Name: mapping protein interaction networks
Uploaded: 2023-04-30T18:28:44.000Z
Duration: 2 min 26 s
Channel: JoVE

K12 Standards

Next Generation Science Standards

High School

Life Science

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

HS-LS1-1

Protein Networks

Ein einzelner Organismus kann Tausende verschiedener Proteine enthalten, und die meisten dieser Proteine müssen mit anderen Proteinen interagieren, um ihre Funktionen zu erfüllen.
Viele Proteine haben mehrere Bindungspartner, was zu einem komplexen Netzwerk von Proteininteraktionen führt.
Verschiedene Labortechniken, darunter sowohl biochemische als auch computergestützte Methoden, helfen den Wissenschaftlern, diese Proteinnetzwerke zu verstehen.
Affinitätsmarkierung ist eine Methode, die häufig verwendet wird, um ein Protein zusammen mit anderen interagierenden Molekülen zu isolieren. Ein Affinitäts-Tag ist ein Aminosäuremotiv, das genetisch zu dem Protein von Interesse hinzugefügt wird. Diese Markierung kann verwendet werden, um das Zielprotein zusammen mit anderen Proteinen, die mit ihm assoziiert sind, zu isolieren. 
Proteine, die mit dem markierten Protein interagieren, können analysiert werden, um ihre Identität und neue Wechselwirkungen zu bestimmen.
Eine Methode, um diese unbekannten Proteinwechselwirkungen zu analysieren, besteht darin, die Proteine in kurze Segmente zu zerlegen und mit einem Massenspektrometer zu analysieren, um die Aminosäuresequenzen zu bestimmen. Diese Sequenzen können mit bestehenden Proteinsequenzdatenbanken verglichen werden, um unbekannte assoziierte Proteine zu identifizieren. 
Darüber hinaus stehen in frei verfügbaren Datenbanken wie IntAct Protein-Protein-Interaktionsdaten, die von Forschern weltweit hochgeladen wurden, zum Vergleich zur Verfügung. Andere Datenbanken in Verbindung mit einer wachsenden Anzahl fortschrittlicher Bioinformatik-Tools können verwendet werden, um die molekularen Wechselwirkungen eines unbekannten Proteins vorherzusagen
Protein-Protein-Interaktionsnetzwerkkarten werden verwendet, um diese Wechselwirkungen zwischen Proteinen in einer Zelle zu visualisieren. Die Kreise sind Knoten, die ein bestimmtes Protein repräsentieren, und Linien sind Kanten, die ein Protein mit den anderen interagierenden Proteinen verbinden. 
Die Untersuchung von Proteininteraktionskarten kann helfen, Proteinfunktionen vorherzusagen. Wenn das Interaktionsmuster eines unbekannten Proteins aus Verbindungskanten dem eines anderen Knotens ähnlich ist, können sich diese beiden Knoten ähnlich verhalten.
Einige Knoten werden als hochgradig vernetzte Knotenpunkte erscheinen, deren Untersuchung zur Entdeckung grundlegender Mechanismen zur Erhaltung der Gesundheit der Zelle führen und so die Arzneimittelentwicklung unterstützen kann.

<ol>
	<li>Alberts et al., 6. Auflage; Seiten 166-169</li>
	<li>Morris, J. H., Knudsen, G. M., Verschueren, E., Johnson, J. R., Cimermancic, P., Greninger, A. L., & Pico, A. R. (2014). Affinitätsreinigung – Massenspektrometrie und Netzwerkanalyse zum Verständnis von Protein-Protein-Wechselwirkungen. Naturprotokolle, 9(11), 2539.</li>
	<li>Ottman, C. (2013). Protein-Protein-Wechselwirkungen: ein Überblick. Protein-Protein-Wechselwirkungen in der Arzneimittelforschung.</li>
	<li>Jordán, F., Nguyen, T. P., & Liu, W. C. (2012). Untersuchung von Protein-Protein-Interaktionsnetzwerken: eine systemische Sicht auf Krankheiten. Briefings in funktioneller Genomik, 11(6), 497-504.</li>
	<li>Berggård, T., Linse, S., & James, P. (2007). Methoden zum Nachweis und zur Analyse von Protein-Protein-Wechselwirkungen. Proteomik, 7(16), 2833-2842.</li>
	<li>Gingras, A. C., Gstaiger, M., Raught, B., & Aebersold, R. (2007). Analyse von Proteinkomplexen mittels Massenspektrometrie. Nature Reviews Molekulare Zellbiologie, 8(8), 645.</li>
</ol>

