1. Herstellung von Lösungen und Materialien Diese Schritte sollten durchgeführt werden, mehrere Tage im Voraus. <ol><li> Deckgläser. Wasser, bei einer 1 gemischt: Die Deckgläser wurden durch Untertauchen für 10 Minuten in eine Lösung von Linbro 7X Reinigungsmittel gesäubert 3-Verhältnis und unter Rühren erhitzt, bis klar. Deckgläser wurden ausgiebig mit deionisiertem Wasser gespült und anschließend bei 450 ° C für 6 Stunden gebacken. Loading Deckgläser in keramische Färbegestelle (siehe Reagenzien) vereinfacht diesen Prozess. </li><li> Protein-Lösung für Stanz. Rekonstituieren Fibronektin folgenden Anweisungen des Herstellers, um eine Stammlösung von 1 mg / ml Konzentration. </li></ol> 2. Cast Briefmarken aus der topologischen Meister Diese Schritte können durchgeführt werden, mehrere Tage im Voraus. Shop Briefmarken Muster-up in einer Schale mit Deckel, wie ein Gewebe Kulturschale. <ol><li> Entfernen Sie den Staub vom Meister mit einem Strom von Druckluft, gefilterte Luft oder Inertgas. </li><li> Setzen Sie den Meister, gemusterten Seite nach oben in den Boden einer Plastikschale nur größer als der Meister. 60 - oder 100-mm Gewebekulturschalen sind für diesen Zweck gut geeignet. </li><li> In einem Polystyrol 50 ml Zentrifugenröhrchen, kombinieren die Sylgard Komponenten in einem Verhältnis von Härter: Elastomer Basis von 1: 10 nach Gewicht. Nach gründlichem Mischen mit einem Kunststoff-Gerät, wie ein Einweg-Pipette. Bereiten Sie mindestens 0,2 ml aus Elastomer pro Quadratzentimeter Gericht Bereich. </li><li> Zentrifugieren Sie die 50 ml Tube mit 300 g für 5 min, um Luftblasen zu entfernen. </li><li> Gießen Sie das Elastomer über den Master, dann in einem Exsikkator Platz unter Vakuum für 30 Minuten. </li><li> Cure das Elastomer in einem Ofen bei 65 ° C für mindestens 2 Stunden. Aushärtung bei höheren Temperaturen und längeren Zeiten Ergebnisse in steifer Elastomer. Lassen Sie auf Raumtemperatur abkühlen. </li><li> Separate das Blatt Briefmarken aus dem Master. </li></ol> 3. Mikrokontaktdruck von Fibronektin auf Glas <ol><li> Schneiden Sie einen einzigen Stempel. Briefmarken von 4 mm x 4 mm bis 1 cm x 1 cm groß und 1 bis 2 mm dick sind am einfachsten zu starten. Legen Sie Muster nach oben auf eine Glasplatte oder kleine Plastikschale. </li><li> Ort Stempel in einen Plasma-Reiniger und Verfahren unter Vakuum für 30 Sekunden. Ein Harrick Scientific Plasma-Reiniger (siehe Ausstattung), am höchsten Output Einstellung gesetzt wird machen die PDMS-Oberfläche hydrophil. Längere Zeiten führen zu Rissen des Elastomers. </li><li> Verdünnen Sie die Fibronektin-Lösung mit deionisiertem Wasser auf eine Stanz-Konzentration von 50 ug / ml. </li><li> Legen Sie einen kleinen Tropfen (10 bis 50 ul) von Stanz-Lösung auf den Stempel. Es wird über die hydrophile Oberfläche verteilt. Fügen Sie nur soviel Lösung, dass der Rückgang der Stempel deckt, aber nicht über die Kanten laufen. Lassen Protein adsorbieren für 5 Minuten zu stempeln. </li><li> Mit einem Kimwipe ® oder anderen sauberen Papiertuch, Docht aus die meisten der Protein-Lösung aus dem Stempel, ohne die strukturierten Gebiet. </li><li> Trocknen Sie die restliche Lösung aus der Stempel unter einem Strom von sauberen, trockenen, inerten Gas wie Stickstoff. </li><li> Mit Pinzette, entfernen Sie den Stempel aus der Glas-Objektträger, umzukehren, und in Kontakt mit dem gereinigten Deckglas (die Oberfläche strukturiert werden). Legen Sie ein Gewicht auf einen guten Kontakt zu fördern. Das spezifische Gewicht, dass die besten Strukturierung bietet, ist abhängig von den Stempel Größe und Muster; beginnen mit einem 5 g Gewicht und passen zwischen Stanzteile. Lassen Sie Stempel in Kontakt mit der Oberfläche für 1 Minute. </li><li> Vorsichtig zerlegen den Stack und separaten Stempel aus Deckglas. </li><li> Kräftig spülen gemusterten Deckglas in PBS, durch deionisiertes Wasser gefolgt, um Protein, das nicht an der Oberfläche adsorbiert ist zu entfernen. Dry Deckglas unter Stickstoffstrom. </li></ol> Repräsentative Ergebnisse Mikrokontaktdruck ist ein leistungsfähiges Verfahren zur Strukturierung Molekülen auf Oberflächen. Dieser Prozess hat die Fähigkeit, Funktionen mit Abmessungen von zehn Mikrometern bis einigen hundert Nanometern zu schaffen; in Abb.. 1A, sind die Logos auf der linken Seite jeweils 200 pm in der Höhe, während die grünen Flecken in Abb. dargestellt. 1B 1 ​​um Durchmesser und Abstand bei 4 um Intervalle, gemessen von Mitte zu Mitte. Abb.. 1B zeigt auch eine leistungsfähige Immobilien Mikrokontaktprägen, nämlich, dass es ist und additiven Prozess. Mehrere Runden von Mikrokontaktdrucken kann eine einzelne Fläche in Mehrkomponenten-Systeme 3 erstellen angewendet werden. <img src="/files/ftp_upload/old/1065_2008_11_24_3/Figure_a.jpg" alt="Abbildung A" /><img src="/files/ftp_upload/old/1065_2008_11_24_4/FIGURE_B.jpg" alt="Abbildung B" />

