Name: molecular spring constant analysis by biomembrane force probe spectroscopy
Uploaded: 2021-11-20T13:00:00
Description: Watch this Scientific Journal Video about Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy at JoVE.com

We thank Guillaume Troadec for helpful discussion, Zihao Wang for hardware consultation, and Sydney Manufacturing Hub, Gregg Suaning and Simon Ringer for support of our lab startup. This work was supported by Australian Research Council Discovery Project (DP200101970 - L.A.J.), NSW Cardiovascular Capacity Building Program (Early-Mid Career Researcher Grant - L.A.J.), Sydney Research Accelerator prize (SOAR - L.A.J.), Ramaciotti Foundations Health Investment Grant (2020HIG76 - L.A.J.), National Health and Medical Research Council Ideas Grant (APP2003904 - L.A.J.), and The University of Sydney Faculty of Engineering Startup Fund and Major Equipment Scheme (L.A.J.). Lining Arnold Ju is an Australian Research Council DECRA fellow (DE190100609).

1. Obtain Analyzable DFS Events
<ol>
	<li>Start the experiment in the software (e.g., LabVIEW VI) for the BFP control and parameter setting (Figure S1A).</li>
	<li>Observe the repetitive probe bead-target bead/cell touches in the software for BFP Monitor (Figure S1B).</li>
	<li>Test and achieve the adhesion frequency &#8804; 20% within the first 50 touches by tuning the impingement force and contact time, by which it ensures that &#8805; 89% of DFS adhesion event are mediated by single...