protein-netzwerke

Ein Organismus kann Tausende verschiedener Proteine besitzen, und diese Proteine müssen zusammenarbeiten, um die Gesundheit des Organismus zu gewährleisten. Proteine binden an andere Proteine und bilden Komplexe, um ihre Funktionen auszuführen. Viele Proteine interagieren mit mehreren anderen Proteinen und bilden so ein komplexes Netzwerk von Proteininteraktionen.

Diese Interaktionen können durch Karten dargestellt werden, die Protein-Protein-Interaktionsnetzwerke zeigen, repräsentiert durch Knoten und Kanten. Knoten sind Kreise, die ein Protein darstellen, und Kanten sind Linien, die zwei interagierende Proteine verbinden. Diese Netzwerke bieten eine Möglichkeit, die Komplexität der Protein-Protein-Wechselwirkungen in einem System zu visualisieren. Diese Karten können sowohl stabile Interaktionen, wie die in Proteinkomplexen gebildeten, als auch transiente Interaktionen umfassen. Die Proteininteraktionen, die in einer Zelle, einem Organismus oder einem spezifischen biologischen Kontext stattfinden, können kollektiv als 'Interaktom' bezeichnet werden.

Proteinnetzwerke können mit verschiedenen biochemischen und computergestützten Methoden untersucht werden. Ein erster Schritt beim Studium von Proteininteraktionen besteht darin, ein Protein von Interesse zusammen mit den anderen assoziierten Proteinen zu isolieren. Dies kann durch das Markieren des Proteins von Interesse mit einem Affinitäts-Tag, wie einem Histidin-Tag, durchgeführt werden. Dieses Tag kann dann verwendet werden, um das Protein zusammen mit den anderen Proteinen mittels Affinitätschromatographie zu separieren. Isolierte Proteine werden anschließend mit einer Protease, wie Trypsin, verdaut und mittels Flüssigkeitschromatographie-Massenspektrometrie (LC-MS) analysiert. Die Peptidmasse kann dann mit einer Datenbank bekannter Proteinsequenzen verglichen werden, um ihre Identität zu bestimmen.

Computergestützt können Protein-Protein-Wechselwirkungen unter Verwendung von Datenbanken sowie Vorhersagewerkzeugen analysiert werden. Es gibt verschiedene Datenbanken, wie IntAct, die vom EMBL-EBI verwaltet wird und experimentell validierte sowie vorhergesagte Proteininteraktionen enthält. Andere Werkzeuge wie STRING vom Schweizer Institut für Bioinformatik können verwendet werden, um diese Interaktionsnetzwerke vorherzusagen.

Das Studium von Proteinnetzwerken kann zu wissenschaftlichen Entdeckungen führen, wie beispielsweise der Bestimmung der Funktion eines unbekannten Proteins. Die Untersuchung der Veränderungen in diesen Netzwerken kann helfen, die Unterschiede zwischen gesunden und kranken Zellen zu verdeutlichen. Diese Informationen können auch für wichtige Anwendungen wie die Entwicklung von Medikamenten zur Behandlung von Krankheiten genutzt werden. Die Analyse von Proteinnetzwerken kann hochvernetzte Knoten identifizieren, die für das Überleben der Zelle entscheidend sein können und die bei Krebs und Krankheiten, bei denen der Zelltod erwünscht ist, ins Visier genommen werden können, was jedoch für die meisten Krankheiten ungeeignet wäre. Andererseits könnten weniger vernetzte Knoten, die nur mit wenigen spezifischen Wegen interagieren, angezielt werden, wenn eine bestimmte Zellfunktion beeinträchtigt ist, und die Entwicklung von Medikamenten, die mit diesen weniger vernetzten Knoten interagieren, könnte zu weniger Nebenwirkungen führen.

