Name: flexural rigidity measurements of biopolymers using gliding assays
Uploaded: 2012-11-09T13:00:00
Description: Watch this Scientific Journal Video about Flexural Rigidity Measurements of Biopolymers Using Gliding Assays at JoVE.com

Мы благодарим Мелисса Klocke за помощь подготовке Рисунок 1 и Анна Ratliff для демонстрации протокол. Эта работа была поддержана Research Corporation по науке улучшению.

1. Микротрубочек Gliding анализа растворов Подготовка перед анализом скольжения. <ol><li> Полимеризации 0,5 мг микротрубочек редко помечены яркой органических флуорофоров 22. Концентрацией целевой метки составляет 1 флуорофора в микрометра микротрубочек, или маркировки ...

<ol>
	<li>Hawkins, T., Mirigian, M., Selcuk Yasar, M., Ross, 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=Mechanics+of+microtubules.">Mechanics of microtubules.</a> Journal of biomechanics. 43, 23-30 (2010).</li><li>Pampaloni, 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=Thermal+fluctuations+of+grafted+microtubules+provide+evidence+of+a+length-dependent+persistence+length.">Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length.</a> Proceedings of the national academy of sciences U S A. 103, 10248-10253 (2006).</li><li>Taute, K. M., Pampaloni, F., Frey, E., Florin, E. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microtubule+dynamics+depart+from+the+wormlike+chain+model.">Microtubule dynamics depart from the wormlike chain model.</a> Physical review letters. 100, 028102 (2008).</li><li>Van den Heuvel, M. G., de Graaff, M. P., Dekker, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microtubule+curvatures+under+perpendicular+electric+forces+reveal+a+low+persistence+length.">Microtubule curvatures under perpendicular electric forces reveal a low persistence length.</a> Proceedings of the national academy of sciences U.S.A. 105, 7941-7946 (2008).</li><li>Gittes, F., Mickey, B., Nettleton, J., Howard, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flexural+rigidity+of+microtubules+and+actin+filaments+measured+from+thermal+fluctuations+in+shape.">Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape.</a> Journal of cell biology. 120, 923-934 (1993).</li><li>Brangwynne, C. P., 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=Bending+dynamics+of+fluctuating+biopolymers+probed+by+automated+high-resolution+filament+tracking.">Bending dynamics of fluctuating biopolymers probed by automated high-resolution filament tracking.</a> Biophysical journal. 93, 346-359 (2007).</li><li>Cassimeris, L., Gard, D., Tran, P. T., Erickson, H. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=XMAP215+is+a+long+thin+molecule+that+does+not+increase+microtubule+stiffness.">XMAP215 is a long thin molecule that does not increase microtubule stiffness.</a> Journal of cell science. 114, 3025-3033 (2001).</li><li>Valdman, D., Atzberger, P. J., Yu, D., Kuei, S., Valentine, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectral+analysis+methods+for+the+robust+measurement+of+the+flexural+rigidity+of+biopolymers.">Spectral analysis methods for the robust measurement of the flexural rigidity of biopolymers.</a> Biophysical. 102, 1144-1153 (2012).</li><li>van Mameren, J., Vermeulen, K. C., Gittes, F., Schmidt, C. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Leveraging+single+protein+polymers+to+measure+flexural+rigidity.">Leveraging single protein polymers to measure flexural rigidity.</a> Journal of physical chemistry b. 113, 3837-3844 (2009).</li><li>Hua, W., Chung, J., Gelles, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distinguishing+inchworm+and+hand-over-hand+processive+kinesin+movement+by+neck+rotation+measurements.">Distinguishing inchworm and hand-over-hand processive kinesin movement by neck rotation measurements.</a> Science. 295, 844-848 (2002).</li><li>Duke, T., Holy, T. E., Leibler, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="Gliding+assays"+for+motor+proteins:+A+theoretical+analysis.">"Gliding assays" for motor proteins: A theoretical analysis.</a> Physical review letters. 74, 330-333 (1995).</li><li>Mehrbod, M., Mofrad, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+significance+of+microtubule+flexural+behavior+in+cytoskeletal+mechanics.">On the significance of microtubule flexural behavior in cytoskeletal mechanics.</a> PLoS one. 6, e25627 (2011).</li><li>Szarama, K. B., Gavara, N., Petralia, R. S., Kelley, M. W., Chadwick, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytoskeletal+changes+in+actin+and+microtubules+underlie+the+developing+surface+mechanical+properties+of+sensory+and+supporting+cells+in+the+mouse+cochlea.">Cytoskeletal changes in actin and microtubules underlie the developing surface mechanical properties of sensory and supporting cells in the mouse cochlea.</a> Development. 139, 2187-2197 (2012).</li><li>Gal, N., Weihs, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intracellular+Mechanics+and+Activity+of+Breast+Cancer+Cells+Correlate+with+Metastatic+Potential.">Intracellular Mechanics and Activity of Breast Cancer Cells Correlate with Metastatic Potential.</a> Cell biochemistry and biophysics. , (2012).</li><li>Volokh, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+tensegrity+in+cell+mechanics.">On tensegrity in cell mechanics.</a> Mol. Cell Biomech. 8, 195-214 (2011).</li><li>Kasas, S., Dietler, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Techniques+for+measuring+microtubule+stiffness.">Techniques for measuring microtubule stiffness.</a> Current nanoscience. 3, 85-96 (2007).</li><li>Kikumoto, M., Kurachi, M., Tosa, V., Tashiro, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flexural+rigidity+of+individual+microtubules+measured+by+a+buckling+force+with+optical+traps.">Flexural rigidity of individual microtubules measured by a buckling force with optical traps.</a> Biophysical journal. 90, 1687-1696 (2006).</li><li>Venier, P., Maggs, A. C., Carlier, M. F., Pantaloni, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+microtubule+rigidity+using+hydrodynamic+flow+and+thermal+fluctuations.">Analysis of microtubule rigidity using hydrodynamic flow and thermal fluctuations.</a> Journal of biological chemistry. 269, 13353-13360 (1994).</li><li>van den Heuvel, M. G., Bolhuis, S., Dekker, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Persistence+length+measurements+from+stochastic+single-microtubule+trajectories.">Persistence length measurements from stochastic single-microtubule trajectories.</a> Nano letters. 7, 3138-3144 (2007).</li><li>Phillips, R., Kondev, J., Theriot, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Physical biology of the cell. , (2008).</li><li>Berliner, E., Young, E. C., Anderson, K., Mahtani, H. 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S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+fluorescent+GTP+analog+as+a+specific,+high-precision+label+of+microtubules.">A fluorescent GTP analog as a specific, high-precision label of microtubules.</a> Biotechniques. 51, 43-48 (2011).</li><li>Hyman, A. <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+modified+tubulins.">Preparation of modified tubulins.</a> Methods in enzymology. 196, 478-485 (1991).</li><li>Lee, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Curve+reconstruction+from+unorganized+points.">Curve reconstruction from unorganized points.</a> Computer aded geometric design. 17, 161-177 (2000).</li><li>Yildiz, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Myosin+V+walks+hand-over-hand:+Single+fluorophore+imaging+with+1.5-nm+localization.">Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization.</a> Science. 300, 2061-2065 (2003).</li><li>Friedman, L. 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Постоянство измерений длины являются хорошей характеристикой механических свойств отдельных биополимеров. В этой статье мы описали метод измерения с сохранением длины микротрубочек. Как отмечалось во введении, этот метод легко распространить на изучение механических свойств микро?...

