mol Biol. 736, 31-43 (2011).</li><li>Lee, M. -. T., Chen, F. -. Y., Huang, H. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Energetics+of+Pore+Formation+Induced+by+Membrane+Active+Peptides.">Energetics of Pore Formation Induced by Membrane Active Peptides.</a> Biochemistry-US. 43, 3590-3599 (2004).</li><li>Henriksen, J. R., Ipsen, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+membrane+elasticity+by+micro-pipette+aspiration.">Measurement of membrane elasticity by micro-pipette aspiration.</a> The European physical journal. E, Soft matter. 14, 149-167 (2004).</li><li>Nichols-Smith, S., Teh, S. -. Y., Kuhl, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermodynamic+and+mechanical+properties+of+model+mitochondrial+membranes.">Thermodynamic and mechanical properties of model mitochondrial membranes.</a> BBA-Biomembranes. 1663, 82-88 (2004).</li><li>Tian, A., Johnson, C., Wang, W., Baumgart, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Line+Tension+at+Fluid+Membrane+Domain+Boundaries+Measured+by+Micropipette+Aspiration.">Line Tension at Fluid Membrane Domain Boundaries Measured by Micropipette Aspiration.</a> Phys. Rev. Lett. 98, (2007).</li><li>Rigaud, J. -. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane+proteins:+functional+and+structural+studies+using+reconstituted+proteoliposomes+and+2-D+crystals.">Membrane proteins: functional and structural studies using reconstituted proteoliposomes and 2-D crystals.</a> Brazilian Journal of Medical and Biological Research. 35, 753-766 (2002).</li></ol>

The authors declare that they have no competing financial interests.

SLBs composed of DOPC:SM:Chol (2:2:1) were formed on mica after vesicle adsorption and rupture induced by calcium chloride. This lipid composition separated into Ld and Lo phases. The Lo phase is enriched in sphingomyelin and cholesterol and is less fluid/more viscous (Figure 1A) than the Ld phase11. The separation of Lo from Ld phase manifests as circular structures elevated above the surrounding (Figure 1B, C)...