<ol>
	<li>Chen, Y., 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=Fluorescence+Biomembrane+Force+Probe:+Concurrent+Quantitation+of+Receptor-ligand+Kinetics+and+Binding-induced+Intracellular+Signaling+on+a+Single+Cell.">Fluorescence Biomembrane Force Probe: Concurrent Quantitation of Receptor-ligand Kinetics and Binding-induced Intracellular Signaling on a Single Cell.</a> The Journal of Visualized Experiments. (102), e52975 (2015).</li><li>Su, Q. P., Ju, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biophysical+nanotools+for+single-molecule+dynamics.">Biophysical nanotools for single-molecule dynamics.</a> Biophysics Reviews. 10 (5), 1349-1357 (2018).</li><li>Ju, L. <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+Analysis+on+the+Redox+States+of+Protein+Disulphide+Bonds.">Dynamic Force Spectroscopy Analysis on the Redox States of Protein Disulphide Bonds.</a> Methods in Molecular Biology. 1967, 115-131 (2019).</li><li>An, C., 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=Ultra-stable+Biomembrane+Force+Probe+for+Accurately+Determining+Slow+Dissociation+Kinetics+of+PD-1+Blockade+Antibodies+on+Single+Living+Cells.">Ultra-stable Biomembrane Force Probe for Accurately Determining Slow Dissociation Kinetics of PD-1 Blockade Antibodies on Single Living Cells.</a> Nano Letters. 20 (7), 5133-5140 (2020).</li><li>Chen, Y., Ju, L., Rushdi, M., Ge, C., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Receptor-mediated+cell+mechanosensing.">Receptor-mediated cell mechanosensing.</a> Molecular Biology of the Cell. 28 (23), 3134-3155 (2017).</li><li>Ju, L., Chen, Y., Rushdi, M. N., Chen, W., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-Dimensional+Analysis+of+Cross-Junctional+Molecular+Interaction+by+Force+Probes.">Two-Dimensional Analysis of Cross-Junctional Molecular Interaction by Force Probes.</a> Methods in Molecular Biology. 1584, 231-258 (2017).</li><li>Evans, E., Ritchie, K., Merkel, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensitive+force+technique+to+probe+molecular+adhesion+and+structural+linkages+at+biological+interfaces.">Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces.</a> Biophysical Journal. 68 (6), 2580-2587 (1995).</li><li>Ju, L., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Benchmarks+of+Biomembrane+Force+Probe+Spring+Constant+Models.">Benchmarks of Biomembrane Force Probe Spring Constant Models.</a> Biophysical Journal. 113 (12), 2842-2845 (2017).</li><li>Evans, E., Ritchie, K., Merkel, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensitive+Force+Technique+to+Probe+Molecular+Adhesion+and+Structural+Linkages+at+Biological+Interfaces.">Sensitive Force Technique to Probe Molecular Adhesion and Structural Linkages at Biological Interfaces.</a> Biophysical Journal. 68, 2580 (1995).</li><li>Fiore, V. F., Ju, L., Chen, Y., Zhu, C., Barker, T. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+catch+of+a+Thy-1-alpha5beta1+syndecan-4+trimolecular+complex.">Dynamic catch of a Thy-1-alpha5beta1+syndecan-4 trimolecular complex.</a> Nature Communications. 5, 4886 (2014).</li><li>Passam, F., 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=Mechano-redox+control+of+integrin+de-adhesion.">Mechano-redox control of integrin de-adhesion.</a> Elife. 7, (2018).</li><li>Chen, Y., 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=An+integrin+alphaIIbbeta3+intermediate+affinity+state+mediates+biomechanical+platelet+aggregation.">An integrin alphaIIbbeta3 intermediate affinity state mediates biomechanical platelet aggregation.</a> Nature Materials. 18 (7), 760-769 (2019).</li><li>Chen, Y., Lee, H., Tong, H., Schwartz, M., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Force+regulated+conformational+change+of+integrin+&#945;V&#946;3.">Force regulated conformational change of integrin &#945;V&#946;3.</a> Matrix Biology. 60, 70-85 (2017).</li><li>Liu, B., Chen, W., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+force+spectroscopy+on+cells.">Molecular force spectroscopy on cells.</a> Annual Review of Physical Chemistry. 66, 427-451 (2015).</li><li>Piper, J. W., Swerlick, R. A., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determining+force+dependence+of+two-dimensional+receptor-ligand+binding+affinity+by+centrifugation.">Determining force dependence of two-dimensional receptor-ligand binding affinity by centrifugation.</a> Biophysical Journal. 74 (1), 492-513 (1998).</li><li>Ju, L., Dong, J. -. f., Cruz, M. A., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+N-terminal+flanking+region+of+the+A1+domain+regulates+the+force-dependent+binding+of+von+Willebrand+factor+to+platelet+glycoprotein+Ib&#945;.">The N-terminal flanking region of the A1 domain regulates the force-dependent binding of von Willebrand factor to platelet glycoprotein Ib&#945;.</a> Journal of Biological Chemistry. 288 (45), 32289-32301 (2013).</li><li>Ju, L., Chen, Y., Xue, L., Du, X., Zhu, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cooperative+unfolding+of+distinctive+mechanoreceptor+domains+transduces+force+into+signals.">Cooperative unfolding of distinctive mechanoreceptor domains transduces force into signals.</a> Elife. 5, 15447 (2016).</li></ol>

In summary, we have provided a detailed data analysis protocol for preprocessing the DFS raw data and deriving molecular spring constants in the BFP Bead-Bead and Bead-Cell analysis modes. Biomechanical models and equations required for determining molecular and cellular spring constants are presented. Albeit different integrins are studied, the kmol measured by the Bead-Bead mode and the Bead-Cell mode possesses significant range differences (Figure 3A vs. <strong class=...