<ol>
	<li>Chen, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Geometric+control+of+cell+life+and+death.">Geometric control of cell life and death.</a> Science. 276, 1425-1425 (1997).</li><li>Kumar, A., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Features+of+Gold+Having+Micrometer+to+Centimeter+Dimensions+can+be+Formed+Through+a+Combination+of+Stamping+with+an+Elastomeric+Stamp+and+an+Alkanethiol+"Ink"+Followed+by+Chemical+Etching.">Features of Gold Having Micrometer to Centimeter Dimensions can be Formed Through a Combination of Stamping with an Elastomeric Stamp and an Alkanethiol "Ink" Followed by Chemical Etching.</a> Applied Physics Letters. 63, 4-4 (1993).</li><li>St. John, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preferential+Glial+Cell+Attachment+to+Microcontact-printed+Surfaces.">Preferential Glial Cell Attachment to Microcontact-printed Surfaces.</a> Journal of Neuroscience Methods. 75, 171-171 (1997).</li><li>Kam, L., Boxer, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+adhesion+to+protein-micropatterned-supported+lipid+bilayer+membranes.">Cell adhesion to protein-micropatterned-supported lipid bilayer membranes.</a> Journal of Biomedical Materials Research. 55, 487-487 (2001).</li><li>Kung, L. A., Kam, L., Hovis, J. S., Boxer, S. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patterning+Hybrid+Surfaces+of+Proteins+and+Supported+Lipid+Bilayers.">Patterning Hybrid Surfaces of Proteins and Supported Lipid Bilayers.</a> Langmuir. 16, 6773-6773 (2000).</li><li>Shen, K., Thomas, V. K., Dustin, M. L., Kam, 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=Micropatterning+of+costimulatory+ligands+enhances+CD4++T+cell+function.">Micropatterning of costimulatory ligands enhances CD4+ T cell function.</a> Proceedings of the National Academy of Sciences. 105, 7791-7791 (2008).</li><li>Shi, P., Shen, K., Kam, 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=Local+presentation+of+L1+and+N-cadherin+in+multicomponent,+microscale+patterns+differentially+direct+neuron+function+in+vitro.">Local presentation of L1 and N-cadherin in multicomponent, microscale patterns differentially direct neuron function in vitro.</a> Developmental Neurobiology. 67, 1765-1765 (2007).</li></ol>

The authors have nothing to disclose.