Atomic Force Microscopy (AFM) generates an image of a surface by scanning across an area of the sample using a cantilever with a very sharp tip1. The movement of the cantilever probes the surface topology of the sample. AFM has been widely applied to biological molecules &#8212; including proteins, DNA, and membranes, owing to its versatility in analyzing fixed samples in air or near-native state in liquid2-5.
Apart from its high-resolution imaging capability in the nanometer range, the AFM cantilever acts as a spring to probe interaction forces (adhesion and repulsion) and mechanical properties of the sample5,6. This is known as force spectroscopy. In this mode, the probe first approaches the sample and exerts a force on it, then is retracted until it loses contact with the sample (Figure 1A). The generated curves show force as a function of distance of the cantilever for both the approach and retraction. Several properties including the elastic modulus to measure the stiffness of a material, and adhesion forces can be derived.
Supported lipid bilayers are biological model membranes lying on top of a solid support &#8212; usually mica, borosilicate glass, fused silica, or oxidized silicon7. They are prepared using various techniques like vesicle deposition, Langmuir-Blodgett method and spin-coating8,9. AFM imaging has been used to follow the formation of these supported bilayers10, and probe different structures formed by membranes of different compositions11-15.
Performing force spectroscopy on supported bilayers results in a peak in the approach curve. This peak indicates the force needed to pierce the bilayer, and is called breakthrough force. The bilayer thickness can also be measured using the force curve6 . The typical breakthrough force of bilayers range between 1-50 nN6. These properties depend on lipid packing (liquid or gel phase) and structure (acyl chain length and degree of unsaturation) and altered by membrane-active agents16. The theory behind the rupture has been explained17 and other experimental parameters such as cantilever softness, tip radius and approach speed also affect the breakthrough force15,16,18. Force spectroscopy has been used to analyze properties of different lipid phases11,19, composition-dependent changes12,20, as well as effects of other biomolecules, like peptides, on the stability of the membrane21.
The flat orientation of supported bilayers is advantageous for combining AFM with other methods such as surface plasmon resonance22 and fluorescence microscopy11,19 to better characterize structure and properties of membranes.
This detailed video protocol is intended to prepare supported lipid bilayers using vesicle deposition and analyze them with AFM and force spectroscopy. While vesicles of various sizes may be used to prepare bilayers, this protocol focuses on small and large unilamellar vesicles. Supported bilayers that phase separate into liquid ordered (Lo) and liquid disordered (Ld) phases were characterized11,15. The membrane is composed of di-oleoyl-phosphatidylcholine (DOPC), sphingomyelin (SM), and cholesterol (Chol) at 2:2:1 ratio. This composition models the lipid rafts, which are proposed to behave as platforms important for protein trafficking and sorting, cell signaling and other cellular processes23,24.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>1,2-dioleoyl-sn-glycero-3-phosphocholine</td>
			<td>Avanti Polar Lipids, Inc.</td>
			<td>850375P</td>
			<td>Comes as lyophilized powder in sealed vials. Dissolve all powder in chloroform upon opening. Store extra as dried lipid films, under inert atmosphere, at -20&#176;C. For more information on storage and handling visit http://www.avantilipids.com/index.php?option=com_content&#38;view=article&#38;id=1679&#38;Itemid=398</td>
		</tr>
		<tr>
			<td>Sphingomyelin (Brain, Porcine)</td>
			<td>Avanti Polar Lipids, Inc.</td>
			<td>860062P</td>
			<td>Comes as lyophilized powder in large sealed plastic containers. Dissolve a spatula point of powder powder in chloroform upon opening. Store extra as dried lipid films, under inert atmosphere, at -20&#176;C.&#160; For more information on storage and handling visit http://www.avantilipids.com/index.php?option=com_content&#38;view=article&#38;id=1679&#38;Itemid=398</td>
		</tr>
		<tr>
			<td>Cholesterol</td>
			<td>Avanti Polar Lipids, Inc.</td>
			<td>700000P</td>
			<td>Comes as lyophilized powder in large sealed plastic containers. Dissolve a spatula point of powder powder in chloroform upon opening. Store extra as dried lipid films, under inert atmosphere, at -20&#176;C.&#160; For more information on storage and handling visit http://www.avantilipids.com/index.php?option=com_content&#38;view=article&#38;id=1679&#38;Itemid=398</td>
		</tr>
		<tr>
			<td>Sodium chloride (NaCl), 99.8%</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>9265.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium chloride (KCl), 88%</td>
			<td>Sigma</td>
			<td>P9541</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydrogenphosphate (Na2HPO4), &#62;99%</td>
			<td>AppliChem GmbH</td>
			<td>A1046</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium dihydrogenphosphate (KH2PO4), 99%</td>
			<td>Carl Roth GmbH + Co. KG</td>
			<td>3904.1</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium chloride dihydrate (CaCl2), molecular biology grade</td>
			<td>AppliChem GmbH</td>
			<td>A4689</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES, molecular biology grade</td>
			<td>AppliChem GmbH</td>
			<td>A3724</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass coverslip, 24x60 mm, 1mm thickness</td>
			<td>Duran Group</td>
			<td>2355036</td>
			<td></td>
		</tr>
		<tr>
			<td>Mica blocks</td>
			<td>NSC Mica Exports Ltd.</td>
			<td></td>
			<td>These are mica pieces at least 1 sq. Inches in area and thickness randing from 0.006 inches to 0.016 inches. They are cut to a specific size by the company for shipping. Small mica discs can be punched from the mica blocks using the punch and die set.&#160; Always handle mica with gloves or tweezers.</td>
		</tr>
		<tr>
			<td>Punch and Die Set</td>
			<td>Precision Brand Products, Inc</td>
			<td>40105</td>
			<td></td>
		</tr>
		<tr>
			<td>Optical Adhesive</td>
			<td>Norland Products, Inc.</td>
			<td>NOA 88</td>
			<td>Liquid adhesive that hardens when cured under long wavelength UV light.&#160;</td>
		</tr>
		<tr>
			<td>Laboratory Equipment Grease</td>
			<td>Borer Chemie AG</td>
			<td>Glisseal N</td>
			<td></td>
		</tr>
		<tr>
			<td>Liposome Extruder</td>
			<td>Avestin</td>
			<td>LiposoFast-Basic</td>
			<td>As an alternative one can also look at offers from Northern Lipids, Inc.</td>
		</tr>
		<tr>
			<td>Adhesive Tape</td>
			<td>3M</td>
			<td>Scotch(R) Magic (TM) Tape 810 (1-inch)</td>
			<td></td>
		</tr>
		<tr>
			<td>Bath Sonicator</td>
			<td>Bandelin Sonorex Digitec</td>
			<td>DT-31</td>
			<td>No heating, Frequency: 35 kHz, Ultrasonic Peak Output: 160 W, HF Power: 40 W. http://www.bandelin.com/datenblaetter/dt/DT_31_H_1798d_DE_GB_FR_BANDELIN.pdf</td>
		</tr>
		<tr>
			<td>Silicon Nitride AFM Cantilever&#160;</td>
			<td>Bruker AFM Probes</td>
			<td>DNP-10</td>
			<td>Each cantilever has four tips and their nominal tip radius is 20 nm (with possible maximum at 60 nm). Based on the specifications, we use tip D with resonance frequency of 18 kHz, and nominal spring constant of 0.06 N/m.</td>
		</tr>
		<tr>
			<td>AFM</td>
			<td>JPK</td>
			<td>JPK Nanowizard II mounted on Zeiss Axiovert 200</td>
			<td></td>
		</tr>
	</tbody>
</table>