As a live-cell DFS technique, BFP engineers a human red blood cell (RBC; Figure 1) into an ultrasensitive and tunable force transducer with a compatible spring constant range at 0.1-3 pN/nm1,2,3. To probe ligand-receptor interaction, BFP enables DFS measurements at ~1 pN (10-12 N), ~3 nm (10-9 m), and ~0.5 ms (10-3 s) in force, spatial, and temporal resolution4,5. Its experimental configuration consists of two opposing micropipettes, namely the Probe and the target. The Probe micropipette aspirates a RBC and a bead is glued at its apex via a biotin-streptavidin interaction. The bead is coated with the ligand of interest (Figure 1A). The Target micropipette aspirates either a cell or a bead bearing the receptor of interest, corresponding to the Bead-Cell (Figure 1B) and Bead-Bead (Figure 1C) modes, respectively5.
BFP construction, assembly and the DFS experimental protocols were described in detail previously1,6. Briefly, a BFP touch cycle consists of 5 stages: Approach, Impinge, Contact, Retract and Dissociate (Figure 1D). The horizontal RBC apex position is denoted as &#916;xRBC. At the beginning, the unstressed (zero-force) RBC deformation &#916;xRBC is 0 (Table 1). The Target is then driven by a piezotranslator to impinge on and retract from the Probe bead (Figure 1D). The RBC probe is first compressed by the Target with negative RBC deformation &#916;xRBC&#160;&#60; 0. In a Bond event, the Retract stage transitions from a compressive to a tensile phase with positive RBC deformation &#916;xRBC&#160;&#62; 0 (Figure 2C and D). According to Hooke&#39;s law, the BFP bearing force is able to be measured as F = kRBC&#160;&#215;&#160;&#916;xRBC, where kRBC (Table 1) is the RBC spring constant of the BFP. Upon bond rupture and the completion of one touch cycle, the probe bead returns to zero-force position with &#916;xRBC&#160;= 0 (Figure 1D).
To determine the kRBC, we measure and record the radii of the probe micropipette inner orifice (Rp), the RBC (R0) and the circular contact area (Rc) between the RBC and the probe bead (Figure 1A). Then kRBC is calculated according to the Evan&#39;s model (Eq. 1)7,8 using a LabVIEW program that acts as a virtual instrument (VI) to operate the BFP (Figure S1A)8,9.
<img alt="Equation 1" src="/files/ftp_upload/62490/62490eq01.jpg" /> (Eq. 1)
With a BFP established and DFS raw data obtained, hereby we present how to analyze the spring constant of ligand-receptor pair or cells. The DFS raw data on the interaction of the glycosylated protein Thy-1 and K562 cell bearing integrin &#945;5&#946;1 (Thy-1-&#945;5&#946;1; Figures 3A and 3B)10 and that of the fibrinogen and bead coated integrin &#945;IIb&#946;3 (FGN-&#945;IIb&#946;3; Figure 3C)11,12 have been used to demonstrate the Bead-Cell and Bead-Bead analysis modes, respectively.
BFP Experimental Preparation 
For details of BFP experimental preparation and instrumentation, please refer to the previously published protocols3. In brief, human RBC has been biotinylated using the Biotin-PEG3500-NHS in the carbon/bicarbonate buffer. Proteins of interest have been covalently coupled to the borosilicate glass beads using MAL-PEG3500-NHS in the phosphate buffer. To attach to the biotinylated RBC, the probe bead is also coated with streptavidin (SA) using the MAL-SA. Please see the Table of Materials and Table 2.
To assemble the BFP (Figure 1, left), the third micropipette termed &#39;Helper&#39; will be used to deliver the probe bead and glue it to the RBC&#39;s apex1,3. The covalent interaction between the SA coated probe bead and biotinylated RBC is much stronger than the ligand-receptor bond of interest. Thus, the Dissociate stage can be interpreted as the ligand-receptor bond rupture rather than the detachment of Probe bead from the RBC.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>3-Mercaptopropyltrimethoxysilane (MPTMS)</td>
			<td>Uct, Specialties, llc</td>
			<td>4420-74-0</td>
			<td>Glass bead functionalization</td>
		</tr>
		<tr>
			<td>Anhy. Sodium Phosphate Dibasic (Na2HPO4)</td>
			<td>Sigma-Aldrich</td>
			<td>S7907</td>
			<td>Phosphate buffer preparation</td>
		</tr>
		<tr>
			<td>BFP data acquisition VI</td>
			<td>LabVIEW</td>
			<td></td>
			<td>BFP control and parameter setting</td>
		</tr>
		<tr>
			<td>BFP data analysis VI</td>
			<td>LabVIEW</td>
			<td></td>
			<td>BFP raw data analysis</td>
		</tr>
		<tr>
			<td>Biotin-PEG3500-NHS</td>
			<td>JenKem</td>
			<td>A5026-1</td>
			<td>RBC biotinylation</td>
		</tr>
		<tr>
			<td>Borosilicate Glass beads</td>
			<td>Distrilab Particle Technology, Netherlands</td>
			<td>9002</td>
			<td>Glass bead functionalization</td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Sigma-Aldrich</td>
			<td>A0336</td>
			<td>Ligand functionalization</td>
		</tr>
		<tr>
			<td>Camera VI</td>
			<td>LabVIEW</td>
			<td></td>
			<td>BFP monitoring</td>
		</tr>
		<tr>
			<td>D-glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G7021</td>
			<td>Tyrode&#8217;s buffer preparation</td>
		</tr>
		<tr>
			<td>Hepes</td>
			<td>Sigma-Aldrich</td>
			<td>H3375</td>
			<td>Tyrode&#8217;s buffer preparation</td>
		</tr>
		<tr>
			<td>MAL-PEG3500-NHS</td>
			<td>JenKem</td>
			<td>A5002-1</td>
			<td>Glass bead functionalization</td>
		</tr>
		<tr>
			<td>Potassium Chloride (KCl)</td>
			<td>Sigma-Aldrich</td>
			<td>P9541</td>
			<td>Tyrode&#8217;s buffer preparation</td>
		</tr>
		<tr>
			<td>Sodium Bicarbonate (NaHCO3)</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td>Carbonate/bicarbonate buffer preparation; Tyrode&#8217;s buffer preparation</td>
		</tr>
		<tr>
			<td>Sodium Carbonate (Na2CO3)</td>
			<td>Sigma-Aldrich</td>
			<td>S2127</td>
			<td>Carbonate/bicarbonate buffer preparation</td>
		</tr>
		<tr>
			<td>Sodium Chloride (NaCl)</td>
			<td>Sigma-Aldrich</td>
			<td>S7653</td>
			<td>Tyrode&#8217;s buffer preparation</td>
		</tr>
		<tr>
			<td>Sodium Phosphate Monobasic Monohydrate (NaH2PO4&#8226;H2O)</td>
			<td>Sigma-Aldrich</td>
			<td>S9638</td>
			<td>Phosphate buffer preparation</td>
		</tr>
		<tr>
			<td>Streptavidin-Maleimide</td>
			<td>Sigma-Aldrich</td>
			<td>S9415</td>
			<td>Glass bead functionalization</td>
		</tr>
	</tbody>
</table>