Protein-Netzwerke

Ein Organismus kann Tausende von verschiedenen Proteinen haben, und diese Proteine müssen zusammenarbeiten, um die Gesundheit eines Organismus zu gewährleisten. Proteine binden an andere ...

Education

Lehre

JoVE Core

Cell Biology

Zellbiologie

Unit 1

Einheit 1

Protein Function

Proteinfunktion

KEY TERMS AND CONCEPTS

KERNBEGRIFFE UND KONZEPTE

mapping protein interaction networks

Protein interaction networks show how proteins work together inside a cell. These networks help scientists see which proteins connect with each other and how those links support cell activity.

Researchers often use online tools to build and study these networks. The transcript points to IntAct and STRING as examples of resources that can help predict and organize protein interactions. These tools make it easier to compare protein links and look for patterns in the network.

Protein networks are useful for understanding biological function. They can also help students see that proteins do not act alone. Instead, many proteins form connected systems that support specific cell processes.

Mapping Protein Interaction Networks

ligand binding sites

Ligand Binding Sites in Proteins

Ligand binding sites are specific parts of a protein where a ligand can attach. A ligand is a molecule that binds to another molecule, often to help start or change a biological process. These sites matter because the shape and chemistry of the protein help determine which ligands can fit and bind. Proteins do not bind every ligand in the same way. The binding site provides a matching surface that supports a close interaction. In many cases, this interaction is important for how cells respond...

protein-protein interfaces

Protein Binding Surfaces and Contacts

Protein binding surfaces and contacts help proteins recognize and attach to each other. These interfaces are the regions where two proteins meet and interact. They are important for many cell processes and for how proteins work together. A protein-protein interface is not just a random touch point. It is shaped by the three-dimensional form of each protein. The matching surfaces allow a stable interaction to form when the proteins fit together well. Studying these interfaces helps explain how...

conserved binding sites

Conserved Binding Sites in Protein Families

Conserved binding sites are regions on proteins that stay similar across related proteins. These shared areas often help proteins interact with the same molecules. For this reason, they are useful clues when comparing protein families. A conserved site can help identify where a protein binds. It can also show which parts of the protein are important for function. When the same pattern appears in several proteins, it suggests that the site has been kept through evolution. Scientists look at...

cofactors and coenzymes

Enzyme Helpers: Metals and Vitamins

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cooperative allosteric transitions

Allosteric Changes in Protein Shape

Allosteric changes in protein shape help explain how some proteins switch between active and inactive states. These transitions are cooperative, which means a change in one part of the protein can affect other parts of the same molecule. The video focuses on how these shifts in shape support protein function. It also shows that allosteric transitions can be described with different models. In the concerted model, the protein changes shape as a whole. In the sequential model, the change happens...

protein kinases and phosphatases

Protein Kinases and Phosphatases in Cell Control

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gtpases and their regulation

GTPase Molecular Switches and Control

GTPases are molecular switches that help control cell activity. They bind guanosine triphosphate, or GTP, and can change between active and inactive states. This switch-like behavior makes them important in many cell processes. The protein is active when GTP is bound and inactive when guanosine diphosphate, or GDP, is bound. GTPases can also turn themselves off by breaking down GTP into GDP. This built-in control helps cells regulate when the protein is on or off. Their activity is regulated...

covalently linked protein regulators

Protein Regulation by Covalent Bonds

Protein regulation by covalent bonds helps control how cells respond to changing conditions. A covalent bond is a strong chemical link, and in this context it can change how a protein behaves. Some regulators work by attaching a chemical group directly to a protein. This covalent change can alter the protein's activity, its location in the cell, or how long it stays active. Because the change is built into the protein itself, it can have a strong effect on cell function. Covalently linked...