atomic force microscopy imaging and force spectroscopy of supported lipid bilayers

Atomic force microscopy (AFM) is a versatile, high-resolution imaging technique that allows visualization of biological membranes. It has sufficient magnification to examine membrane substructures and even individual molecules. AFM can act as a force probe to measure interactions and mechanical properties of membranes. Supported lipid bilayers are conventionally used as membrane models in AFM studies. In this protocol, we demonstrate how to prepare supported bilayers and characterize their structure and mechanical properties using AFM. These include bilayer thickness and breakthrough force. 
The information provided by AFM imaging and force spectroscopy help define mechanical and chemical properties of membranes. These properties play an important role in cellular processes such as maintaining cell hemostasis from environmental stress, bringing membrane proteins together, and stabilizing protein complexes.

Supported lipid bilayers composed of DOPC:SM:Chol (2:2:1) were imaged in AFM (Figure 2 A-C). Because of the lipid composition, SM/Chol-rich Lo and DOPC-rich Ld phases were observed. The height profile from the AFM imaging can provide important information on the membrane structure. By looking at the height profile, the bilayer thickness can be measured in presence of defects in the membrane (Figure 2B), or the difference in height between the Lo/Ld</...

Watch this Scientific Journal Video about Atomic Force Microscopy Imaging and Force Spectroscopy of Supported Lipid Bilayers at JoVE.com

Atomic Force Microscopy Imaging and Force Spectroscopy of Supported Lipid Bilayers

We describe a protocol for preparation of supported lipid bilayers and its characterization using atomic force microscopy and force spectroscopy.

Atomic force microscopy (AFM) is a versatile, high-resolution imaging technique that allows visualization of biological membranes. It has sufficient ...

atomic-force-microscopy-imaging-force-spectroscopy-supported-lipid

Research

JoVE Journal

Bioengineering

14.6K Views.  Interfaculty Institute for Biochemistry. We describe a protocol for preparation of supported lipid bilayers and its characterization using atomic force microscopy and force spectroscopy.