The cytoskeleton, a network of biopolymers found in most eukaryotic cells, plays a role in cellular organization, intracellular transport, and cell mechanics. The mechanical characteristics of the biopolymers of the cytoskeleton (primarily actin and microtubules) play a significant role in determining the mechanical characteristics of the cell as a whole12. Since whole cell mechanics can characterize healthy and diseased cells13,14 and is involved in cellular motility15, the mechanical properties of the underlying cytoskeletal components have been an active area of study for the past two decades1.
The flexibility (or stiffness) of biopolymers is characterized by the persistence length, the length of polymer which bends by approximately one radian under thermal fluctuations at ambient temperature. A number of techniques have been developed to measure persistence length16, for example active techniques which involve bending the polymer using hydrodynamic flow, optical traps, or electric fields4,17,18 , and passive techniques which measure the fluctuations of free polymers in solution5,6 . The active measurements, however, require specialized setups to implement known forces on the micrometer scale, and the free-fluctuation measurements can be challenging due to diffusion out of the plane of focus of the microscope used.
In this article, we describe a complementary, passive, technique to measure the persistence length of microtubules, a cytoskeletal polymer. The technique involves gliding assays, which ensure that the polymer always remains in the focal plane19. Moreover, it involves tracking single fluorophores attached permanently to the polymer of interest, so that specific locations along the polymer are well characterized.
A cartoon of the method is shown in Figure 1. Kinesin moves specifically toward the + end of microtubules, so the microtubules in a gliding assay are propelled unidirectionally. The leading end of the microtubule, beyond the last kinesin attached, is free to fluctuate under the thermal forces of the surrounding solution. As the microtubule is propelled forward, the end fluctuates until binding to a new kinesin molecule further along the glass slide freezes in a given fluctuation. Because kinesin attaches microtubules very strongly, the microtubule is constrained to follow the path of the leading end. Therefore, the statistical fluctuations frozen into the microtubule trajectory are the same as the statistical fluctuations of the free end of microtubules11, and can therefore be used to calculate the persistence length according to20
<img alt="Equation 1" fo:content-width="1in" fo:src="/files/ftp_upload/50117/50117eq1highres.jpg" src="/files/ftp_upload/50117/50117eq1.jpg" /> 
where lp is the persistence length of the microtubule, &theta;s is the angle between tangents to the trajectory separated by a contour length s, and &lt;&gt; denotes an average over all pairs of positions separated by a contour length s.
The gliding assay itself uses kinesin biotinylated at the coiled-coil21 specifically bound to the glass slide via a streptavidin-biotin linkage. This attachment ensures that the motor domains are free to bind to and propel microtubules. In order to follow microtubule trajectories, microtubules are sparsely labeled with organic fluorophores22,23 - the labels must be sparse enough that single fluorophores are resolvable using single molecule fluorescence microscopy. Single fluorophores are tracked using image analysis routines written in IDL. The trajectories of each fluorophore bound to a given microtubule are combined into a composite microtubule trajectory automatically24. The tangent angles &theta; to each point along a trajectory are calculated; from these tangent angles the &lt;cos&theta;s&gt; value is calculated for each contour length s. Finally, these data are fit to Eq. 1 in order to extract a persistence length for a given microtubule, or for many microtubules in the same gliding assay.
The method is robust enough to work with microtubules prepared in a wide variety of conditions (with different stabilizing agents or other small molecules bound to the microtubule, with bound microtubule associated proteins (MAPs), or with a variety of viscous solutions). In our lab, the technique has been used to characterize the persistence length of microtubules as a function of length along the microtubules and microtubules with different stabilizing agents. The main restriction is that the microtubules must still support kinesin motility. Since kinesin is a robust motor enzyme, this is a fairly loose restriction. By replacing microtubules with actin and kinesin with a myosin family enzyme, the persistence length of actin can be measured using the same technique.