protein complexes with interchangeable parts

protein-complexes-with-interchangeable-parts

Modular Protein Complexes in Cells

Protein complexes in cells can be built from interchangeable parts. This modular design lets some complexes share common subunits while still changing their behavior. A well-known example is the ubiquitin ligase complex called SCF. SCF stands for Skp1-Cullin-F-box, and it helps attach ubiquitin, a small protein tag, to target proteins. The core of SCF stays the same, but the F-box protein can change. The interchangeable F-box subunit gives the complex its specificity. Different F-box proteins...

mechanical protein function

Proteins That Generate Cell Movement

Mechanical proteins help cells and tissues move. They turn chemical energy into force and motion. This process is important in many biological systems. These proteins are also called motor proteins. They interact with cell structures and can produce directed movement. In muscle cells, they support contraction. In other cells, they help with transport and shape changes. Mechanical protein function is a key part of how living systems work. It links protein activity to movement at the cellular...

structural protein function

Structural Proteins in Cells and Tissues

Structural proteins help cells and tissues keep their shape and strength. They are an important part of living systems because they provide support where it is needed most. Many structural proteins form fibers or other sturdy forms that resist stretching and wear. These proteins work as building materials in the body and help keep structures stable over time. Examples of structural proteins include collagen, actin, myosin, and keratin. Each one supports a different part of the body, but all...

protein networks

Protein interaction networks show how proteins work together inside a cell. These networks help scientists see which proteins connect with each other and how those links support cell activity. Researchers often use online tools to build and study these networks. The transcript points to IntAct and STRING as examples of resources that can help predict and organize protein interactions. These tools make it easier to compare protein links and look for patterns in the network. Protein networks...

key terms and concepts

Learn how protein interaction networks reveal links between proteins in cells, and how tools like IntAct and STRING help predict and study those connections.

Mapping Protein Interaction Networks | JoVE K12

cell biology

JoVE Core Zellbiologie veranschaulicht komplexe zelluläre Prozesse in leicht verständlichen und dennoch umfassenden animierten Videolektionen. Diese Sammlung konzentriert sich auf die wesentlichen Bestandteile und Funktionen von Zellen, einschließlich Organellen und Membranen, Zelltransport und Zellenergie. Ergänzt wird sie durch Videos von Wissenschaftlern in Aktion, die die Anwendung der Zellbiologie in realen Forschungsexperimenten demonstrieren.

Characteristics of Life

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Covalently Linked Protein Regulators

Protein Complexes with Interchangeable Parts

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Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins, which carry out the essential functions of life through systems of specialized cells. [Assessment Boundary: Assessment does not include identification of specific cell or tissue types, whole body systems, specific protein structures and functions, or the biochemistry of protein synthesis.]

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Develop and use a model to illustrate the hierarchical organization of interacting systems that provide specific functions within multicellular organisms. [Clarification Statement: Emphasis is on functions at the organism system level such as nutrient uptake, water delivery, and organism movement in response to neural stimuli. An example of an interacting system could be an artery depending on the proper function of elastic tissue and smooth muscle to regulate and deliver the proper amount of blood within the circulatory system.] [Assessment Boundary: Assessment does not include interactions and functions at the molecular or chemical reaction level.]

HS-LS1-2

What is Homeostasis?

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Negative and Positive Feedback

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Homeostasis is the maintenance of a stable internal environment within the body, which is crucial for the proper functioning of cells, tissues, organs, ...

Plan and conduct an investigation to provide evidence that feedback mechanisms maintain homeostasis. [Clarification Statement: Examples of investigations could include heart rate response to exercise, stomate response to moisture and temperature, and root development in response to water levels.] [Assessment Boundary: Assessment does not include the cellular processes involved in the feedback mechanism.]

HS-LS1-3

Mapping Protein Interaction Networks

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