Video: Atomic Force Microscopy Imaging and Force Spectroscopy of Supported Lipid Bilayers

Bacterial Immobilization for Imaging by Atomic Force Microscopy

AFM is a high-resolution (nm scale) imaging tool that mechanically probes a surface. It has the ability to image cells and biomolecules, in a liquid environment, without the need to chemically treat the sample. In order to accomplish this goal, the sample must sufficiently adhere to the mounting surface to prevent removal by forces exerted by the scanning AFM cantilever tip. In many instances, successful imaging depends on immobilization of the sample to the mounting surface. Optimally, immobilization should be minimally invasive to the sample such that metabolic processes and functional attributes are not compromised. By coating freshly cleaved mica surfaces with porcine (pig) gelatin, negatively charged bacteria can be immobilized on the surface and imaged in liquid by AFM. Immobilization of bacterial cells on gelatin-coated mica is most likely due to electrostatic interaction between the negatively charged bacteria and the positively charged gelatin. Several factors can interfere with bacterial immobilization, including chemical constituents of the liquid in which the bacteria are suspended, the incubation time of the bacteria on the gelatin coated mica, surface characteristics of the bacterial strain and the medium in which the bacteria are imaged. Overall, the use of gelatin-coated mica is found to be generally applicable for imaging microbial cells.

Live Gram-negative and Gram-positive bacteria can be immobilized on gelatin-coated mica and imaged in liquid using Atomic Force Microscopy (AFM).

AFM is a high-resolution (nm scale) imaging tool that mechanically probes a surface.  It has the ability to image cells and biomolecules, in a liquid ...

Visualization of Recombinant DNA and Protein Complexes Using Atomic Force Microscopy

Atomic force microscopy (AFM) allows for the visualizing of individual proteins, DNA molecules, protein-protein complexes, and DNA-protein complexes. On the end of the microscope's cantilever is a nano-scale probe, which traverses image areas ranging from nanometers to micrometers, measuring the elevation of macromolecules resting on the substrate surface at any given point. Electrostatic forces cause proteins, lipids, and nucleic acids to loosely attach to the substrate in random orientations and permit imaging. The generated data resemble a topographical map, where the macromolecules resolve as three-dimensional particles of discrete sizes (Figure 1) 1,2. Tapping mode AFM involves the repeated oscillation of the cantilever, which permits imaging of relatively soft biomaterials such as DNA and proteins. One of the notable benefits of AFM over other nanoscale microscopy techniques is its relative adaptability to visualize individual proteins and macromolecular complexes in aqueous buffers, including near-physiologic buffered conditions, in real-time, and without staining or coating the sample to be imaged. 
The method presented here describes the imaging of DNA and an immunoadsorbed transcription factor (i.e. the glucocorticoid receptor, GR) in buffered solution (Figure 2). Immunoadsorbed proteins and protein complexes can be separated from the immunoadsorbing antibody-bead pellet by competition with the antibody epitope and then imaged (Figure 2A). This allows for biochemical manipulation of the biomolecules of interest prior to imaging. Once purified, DNA and proteins can be mixed and the resultant interacting complex can be imaged as well. Binding of DNA to mica requires a divalent cation 3,such as Ni2+ or Mg2+, which can be added to sample buffers yet maintain protein activity. Using a similar approach, AFM has been utilized to visualize individual enzymes, including RNA polymerase 4 and a repair enzyme 5, bound to individual DNA strands. These experiments provide significant insight into the protein-protein and DNA-protein biophysical interactions taking place at the molecular level. Imaging individual macromolecular particles with AFM can be useful for determining particle homogeneity and for identifying the physical arrangement of constituent components of the imaged particles. While the present method was developed for visualization of GR-chaperone protein complexes 1,2 and DNA strands to which the GR can bind, it can be applied broadly to imaging DNA and protein samples from a variety of sources.

A tapping mode atomic force microscope (AFM) method for the visualization of plasmid DNA, cytoplasmic proteins, and DNA-protein complexes is described. The method includes alternate approaches for preparing samples for AFM imaging following biochemical manipulation. DNA containing specific protein interacting regions are observed in near-physiologic buffer conditions.

Atomic force microscopy (AFM) allows for the visualizing of individual proteins, DNA molecules, protein-protein complexes, and DNA-protein complexes. On ...