<table border="1">
	<tbody>
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 <td>Reagents </td>
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 <td>imidazole</td>
 <td>Sigma-Aldrich</td>
 <td>I2399 </td>
 <td></td>
 </tr>
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 <td>potassium chloride</td>
 <td>Sigma-Aldrich</td>
 <td>P9541 </td>
 <td></td>
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 <td>magnesium chloride</td>
 <td>Sigma-Aldrich</td>
 <td>M8266 </td>
 <td></td>
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 <td>EGTA</td>
 <td>Sigma-Aldrich</td>
 <td>E3889 </td>
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 <td>BSA</td>
 <td>Calbiochem</td>
 <td>126615</td>
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 <td>biotinylated BSA</td>
 <td>Thermo Scientific</td>
 <td>29130</td>
 <td></td>
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 <td>&alpha;-casein</td>
 <td>Sigma-Aldrich</td>
 <td>C6780 </td>
 <td></td>
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 <td>streptavidin</td>
 <td>Thermo Scientific</td>
 <td>21125</td>
 <td></td>
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 <td>dithiothreitol</td>
 <td>Sigma-Aldrich</td>
 <td>D0632 </td>
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 <td>paclitaxel</td>
 <td>LC Laboratories</td>
 <td>P-9600</td>
 <td></td>
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 <td>glucose oxidase</td>
 <td>Sigma-Aldrich</td>
 <td>G2133</td>
 <td></td>
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 <td>catalase</td>
 <td>Sigma-Aldrich</td>
 <td>C100</td>
 <td></td>
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 <td>glucose</td>
 <td>Sigma-Aldrich</td>
 <td>G8270</td>
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 <td>ATP</td>
 <td>Sigma-Aldrich</td>
 <td>A2383 </td>
 <td></td>
 </tr>
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 <td>2-mercaptoethanol</td>
 <td>Sigma-Aldrich</td>
 <td>M3148 </td>
 <td>Toxic. Buy small amount.</td>
 </tr>
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 <td>24X60 mm No. 1 1/2 cover glass</td>
 <td>VWR</td>
 <td>48393-252</td>
 <td></td>
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 <td>22X22 mm No. 1 cover glass</td>
 <td>Gold Seal</td>
 <td>3306</td>
 <td></td>
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 <td>High Vacuum Grease</td>
 <td>Dow-Corning</td>
 <td>NA</td>
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 <td>Equipment </td>
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 <td>TIRF microscope</td>
 <td>many</td>
 <td>NA</td>
 <td>The TIRF microscope used in this method was home-made.</td>
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 <td>IDL (software)</td>
 <td>Exelis</td>
 <td>NA</td>
 <td>Could substitute MATLAB, ImageJ, or other image analysis software.</td>
 </tr>
	 </tbody>
 </table>