molecular spring constant analysis by biomembrane force probe spectroscopy

A biomembrane force probe (BFP) has recently emerged as a native-cell-surface or in situ dynamic force spectroscopy (DFS) nanotool that can measure single-molecular binding kinetics, assess mechanical properties of ligand-receptor interactions, visualize protein dynamic conformational changes and more excitingly elucidate receptor mediated cell mechanosensing mechanisms. More recently, BFP has been used to measure the spring constant of molecular bonds. This protocol describes the step-by-step procedure to perform molecular spring constant DFS analysis. Specifically, two BFP operation modes are discussed, namely the Bead-Cell and Bead-Bead modes. This protocol focuses on deriving spring constants of the molecular bond and cell from DFS raw data.

In this work, we have demonstrated the protocol of the BFP spring constant analysis. For the Bead-Cell analysis mode, we analyzed the kmol&#160;of the molecular bond between the glycosylated protein Thy-1 coated on the Probe bead and the integrin &#945;5&#946;1 expressed on the Target K562 cell (Thy-1-integrin &#945;5&#946;1; Figure 3A)10. The kcell is also derived from the Bead-Cell m...

Watch this Scientific Journal Video about Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy at JoVE.com

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

A biomembrane force probe (BFP) is an in situ dynamic force spectroscopy (DFS) technique. BFP can be used to measure the spring constant of molecular interactions on living cells. This protocol presents spring constant analysis for molecular bonds detected by BFP.

A biomembrane force probe (BFP) has recently emerged as a native-cell-surface or in situ dynamic force spectroscopy (DFS) nanotool that can measure ...