Quantifying the Mechanical Properties of the Endothelial Glycocalyx with Atomic Force Microscopy

Our understanding of the interaction of leukocytes and the vessel wall during leukocyte capture is limited by an incomplete understanding of the mechanical properties of the endothelial surface layer. It is known that adhesion molecules on leukocytes are distributed non-uniformly relative to surface topography 3, that topography limits adhesive bond formation with other surfaces 9, and that physiological contact forces (&asymp; 5.0 &minus; 10.0 pN per microvillus) can compress the microvilli to as little as a third of their resting length, increasing the accessibility of molecules to the opposing surface 3, 7. We consider the endothelium as a two-layered structure, the relatively rigid cell body, plus the glycocalyx, a soft protective sugar coating on the luminal surface 6. It has been shown that the glycocalyx can act as a barrier to reduce adhesion of leukocytes to the endothelial surface 4. In this report we begin to address the deformability of endothelial surfaces to understand how the endothelial mechanical stiffness might affect bond formation. Endothelial cells grown in static culture do not express a robust glycocalyx, but cells grown under physiological flow conditions begin to approximate the glycocalyx observed in vivo 2. The modulus of the endothelial cell body has been measured using atomic force microscopy (AFM) to be approximately 5 to 20 kPa 5. The thickness and structure of the glycocalyx have been studied using electron microscopy 8, and the modulus of the glycocalyx has been approximated using indirect methods, but to our knowledge, there have been no published reports of a direct measurement of the glycocalyx modulus in living cells. In this study, we present indentation experiments made with a novel AFM probe on cells that have been cultured in conditions to maximize their glycocalyx expression to make direct measurements of the modulus and thickness of the endothelial glycocalyx.

The mechanical characteristics of endothelial glycocalyx were measured by indentation using micron sized spheres on AFM cantilevers. Endothelial cells were cultured in a custom chamber under physiological flow conditions to induce glycocalyx expression. Data were analyzed using a thin film model to determine the glycocalyx thickness and modulus.

Our  understanding of the interaction of leukocytes and the vessel wall during  leukocyte capture is limited by an incomplete understanding of the ...

Measuring the Mechanical Properties of Living Cells Using Atomic Force Microscopy

Mechanical properties of cells and extracellular matrix (ECM) play important roles in many biological processes including stem cell differentiation, tumor formation, and wound healing. Changes in stiffness of cells and ECM are often signs of changes in cell physiology or diseases in tissues. Hence, cell stiffness is an index to evaluate the status of cell cultures. Among the multitude of methods applied to measure the stiffness of cells and tissues, micro-indentation using an Atomic Force Microscope (AFM) provides a way to reliably measure the stiffness of living cells. This method has been widely applied to characterize the micro-scale stiffness for a variety of materials ranging from metal surfaces to soft biological tissues and cells. The basic principle of this method is to indent a cell with an AFM tip of selected geometry and measure the applied force from the bending of the AFM cantilever. Fitting the force-indentation curve to the Hertz model for the corresponding tip geometry can give quantitative measurements of material stiffness. This paper demonstrates the procedure to characterize the stiffness of living cells using AFM. Key steps including the process of AFM calibration, force-curve acquisition, and data analysis using a MATLAB routine are demonstrated. Limitations of this method are also discussed.

This paper demonstrates a protocol to characterize the mechanical properties of living cells by means of microindentation using an Atomic Force Microscope (AFM).

Mechanical  properties of cells and extracellular matrix (ECM) play important roles in many  biological processes including stem cell differentiation, ...

Preparation of Mica Supported Lipid Bilayers for High Resolution Optical Microscopy Imaging

Supported lipid bilayers (SLBs) are widely used as a model for studying membrane properties (phase separation, clustering, dynamics) and its interaction with other compounds, such as drugs or peptides. However SLB characteristics differ depending on the support used. 
Commonly used techniques for SLB imaging and measurements are single molecule fluorescence microscopy, FCS and atomic force microscopy (AFM). Because most optical imaging studies are carried out on a glass support, while AFM requires an extremely flat surface (generally mica), results from these techniques cannot be compared directly, since the charge and smoothness properties of these materials strongly influence diffusion. Unfortunately, the high level of manual dexterity required for the cutting and gluing thin slices of mica to the glass slide presents a hurdle to routine use of mica for SLB preparation. Although this would be the method of choice, such prepared mica surfaces often end up being uneven (wavy) and difficult to image, especially with small working distance, high numerical aperture lenses. Here we present a simple and reproducible method for preparing thin, flat mica surfaces for lipid vesicle deposition and SLB preparation. Additionally, our custom made chamber requires only very small volumes of vesicles for SLB formation. The overall procedure results in the efficient, simple and inexpensive production of high quality lipid bilayer surfaces that are directly comparable to those used in AFM studies.