Die Mikrokontaktdrucken Prozess ist konzeptionell einfach und sehr robust, dass die Strukturierung einer Vielzahl von Molekülen auf einer Vielzahl von Substraten aufgebracht. Allerdings bleibt dieser Prozess etwas wie eine Kunst. Die spezielle Geometrie des Musters erstellt werden soll, Eiweiß zu strukturierende, Auflagegewicht und Beschichtung / Stanzen Bedingungen wirken sich auf die Prägequalität. Zum Beispiel, zu wenig Gewicht, auf große Features, führt oft zu Lücken in der Muster wie in der oberen rechten Logo ersichtlich ist. 1...

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<td>Plasma Cleaner</td>
<td>&nbsp;</td>
<td>Harrick Scientific Products, Inc.</td>
<td>PDC-32G</td>
<td>&nbsp;</td>
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<td>Desiccator</td>
<td>&nbsp;</td>
<td>Nalgene</td>
<td>5315-0150</td>
<td>&nbsp;</td>
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<td>PBS</td>
<td>Reagent</td>
<td>Invitrogen</td>
<td>10010-072</td>
<td>&nbsp;</td>
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<td>Protein labeling kit</td>
<td>Reagent</td>
<td>Invitrogen</td>
<td>A30006</td>
<td>&nbsp;</td>
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<td>Fibronectin </td>
<td>Reagent</td>
<td>Sigma-Aldrich</td>
<td>F2006</td>
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<td>Staining rack</td>
<td>Reagent</td>
<td>Thomas Scientific</td>
<td>8542E40</td>
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<td>Coverslips</td>
<td>Reagent</td>
<td>Fisher Scientific</td>
<td>12-544-12</td>
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<td>Sylgard 184</td>
<td>Reagent</td>
<td>Ellsworth Adhesives</td>
<td>184 Sil Elast Kit</td>
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<td>Diffraction Grating</td>
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microcontact printing of proteins for cell biology

Die Fähigkeit, Muster Proteinen und anderen Biomolekülen auf Substrate ist für die Erfassung der räumlichen Komplexität der extrazellulären Umgebung wichtig. Entwicklung von Mikrokontaktdrucken durch die Whitesides Gruppe (<a href="http://gmwgroup.harvard.edu/"&gt; Http://gmwgroup.harvard.edu/</a&gt;) In der Mitte der 1990er Jahre revolutioniert diesem Bereich, indem Mikroelektronik / Mikrofabrikationstechniken zugänglich Labors auf dem Gebiet Life Sciences fokussiert. Erste Implementierungen dieser Methode verwendet Polydimethylsiloxan (PDMS) Briefmarken, um Muster von funktionalisierten Chemikalien auf Materialoberflächen erstellen<sup&gt; 1</sup&gt;. Seitdem haben eine Reihe von innovativen Ansätzen, um Muster anderer Moleküle entwickelt worden, einschließlich Proteinen<sup&gt; 2</sup&gt;. Dieses Video zeigt den grundlegenden Prozess der Erstellung PDMS-Stempel und nutzt sie, um Muster Proteine, wie diese Schritte schwierig, genau in Worte zu fassen sind. Wir konzentrieren uns auf die Strukturierung der extrazellulären Matrix-Protein Fibronektin auf Deckgläschen als ein konkretes Beispiel der Musterung. Ein wichtiger Bestandteil des Mikrokontaktdrucken Prozess ist eine topologische Meister, von denen die Briefmarken abgegeben werden; das Heben und Senken Regionen der Meister in die Stempel gespiegelt und definieren die endgültige Muster. Typischerweise wird ein Kapitän eines Silizium-Wafers mit Fotolack beschichtet und dann strukturiert durch Photolithographie besteht, wie hier geschehen. Erstellung von Meistern, die ein bestimmtes Muster erfordert spezielle Ausrüstung und wird am besten in Absprache mit einem Fertigungszentrum oder Anlage angefahren. Allerdings kann fast jedes Substrat mit Topologie wie ein Meister, wie Kunststoff-Beugungsgitter (siehe Reagenzien für ein Beispiel) verwendet werden, und solche glückliche Meister geben leicht zugänglich, einfache Muster. Dieses Protokoll beginnt mit dem Punkt, der mit einem Master in der Hand.