This video describes step-by-step procedures on using Biomembrane Force Probe, or BFP to measure molecular spring constant. In force probe, BFP has recently emerged in the native cell surface or in SITU Dynamic Force Spectroscopy analysis. The main aim of this technique is to measure single molecule binding genetics.This data analysis procedure is a simple but powerful message and provide mechanical information, specifically the dynamic force and inflammation of the cell membrane expressing molecules. During the BFP experiment cycle, the probe microbiome bet with the red blood cell and probate, the target cell and the ligand receptor molecular bonding between the probe and the target can be considered as a series connected brain system. Based on Hooke's law, the reciprocal of the total spring constant of a series connected spring system is equal to the sum of the inverse spring constant of each single component, as the equation shows.The spring constant of red blood cell is calculated based on events motion, which is dependent to the radial of the probe micropipette in the orifice. The red blood cell, the circular contact area between the red blood cell and the probate and the micro-pipette aspirating pression. The BFP road data is obtained by a homemade left view virtual instrument, which controls the movement of the target micro-pipette by a PAs Translator.A full PFP touch cycle consists of five stages.Approach.Impinge.Contact. Retract and dissociate. In the beginning, does stress the Robusto APICS position is denoted as X equals 0 in black deshine.The target is then driven by a piece or translator to impinge on and compress the robusto to cause negative probate movement. You note it as X smaller than zero in red dash line. In the retract stage, the red busto apex move from the X smaller than zero position back to the X equal to zero position referred to as the compressive phase.If a bond is formed between the ligand receptor molecule complex, the red blood cell would further different to other positive direction. This X greater than zero period is referred to as the tensile phase of the retract stage. The retract stage is the most critical part to determine the spring constant of the molecule of bonding.Collect force versus time road data using the BSP data acquisition platform. Each experiments usually record 50 to 200 touch cycles, Open the PFP data analysis software. Click on the yellow folder icon and select the corresponding row data file by double clicking on them.We're on the program. Then click on the up and down arrow buttons to switch between events. Using the outlier exclusion criteria to screen out invalid events.Select the exporting data type that's forced to time format and choose the appropriate state range of time. Click on the export plot data button. The exported data is saved as text file in default.This text file contains two columns of data. It's the first column representing the time daddies and the second column representing the corresponding force at each time point. Plot the force versus time curve using spreadsheets software to obtain the forced versus displacement curve.Multiply the time value of each data point by the Willow Steel PSO movement. Zero the first data point by subtracting the smallest displacement value from each data point. This horizontal transformation does not affect the subsequent spring constant calculation.In the force versus displacement curve, two distinct actor group was different if the new force slope can be identified. Each representing the compressive phase and the 10 style phase. Fit a regression line to each data group.The line with steeper slope represents the total spring constant at a compressor phase denoted as K1.And the line that was smallest top represents the line at this 10 style phase denoted as K2.As I've mentioned, the total spring constant is the reciprocal of the son of the series spring constant of each component. During the compressive phase of the beat to cell mode, the molecular bonding is not stretched, therefore the molecular bonding spring constant is not taken into consideration. The spring constant of the target cell is described as the equation displayed where K1 represents the total spring constant during the compressor phase.In the 10 style phase of the beat to sell mode, the total spring constant is the sun of the uverse spring constant of the red blood cell molecular bond. And the target cell, use the equation displayed to calculate the moleculer bonding spring constant, which K2 represents the total spring constant. You read the 10 stop phase.In the beat to beat mode, since B deformation is negligible, the term which describes the inverse of the target cell spring constant approach zero, therefore the total spring constant in the compressor phase is equivalent to the red blood cell spring constant showing as the following equation. In the tensile phase, the spring constant of the molecular bonding can be calculated by subtracting the effect of the red blood cell showing as the following equation. Collect spring constants of the side-wind integrating attitude B, Beta 3 complex, the K562 cell and the Febrifugine integrating attitude B Beta three complex, calculate the mean and standard deviation of the derived spring constants at pick a Newton or nanometers scale.Now you should have a better understanding of what are the requirements for measuring and spring constant out of the VFD data. The differences between the beat to cell mode and the beat to beat mode should be noticed. Different molecule presenting service will have different defenses to the measure of spring constant.In conclusion, this step-by-step procedure describes how to perform molecular spring constant analysis using BFP. We foresee future efforts will be made to automate and integrate the BFP data acquisition and DFS analysis into one computer rest program. Making the entire BFP operation data analysis more user friendly and high throughout.