We present a method of preparing mica supported lipid bilayers for high resolution microscopy. Mica is transparent and flat on an atomic scale, but rarely used in imaging because of handling difficulties; our preparation results in even deposition of the mica sheet, and reduces the material used in bilayer preparation.

Supported lipid bilayers (SLBs) are widely used as a model for studying membrane properties (phase separation, clustering, dynamics) and its interaction ...

Surface Potential Measurement of Bacteria Using Kelvin Probe Force Microscopy

Surface potential is a commonly overlooked physical characteristic that plays a dominant role in the adhesion of microorganisms to substrate surfaces. Kelvin probe force microscopy (KPFM) is a module of atomic force microscopy (AFM) that measures the contact potential difference between surfaces at the nano-scale. The combination of KPFM with AFM allows for the simultaneous generation of surface potential and topographical maps of biological samples such as bacterial cells. Here, we employ KPFM to examine the effects of surface potential on microbial adhesion to medically relevant surfaces such as stainless steel and gold. Surface potential maps revealed differences in surface potential for microbial membranes on different material substrates. A step-height graph was generated to show the difference in surface potential at a boundary area between the substrate surface and microorganisms. Changes in cellular membrane surface potential have been linked with changes in cellular metabolism and motility. Therefore, KPFM represents a powerful tool that can be utilized to examine the changes of microbial membrane surface potential upon adhesion to various substrate surfaces. In this study, we demonstrate the procedure to characterize the surface potential of individual methicillin-resistant Staphylococcus aureus USA100 cells on stainless steel and gold using KPFM.

Here, we present a protocol explaining the use of Kelvin probe force microscopy as a tool for generating high resolution nano-scale surface potential maps. This tool was applied to assess the role of surface potential on the binding capacity of microorganisms to substrate surfaces.

Surface potential is a commonly overlooked physical characteristic that plays a dominant role in the adhesion of microorganisms to substrate surfaces. ...

Novel Atomic Force Microscopy Based Biopanning for Isolation of Morphology Specific Reagents against TDP-43 Variants in Amyotrophic Lateral Sclerosis

Because protein variants play critical roles in many diseases including TDP-43 in Amyotrophic Lateral Sclerosis (ALS), alpha-synuclein in Parkinson&#8217;s disease and beta-amyloid and tau in Alzheimer&#8217;s disease, it is critically important to develop morphology specific reagents that can selectively target these disease-specific protein variants to study the role of these variants in disease pathology and for potential diagnostic and therapeutic applications. We have developed novel atomic force microscopy (AFM) based biopanning techniques that enable isolation of reagents that selectively recognize disease-specific protein variants. There are two key phases involved in the process, the negative and positive panning phases. During the negative panning phase, phages that are reactive to off-target antigens are eliminated through multiple rounds of subtractive panning utilizing a series of carefully selected off-target antigens. A key feature in the negative panning phase is utilizing AFM imaging to monitor the process and confirm that all undesired phage particles are removed. For the positive panning phase, the target antigen of interest is fixed on a mica surface and bound phages are eluted and screened to identify phages that selectively bind the target antigen. The target protein variant does not need to be purified providing the appropriate negative panning controls have been used. Even target protein variants that are only present at very low concentrations in complex biological material can be utilized in the positive panning step. Through application of this technology, we acquired antibodies to protein variants of TDP-43 that are selectively found in human ALS brain tissue. We expect that this protocol should be applicable to generating reagents that selectively bind protein variants present in a wide variety of different biological processes and diseases.

Using atomic force microscopy in combination with biopanning technology we created a negative and positive biopanning system to acquire antibodies against disease-specific protein variants present in any biological material, even at low concentrations. We were successful in obtaining antibodies to TDP-43 protein variants involved in Amyotrophic Lateral Sclerosis.