Watch this Scientific Journal Video about Microcontact Printing of Proteins for Cell Biology at JoVE.com

Microcontact Printing of Proteins for Cell Biology

Mikrokontaktdruck ausgiebig in die Muster von Proteinen und anderen Molekülen auf Materialoberflächen eingesetzt. Wir zeigen die wichtigsten Schritte dieses Prozesses, Stanz-Muster von Fibronektin auf Glas.

Mikrokontaktdrucken von Proteinen für Zellbiologie

The ability to pattern proteins and other biomolecules onto substrates is important for capturing the spatial complexity of the extracellular environment. ...

microcontact-printing-of-proteins-for-cell-biology

Research

JoVE Journal

Biology

19.9K Aufrufe.  Columbia University. Mikrokontaktdruck ausgiebig in die Muster von Proteinen und anderen Molekülen auf Materialoberflächen eingesetzt. Wir zeigen die wichtigsten Schritte dieses Prozesses, Stanz-Muster von Fibronektin auf Glas.

Serie: Microcontact Printing of Proteins for Cell Biology

A Gradient-generating Microfluidic Device for Cell Biology

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an enabling experimental tool, because it can precisely manipulate fluid flows, enable high-throughput experiments, and generate stable soluble concentration gradients.  Compared to conventional gradient generators, poly(dimethylsiloxane) (PDMS)-based  microfluidic devices can generate stable concentration gradients of growth factors with well-defined profiles.  Here, we developed simple gradient-generating microfluidic devices with three separate inlets.  Three microchannels combined into one microchannel to generate concentration gradients.  The stability and shape of growth factor gradients were confirmed by fluorescein isothyiocyanate (FITC)-dextran with a molecular weight similar to epidermal growth factor (EGF).  Using this microfluidic device, we demonstrated that fibroblasts exposed to concentration gradients of EGF migrated toward higher concentrations.  The directional orientation of cell migration and motility of migrating cells were quantitatively assessed by cell tracking analysis.  Thus, this gradient-generating microfluidic device might be useful for studying and analyzing the behavior of migrating cells.

We describe a protocol for the microfabrication of the gradient-generating microfluidic device that can generate spatial and temporal gradients in well-defined microenvironment. In this approach, the gradient-generating microfluidic device can be used to study directed cell migration, embryogenesis, wound healing, and cancer metastasis.

Ein Gradient-Erzeugung Mikrofluidikvorrichtung für Zellbiologie

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an ...

Forschung

Biologie

Micro-scale Engineering for Cell Biology

Micro-Maßstab Engineering for Cell Biology

Assessing Two-dimensional Crystallization Trials of Small Membrane Proteins for Structural Biology Studies by Electron Crystallography

Electron crystallography has evolved as a method that can be used either alternatively or in combination with three-dimensional crystallization and X-ray crystallography to study structure-function questions of membrane proteins, as well as soluble proteins. Screening for two-dimensional (2D) crystals by transmission electron microscopy (EM) is the critical step in finding, optimizing, and selecting samples for high-resolution data collection by cryo-EM. Here we describe the fundamental steps in identifying both large and ordered, as well as small 2D arrays, that can potentially supply critical information for optimization of crystallization conditions.
By working with different magnifications at the EM, data on a range of critical parameters is obtained. Lower magnification supplies valuable data on the morphology and membrane size. At higher magnifications, possible order and 2D crystal dimensions are determined. In this context, it is described how CCD cameras and online-Fourier Transforms are used at higher magnifications to assess proteoliposomes for order and size.
While 2D crystals of membrane proteins are most commonly grown by reconstitution by dialysis, the screening technique is equally applicable for crystals produced with the help of monolayers, native 2D crystals, and ordered arrays of soluble proteins. In addition, the methods described here are applicable to the screening for 2D crystals of even smaller as well as larger membrane proteins, where smaller proteins require the same amount of care in identification as our examples and the lattice of larger proteins might be more easily identifiable at earlier stages of the screening.