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Research

JoVE Journal

Bioengineering

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Membrane protein folding is an emerging topic with both fundamental and health-related significance. The abundance of membrane proteins in cells underlies the need for comprehensive study of the folding of this ubiquitous family of proteins. Additionally, advances in our ability to characterize diseases associated with misfolded proteins have motivated significant experimental and theoretical efforts in the field of protein folding. Rapid progress in this important field is unfortunately hindered by the inherent challenges associated with membrane proteins and the complexity of the folding mechanism. Here, we outline an experimental procedure for measuring the thermodynamic property of the Gibbs free energy of unfolding in the absence of denaturant, &Delta;G&deg;H2O, for a representative integral membrane protein from E. coli. This protocol focuses on the application of fluorescence spectroscopy to determine equilibrium populations of folded and unfolded states as a function of denaturant concentration. Experimental considerations for the preparation of synthetic lipid vesicles as well as key steps in the data analysis procedure are highlighted. This technique is versatile and may be pursued with different types of denaturant, including temperature and pH, as well as in various folding environments of lipids and micelles. The current protocol is one that can be generalized to any membrane or soluble protein that meets the set of criteria discussed below.

This video article details the experimental procedure for obtaining the Gibbs free energy of membrane protein folding by tryptophan fluorescence.

Membrane protein folding is an emerging topic with both fundamental and health-related significance.  The abundance of membrane proteins in cells ...

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 ...

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Single-molecule techniques for stretching DNA of contour lengths less than a kilobase are fraught with experimental difficulties. However, many interesting biological events such as histone binding and protein-mediated looping of DNA1,2, occur on this length scale. In recent years, the mechanical properties of DNA have been shown to play a significant role in fundamental cellular processes like the packaging of DNA into compact nucleosomes and chromatin fibers3,4. Clearly, it is then important to understand the mechanical properties of short stretches of DNA. In this paper, we provide a practical guide to a single-molecule optical tweezing technique that we have developed to study the mechanical behavior of DNA with contour lengths as short as a few hundred basepairs.
The major hurdle in stretching short segments of DNA is that conventional optical tweezers are generally designed to apply force in a direction lateral to the stage5,6, (see Fig. 1). In this geometry, the angle between the bead and the coverslip, to which the DNA is tethered, becomes very steep for submicron length DNA. The axial position must now be accounted for, which can be a challenge, and, since the extension drags the microsphere closer to the coverslip, steric effects are enhanced. Furthermore, as a result of the asymmetry of the microspheres, lateral extensions will generate varying levels of torque due to rotation of the microsphere within the optical trap since the direction of the reactive force changes during the extension.
Alternate methods for stretching submicron DNA run up against their own unique hurdles. For instance, a dual-beam optical trap is limited to stretching DNA of around a wavelength, at which point interference effects between the two traps and from light scattering between the microspheres begin to pose a significant problem. Replacing one of the traps with a micropipette would most likely suffer from similar challenges. While one could directly use the axial potential to stretch the DNA, an active feedback scheme would be needed to apply a constant force and the bandwidth of this will be quite limited, especially at low forces.
We circumvent these fundamental problems by directly pulling the DNA away from the coverslip by using a constant force axial optical tweezers7,8. This is achieved by trapping the bead in a linear region of the optical potential, where the optical force is constant-the strength of which can be tuned by adjusting the laser power. Trapping within the linear region also serves as an all optical force-clamp on the DNA that extends for nearly 350 nm in the axial direction. We simultaneously compensate for thermal and mechanical drift by finely adjusting the position of the stage so that a reference microsphere stuck to the coverslip remains at the same position and focus, allowing for a virtually limitless observation period.

We illustrate the use of a constant force axial optical tweezers to explore the mechanical properties of short DNA molecules. By stretching DNA axially, we minimize steric hindrances and artifacts arising in conventional lateral manipulation, allowing us to study DNA molecules as short as ~100 nm.