Because protein variants play critical roles in many diseases including TDP-43 in Amyotrophic Lateral Sclerosis (ALS), alpha-synuclein in ...

Single Molecule Fluorescence Microscopy on Planar Supported Bilayers

In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background in optics and laser physics to a discipline that is now enjoying vivid attention by life-scientists of all venues 1. This is because single molecule imaging has the unique potential to reveal protein behavior in situ in living cells and uncover cellular organization with unprecedented resolution below the diffraction limit of visible light 2. Glass-supported planar lipid bilayers (SLBs) are a powerful tool to bring cells otherwise growing in suspension in close enough proximity to the glass slide so that they can be readily imaged in noise-reduced Total Internal Reflection illumination mode 3,4. They are very useful to study the protein dynamics in plasma membrane-associated events as diverse as cell-cell contact formation, endocytosis, exocytosis and immune recognition. Simple procedures are presented how to generate highly mobile protein-functionalized SLBs in a reproducible manner, how to determine protein mobility within and how to measure protein densities with the use of single molecule detection. It is shown how to construct a cost-efficient single molecule microscopy system with TIRF illumination capabilities and how to operate it in the experiment.

Preparation of protein-functionalized planar glass-supported lipid bilayers, determination of protein mobility within and measurement of protein densities is shown here. A roadmap to building a noise-reduced Total Internal Reflection microscope is outlined, which allows visualizing single bilayer-resident fluorochromes with high spatiotemporal resolution.

In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background ...

Fabrication and Implementation of a Reference-Free Traction Force Microscopy Platform

Quantifying cell-induced material deformation provides useful information concerning how cells sense and respond to the physical properties of their microenvironment. While many approaches exist for measuring cell-induced material strain, here we provide a methodology for monitoring strain with sub-micron resolution in a reference-free manner. Using a two-photon activated photolithographic patterning process, we demonstrate how to generate mechanically and bio-actively tunable synthetic substrates containing embedded arrays of fluorescent fiducial markers to easily measure three-dimensional (3D) material deformation profiles in response to surface tractions. Using these substrates, cell tension profiles can be mapped using a single 3D image stack of a cell of interest. Our goal with this methodology is to make traction force microscopy a more accessible and easier to implement tool for researchers studying cellular mechanotransduction processes, especially newcomers to the field.

This protocol provides instructions for implementing multiphoton lithography to fabricate three-dimensional arrays of fluorescent fiducial markers embedded in poly(ethylene glycol)-based hydrogels for use as reference-free, traction force microscopy platforms. Using these instructions, measurement of 3D material strain and calculation of cellular tractions is simplified to promote high-throughput traction force measurements.

Quantifying cell-induced material deformation provides useful information concerning how cells sense and respond to the physical properties of their ...

Application of Atomic Force Microscopy to Detect Early Osteoarthritis

Biomechanical properties of cells and tissues not only regulate their shape and function but are also crucial for maintaining their vitality. Changes in elasticity can propagate or trigger the onset of major diseases like cancer or osteoarthritis (OA). Atomic force microscopy (AFM) has emerged as a strong tool to qualitatively and quantitatively characterize the biomechanical properties of specific biological target structures on a microscopic scale, measuring forces in a range from as small as the piconewton to the micronewton. Biomechanical properties are of special importance in musculoskeletal tissues, which are subjected to high levels of strain. OA as a degenerative disease of the cartilage results in the disruption of the pericellular matrix (PCM) and the spatial rearrangement of the chondrocytes embedded in their extracellular matrix (ECM). Disruption in PCM and ECM has been associated with changes in the biomechanical properties of cartilage. In the present study we used AFM to quantify these changes in relation to the specific spatial pattern changes of the chondrocytes. With each pattern change, significant changes in elasticity were observed for both the PCM and ECM. Measuring the local elasticity thus allows for drawing direct conclusions about the degree of local tissue degeneration in OA.

We present a method to investigate early osteoarthritic changes at the cellular level in articular cartilage by using atomic force microscopy (AFM).

Biomechanical properties of cells and tissues not only regulate their shape and function but are also crucial for maintaining their vitality. Changes in ...