Evaluating two-dimensional (2D) crystallization trials for the formation of ordered membrane protein arrays is a highly critical and difficult task in electron crystallography. Here we describe our approach in screening for and identifying 2D crystals of predominantly small membrane proteins in the range of 15 &#x2013; 90kDa.

Die Beurteilung Zweidimensionale Kristallisation Trials of Small Membranproteinen für Strukturbiologie Studien Electron Crystallography

Electron crystallography has evolved as a method that can be used either alternatively or in combination with three-dimensional crystallization and X-ray ...

Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. These systems offer a broad selection of fluorescent substrates optimized for a range of imaging instrumentation. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O6-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag labels are dyes conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells.

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again.

Fluoreszenzmarkierung von COS-7 mit dem Ausdruck SNAP-tag-Fusionsproteinen für das Live Cell Imaging

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest ...

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level. There are several methods, both in vitro and in vivo, to evaluate protein binding, and at least two methods that complement the shortcomings of each other should be conducted to obtain reliable insights. 
For an in vivo assay, the bimolecular fluorescence complementation (BiFC) assay represents the most popular and least invasive approach that enables to detect protein-protein interaction within living cells, as well as identify the intracellular localization of the interacting proteins 1,2. In this assay, non-fluorescent N- and C-terminal halves of GFP or its variants are fused to tested proteins, and when the two fusion proteins are brought together due to the tested proteins&#x2019; interactions, the fluorescent signal is reconstituted3-6. Because its signal is readily detectable by epifluorescence or confocal microscopy, BiFC has emerged as a powerful tool of choice among cell biologists for studying about protein-protein interactions in living cells 3. This assay, however, can sometimes produce false positive results. For example, the fluorescent signal can be reconstituted by two GFP fragments arranged as far as 7 nm from each other due to close packing in a small subcellular compartment, rather that due to specific interactions7.
Due to these limitations, the results obtained from live cell imaging technologies should be confirmed by an independent approach based on a different principle for detecting protein interactions. Co-immunoprecipitation (Co-IP) or glutathione transferase (GST) pull-down assays represent such alternative methods that are commonly used to analyze protein-protein interactions in vitro. However, iIn these assays, however, the tested proteins must be readily soluble in the buffer that supportsused for the binding reaction. Therefore, specific interactions involving an insoluble protein cannot be assessed by these techniques.
 Here, we illustrate the protocol for the protein membrane overlay binding assay, which circumvents this difficulty. In this technique, interaction between soluble and insoluble proteins can be reliably tested because one of the proteins is immobilized on a membrane matrix. This method, in combination with in vivo experiments, such as BiFC, provides a reliable approach to investigate and characterize interactions faithfully between soluble and insoluble proteins. In this article, binding between Tobacco mosaic virus (TMV) movement protein (MP), which exerts multiple functions during viral cell-to-cell transport8-14, and a recently identified plant cellular interactor, tobacco ankyrin repeat-containing protein (ANK) 15, is demonstrated using this technique.

Protein Membrane Overlay Assay: A Protocol to Test Interaction Between Soluble and Insoluble Proteins in vitro

Testing protein-protein interaction is indispensable for dissection of protein functionality. Here, we introduce an in vitro protein-protein binding assay to probe a membrane-immobilized protein with a soluble protein. This assay provides a reliable method to test interaction between an insoluble protein and a protein in solution.

Proteinmembran Overlay Assay: Ein Protokoll, die Interaktion zwischen löslichen und unlöslichen Proteinen testen In-vitro-</em

Validating interactions between different proteins is vital for investigation of their biological functions on the molecular level.  There are several ...