Single-molecule techniques for stretching DNA of contour lengths  less than a kilobase are fraught with experimental difficulties. However, many ...

Investigating Receptor-ligand Systems of the Cellulosome with AFM-based Single-molecule Force Spectroscopy

Cellulosomes are discrete multienzyme complexes used by a subset of anaerobic bacteria and fungi to digest lignocellulosic substrates. Assembly of the enzymes onto the noncatalytic scaffold protein is directed by interactions among a family of related receptor-ligand pairs comprising interacting cohesin and dockerin modules. The extremely strong binding between cohesin and dockerin modules results in dissociation constants in the low picomolar to nanomolar range, which may hamper accurate off-rate measurements with conventional bulk methods. Single-molecule force spectroscopy (SMFS) with the atomic force microscope measures the response of individual biomolecules to force, and in contrast to other single-molecule manipulation methods (i.e.&#160;optical tweezers), is optimal for studying high-affinity receptor-ligand interactions because of its ability to probe the high-force regime (&#62;120 pN). Here we present our complete protocol for studying cellulosomal protein assemblies at the single-molecule level. Using a protein topology derived from the native cellulosome, we worked with enzyme-dockerin and carbohydrate binding module-cohesin (CBM-cohesin) fusion proteins, each with an accessible free thiol group at an engineered cysteine residue. We present our site-specific surface immobilization protocol, along with our measurement and data analysis procedure for obtaining detailed binding parameters for the high-affinity complex. We demonstrate how to quantify single subdomain unfolding forces, complex rupture forces, kinetic off-rates, and potential widths of the binding well. The successful application of these methods in characterizing the cohesin-dockerin interaction responsible for assembly of multidomain cellulolytic complexes is further described.

Cellulosomes are multienzyme complexes designed for digesting cellulose. AFM-based SMFS was used to study the mechanical properties and folding configuration of cellulosome-associated protein assemblies. We present a complete workflow for protein immobilization, data acquisition, and data analysis to study the interactions of individual receptor-ligand complexes involved in cellulosome assembly.

Cellulosomes are discrete multienzyme complexes used by a subset of anaerobic bacteria and fungi to digest lignocellulosic substrates. Assembly of the ...

A Microfluidic Technique to Probe Cell Deformability

Here we detail the design, fabrication, and use of a microfluidic device to evaluate the deformability of a large number of individual cells in an efficient manner. Typically, data for ~102 cells can be acquired within a 1 hr experiment. An automated image analysis program enables efficient post-experiment analysis of image data, enabling processing to be complete within a few hours. Our device geometry is unique in that cells must deform through a series of micron-scale constrictions, thereby enabling the initial deformation and time-dependent relaxation of individual cells to be assayed. The applicability of this method to human promyelocytic leukemia (HL-60) cells is demonstrated. Driving cells to deform through micron-scale constrictions using pressure-driven flow, we observe that human promyelocytic (HL-60) cells momentarily occlude the first constriction for a median time of 9.3 msec before passaging more quickly through the subsequent constrictions with a median transit time of 4.0 msec per constriction. By contrast, all-trans retinoic acid-treated (neutrophil-type) HL-60 cells occlude the first constriction for only 4.3 msec before passaging through the subsequent constrictions with a median transit time of 3.3 msec. This method can provide insight into the viscoelastic nature of cells, and ultimately reveal the molecular origins of this behavior.

We demonstrate a microfluidics-based assay to measure the timescale for cells to transit through a sequence of micron-scale constrictions.

Here we detail the design, fabrication, and use of a microfluidic device to evaluate the deformability of a large number of individual cells in an ...