flexural rigidity measurements of biopolymers using gliding assays

Микротрубочки цитоскелета являются полимерами, которые играют важную роль в делении клеток, клеточной механики и внутриклеточного транспорта. Каждая из этих функций требует микротрубочек, которые являются жесткими и прямыми достаточно, чтобы охватить значительную часть клетки диаметра. В результате, длина микротрубочек настойчивость, мера жесткости, активно исследуется в течение последних двух десятилетий 1. Тем не менее, открытыми остаются вопросы: короткие микротрубочки в 10-50 раз менее жесткими, чем длинные микротрубочки 2-4, и даже долго микротрубочек измерили сохранением длины, которые зависят от порядка 5-9. Здесь мы представляем метод для измерения длины микротрубочек настойчивость. Метод основан на кинезин управляемые скольжением микротрубочек анализа 10. Благодаря сочетанию редких флуоресцентные маркировки отдельных микротрубочек с одной отслеживание частиц отдельных флуорофоров прикреплены к микротрубочек, Glidinг траектории одной микротрубочки отслеживаются с нанометрового уровня точности. Сохранение длины траектории так же, как сохранение длины микротрубочек в соответствии с условиями 11. Автоматизированное отслеживание используется для создания микротрубочек траекторий из флуорофоров к отдельным микротрубочки, и сохранением длины этой траектории рассчитывается с использованием процедуры, написанные на IDL. Эта техника быстро реализуемым, и способны измерять сохранение длиной 100 микротрубочек в один день эксперимента. Метод может быть расширен для измерения длины настойчивость в различных условиях, в том числе сохранением длины в зависимости от длины вдоль микротрубочек. Кроме того, анализ процедур, используемых может быть продлен до миозина на основе действующего скольжение анализы, чтобы измерить длину сохранение нитей актина, а также.

A snapshot from a gliding assay is shown in Figure 2. A good microtubule density is 1-10 microtubules per field of view; substantially more will result in mistracking as microtubules cross each other. A plot of the 11 microtubule trajectories from the gliding assay in Figure 2 is shown in Figure 3. Typical trajectories are 10 to 30 &mu;m long; some trajectories have gaps where one microtubule crosses another. These trajectories may be discarded from analysis....

Watch this Scientific Journal Video about Flexural Rigidity Measurements of Biopolymers Using Gliding Assays at JoVE.com

Flexural Rigidity Measurements of Biopolymers Using Gliding Assays

Метод измерения длины сохранение или жесткость на изгиб биополимеров описано. Метод использует кинезин управляемые скольжением микротрубочек анализа экспериментально определить сохранением длины отдельных микротрубочек и адаптируется к актина на основе скользящих анализов.

Жесткость на изгиб измерений биополимеров Использование Gliding Анализы

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Molecular Entanglement and Electrospinnability of Biopolymers

Молекулярная Запутанность и Electrospinnability биополимеров

Electrospinning is a fascinating technique to fabricate micro- to nano-scale fibers from a wide variety of materials. For biopolymers, molecular ...

Methods for the Self-integration of Megamolecular Biopolymers on the Drying Air-LC Interface

Методы самостоятельной интеграции Megamolecular биополимеров на сушильный воздух-LC интерфейс

Living organisms that use water are always prone to drying in the environment. Their activities are driven by biopolymer-based micro- and ...

Power Input Measurements in Stirred Bioreactors at Laboratory Scale

Мощность входных измерения в перемешиваемой биореакторов лабораторного масштаба

The power input in stirred bioreactors is an important scaling-up parameter and can be measured through the torque that acts on the impeller shaft during ...

A Millimeter Scale Flexural Testing System for Measuring the Mechanical Properties of Marine Sponge Spicules

Миллиметр на изгиб тестирования системы шкалы для измерения механических свойств морской губкой спикулы

Many load bearing biological structures (LBBSs)&#8212;such as feather rachises and spicules&#8212;are small (&#60;1 mm) but not microscopic. Measuring the ...