Pull-down of Calmodulin-binding Proteins

Calcium (Ca2+) is an ion vital in regulating cellular function through a variety of mechanisms. Much of Ca2+ signaling is mediated through the calcium-binding protein known as calmodulin (CaM)1,2. CaM is involved at multiple levels in almost all cellular processes, including apoptosis, metabolism, smooth muscle contraction, synaptic plasticity, nerve growth, inflammation and the immune response. A number of proteins help regulate these pathways through their interaction with CaM. Many of these interactions depend on the conformation of CaM, which is distinctly different when bound to Ca2+ (Ca2+-CaM) as opposed to its Ca2+-free state (ApoCaM)3.
While most target proteins bind Ca2+-CaM, certain proteins only bind to ApoCaM. Some bind CaM through their IQ-domain, including neuromodulin4, neurogranin (Ng)5, and certain myosins6. These proteins have been shown to play important roles in presynaptic function7, postsynaptic function8, and muscle contraction9, respectively. Their ability to bind and release CaM in the absence or presence of Ca2+ is pivotal in their function. In contrast, many proteins only bind Ca2+-CaM and require this binding for their activation. Examples include myosin light chain kinase10, Ca2+/CaM-dependent kinases (CaMKs)11 and phosphatases (e.g. calcineurin)12, and spectrin kinase13, which have a variety of direct and downstream effects14.
The effects of these proteins on cellular function are often dependent on their ability to bind to CaM in a Ca2+-dependent manner. For example, we tested the relevance of Ng-CaM binding in synaptic function and how different mutations affect this binding. We generated a GFP-tagged Ng construct with specific mutations in the IQ-domain that would change the ability of Ng to bind CaM in a Ca2+-dependent manner. The study of these different mutations gave us great insight into important processes involved in synaptic function8,15. However, in such studies, it is essential to demonstrate that the mutated proteins have the expected altered binding to CaM.
Here, we present a method for testing the ability of proteins to bind to CaM in the presence or absence of Ca2+, using CaMKII and Ng as examples. This method is a form of affinity chromatography referred to as a CaM pull-down assay. It uses CaM-Sepharose beads to test proteins that bind to CaM and the influence of Ca2+ on this binding. It is considerably more time efficient and requires less protein relative to column chromatography and other assays. Altogether, this provides a valuable tool to explore Ca2+/CaM signaling and proteins that interact with CaM.

Calmodulin (CaM) pull-down assay is an effective way to investigate the interaction of CaM with various proteins. This method uses CaM-sepharose beads for efficient and specific analysis of CaM-binding proteins. This provides an important tool to explore CaM signaling in cellular function.

Pull-down von Calmodulin-bindende Proteine

Calcium (Ca2+) is an ion vital in regulating cellular function through a variety of mechanisms. Much of Ca2+ signaling is mediated through the ...

Modified Yeast-Two-Hybrid System to Identify Proteins Interacting with the Growth Factor Progranulin

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role in a variety of physiologic and disease processes, including early embryogenesis, wound healing 1, inflammation 2, 3, and host defense 4. PGRN also functions as a neurotrophic factor 5, and mutations in the PGRN gene resulting in partial loss of the PGRN protein cause frontotemporal dementia 6, 7. Our recent studies have led to the isolation of PGRN as an important regulator of cartilage development and degradation 8-11. Although PGRN, discovered nearly two decades ago, plays crucial roles in multiple physiological and pathological conditions, efforts to exploit the actions of PGRN and understand the mechanisms involved have been significantly hampered by our inability to identify its binding receptor(s). To address this issue, we developed a modified yeast two-hybrid (MY2H) approach based on the most commonly used GAL4 based 2-hybrid system. Compared with the conventional yeast two-hybrid screen, MY2H dramatically shortens the screen process and reduces the number of false positive clones. In addition, this approach is reproducible and reliable, and we have successfully employed this system in isolating the binding proteins of various baits, including ion channel 12, extracellular matrix protein 10, 13, and growth factor14. In this paper, we describe this MY2H experimental procedure in detail using PGRN as an example that led to the identification of TNFR2 as the first known PGRN-associated receptor 14, 15.