Formation of Biomembrane Microarrays with a Squeegee-based Assembly Method

Lipid bilayer membranes form the plasma membranes of cells and define the boundaries of subcellular organelles. In nature, these membranes are heterogeneous mixtures of many types of lipids, contain membrane-bound proteins and are decorated with carbohydrates. In some experiments, it is desirable to decouple the biophysical or biochemical properties of the lipid bilayer from those of the natural membrane. Such cases call for the use of model systems such as giant vesicles, liposomes or supported lipid bilayers (SLBs). Arrays of SLBs are particularly attractive for sensing applications and mimicking cell-cell interactions. Here we describe a new method for forming SLB arrays. Submicron-diameter SiO2 beads are first coated with lipid bilayers to form spherical SLBs (SSLBs). The beads are then deposited into an array of micro-fabricated submicron-diameter microwells. The preparation technique uses a "squeegee" to clean the substrate surface, while leaving behind SSLBs that have settled into microwells. This method requires no chemical modification of the microwell substrate, nor any particular targeting ligands on the SSLB. Microwells are occupied by single beads because the well diameter is tuned to be just larger than the bead diameter. Typically, more 75% of the wells are occupied, while the rest remain empty. In buffer SSLB arrays display long-term stability of greater than one week. Multiple types of SSLBs can be placed in a single array by serial deposition, and the arrays can be used for sensing, which we demonstrate by characterizing the interaction of cholera toxin with ganglioside GM1. We also show that phospholipid vesicles without the bead supports and biomembranes from cellular sources can be arrayed with the same method and cell-specific membrane lipids can be identified.

Supported lipid bilayers and natural membrane particles are convenient systems that can approximate the properties of cell membranes and be incorporated in a variety of analytical strategies. Here we demonstrate a method for preparing microarrays composed of supported lipid bilayer-coated SiO2 beads, phospholipid vesicles or natural membrane particles.

Lipid bilayer membranes form the plasma membranes of cells and define the boundaries of subcellular organelles. In nature, these membranes are ...

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. ...

Measurement of Maximum Isometric Force Generated by Permeabilized Skeletal Muscle Fibers

Analysis of the contractile properties of chemically skinned, or permeabilized, skeletal muscle fibers offers a powerful means by which to assess muscle function at the level of the single muscle cell. Single muscle fiber studies are useful in both basic science and clinical studies. For basic studies, single muscle fiber contractility measurements allow investigation of fundamental mechanisms of force production, and analysis of muscle function in the context of genetic manipulations. Clinically, single muscle fiber studies provide useful insight into the impact of injury and disease on muscle function, and may be used to guide the understanding of muscular pathologies. In this video article we outline the steps required to prepare and isolate an individual skeletal muscle fiber segment, attach it to force-measuring apparatus, activate it to produce maximum isometric force, and estimate its cross-sectional area for the purpose of normalizing the force produced.

Analysis of the contractile properties of chemically skinned, or permeabilized, skeletal muscle fibers offers a powerful means by which to assess muscle function at the level of the single muscle cell. In this article we outline a valid and reliable technique to prepare and test permeabilized skeletal muscle fibers in vitro.

Analysis of the contractile properties of chemically skinned, or permeabilized, skeletal muscle fibers offers a powerful means by which to assess muscle ...

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.

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 ...

Fluorescence Biomembrane Force Probe: Concurrent Quantitation of Receptor-ligand Kinetics and Binding-induced Intracellular Signaling on a Single Cell

Membrane receptor-ligand interactions mediate many cellular functions. Binding kinetics and downstream signaling triggered by these molecular interactions are likely affected by the mechanical environment in which binding and signaling take place. A recent study demonstrated that mechanical force can regulate antigen recognition by and triggering of the T-cell receptor (TCR). This was made possible by a new technology we developed and termed fluorescence biomembrane force probe (fBFP), which combines single-molecule force spectroscopy with fluorescence microscopy. Using an ultra-soft human red blood cell as the sensitive force sensor, a high-speed camera and real-time imaging tracking techniques, the fBFP is of ~1 pN (10-12 N), ~3 nm and ~0.5 msec in force, spatial and temporal resolution. With the fBFP, one can precisely measure single receptor-ligand binding kinetics under force regulation and simultaneously image binding-triggered intracellular calcium signaling on a single live cell. This new technology can be used to study other membrane receptor-ligand interaction and signaling in other cells under mechanical regulation.

We describe a technique for concurrently measuring force-regulated single receptor-ligand binding kinetics and real-time imaging of calcium signaling in a single T lymphocyte.

Membrane receptor-ligand interactions mediate many cellular functions. Binding kinetics and downstream signaling triggered by these molecular interactions ...