We have modified the conventional yeast two-hybrid screening, an effective genetic tool in identifying protein interaction. This modification markedly shortens the process, reduces the workload, and most importantly, reduces the number of false positives. In addition, this approach is reproducible and reliable.

Modifizierten Hefe-Zwei-Hybrid-System, um Proteine ​​interagieren mit dem Growth Factor Progranulin Identifizieren

Progranulin (PGRN), also known as granulin epithelin precursor (GEP), is a 593-amino-acid autocrine growth factor. PGRN is known to play a critical role ...

Cell Tracking Using Photoconvertible Proteins During Zebrafish Development

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of genetically-encoded fluorescent proteins has proven a valuable strategy for elucidating dynamic morphogenetic processes as they occur in the intact organism. During the past decade, the development of photoactivatable and photoconvertible fluorescent proteins has opened the possibility to investigate the fate of discrete subpopulations of tagged proteins1. Unlike photoactivatable proteins, photoconvertible fluorescent proteins (PCFPs) are readily tracked and imaged in their native emission state prior to photoconversion, making it easier to identify and select regions by optical inspection. PCFPs, such as Kaede2, KikGR3, Dendra4 and EosFP5, can be shifted from green to red upon exposure to UV or blue light due to a His-Tyr-Gly tripeptide sequence which forms a green chromophore that can be photoconverted to a red one by a light-catalyzed &beta;-elimination and subsequent extension of a &pi;-conjugated system3. PCFPs and their monomeric variants are useful tools for tracking cells6-10 and studying protein dynamics11-14, respectively. During recent years, PCFPs have been expressed in different animal model, such as zebrafish6, chicken7,8 and mouse9,10 for cell fate tracking. Here we report a protocol for cell-specific photoconversion of PCFPs in the living zebrafish embryo and further tracking of photoconverted proteins at later developmental stages. This methodology allows studying, in a tissue-specific manner, cell biological events underlying morphogenesis in the zebrafish animal model.

Here, we present a method for the photoactivated switch of photoconvertible fluorescent proteins (PCFPs) in the living zebrafish embryo and further tracking of photoconverted protein at specific time points during development. This methodology allows monitoring of cell biological events underlying different developmental processes in a live vertebrate organism.

Handy-Tracking Mit Photoconvertible Proteine ​​während der Zebrafisch-Entwicklung

Embryogenesis is a dynamic process that is best studied by using techniques that allow the documentation of developmental changes in vivo. The use of ...

The Use of Chemostats in Microbial Systems Biology

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated including macromolecular synthesis, metabolism and ultimately, commitment to the cell division cycle. The chemostat, a method of experimentally controlling cell growth rate, provides a powerful means of systematically studying how growth rate impacts cellular processes - including gene expression and metabolism - and the regulatory networks that control the rate of cell growth. When maintained for hundreds of generations chemostats can be used to study adaptive evolution of microbes in environmental conditions that limit cell growth. We describe the principle of chemostat cultures, demonstrate their operation and provide examples of their various applications. Following a period of disuse after their introduction in the middle of the twentieth century, the convergence of genome-scale methodologies with a renewed interest in the regulation of cell growth and the molecular basis of adaptive evolution is stimulating a renaissance in the use of chemostats in biological research.

Cell growth rate is a regulated process and a primary determinant of cell physiology. Continuous culturing using chemostats enables extrinsic control of cell growth rate by nutrient limitation facilitating the study of molecular networks that control cell growth and how those networks evolve to optimize cell growth.

Der Einsatz von Chemostate in Microbial Systems Biology

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated ...

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology.2,3 To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems.4,5 The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.6 Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted.7 The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters.6,8 Accompanying mathematical models are available.9,10 The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.

Protokolle für die Implementierung einer<em&gt; Escherichia coli</em&gt; Basierend TX-TL Zellfreie Expression System für Synthetische Biologie

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for ...