Name: protein binding surfaces and contacts
Uploaded: 2023-04-30T18:28:43.000Z
Duration: 2 min 4 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-Protein Interfaces

Viele biologische Prozesse hängen von Protein-Protein-Wechselwirkungen ab. Tatsächlich muss eine große Anzahl von Proteinen Proteinkomplexe oder Oligomere bilden, um ihre Funktionen zu erfüllen.
Manchmal bilden zwei oder mehr identische Proteine einen Komplex, wie z. B. dieses Kinesin-Dimer, in anderen Fällen kommen verschiedene Proteine oder Polypeptide zu einer funktionellen Einheit zusammen. 
So bestehen die Mikrotubuli des Zytoskeletts aus Alpha- und Beta-Tubulin-Dimeren. Die Bindungsflächen von Alpha- und Beta-Tubulin-Monomeren haben komplementäre Formen. 
Diese aufeinander abgestimmten Formen ermöglichen es den Monomeren, eine große Anzahl nicht-kovalenter Bindungen miteinander zu bilden, die dann das Alpha- und Beta-Tubulin zusammenhalten. Diese Art von Schnittstelle ist ein Beispiel für eine Oberfläche-Oberfläche-Wechselwirkung.
Ähnlich wie bei Ligandenbindungsstellen können Wechselwirkungen an einer Protein-Protein-Grenzfläche nicht-kovalente Bindungen und hydrophobe Kräfte beinhalten. Kovalente Disulfidbindungen zwischen Cystein-Aminosäuren auf jeder Proteinoberfläche können jedoch auch eine Rolle spielen, um sie zusammenzuhalten.
Doch nicht alle Proteingrenzflächen weisen eng aufeinander abgestimmte Oberflächen auf. So bilden viele Enzyme, wie hier die Proteinkinase A, einen Spalt, der Polypeptidschleifen ihrer Bindungspartner erkennen und binden kann. Diese Art von Schnittstelle wird als Oberfläche-Zeichenfolgen-Interaktion bezeichnet.
Eine andere Art von Grenzfläche, die als Helix-Helix oder Coiled-Coil-Wechselwirkung bekannt ist, entsteht, wenn sich Helices zweier Proteine umeinander wickeln. Diese Grenzfläche wird häufig in Proteinen beobachtet, die Leucin-Zipper-Domänen enthalten, wie z. B. eukaryotische Transkriptionsfaktoren.
Zusammenfassend lässt sich sagen, dass die physikalische Struktur und die chemischen Eigenschaften der wechselwirkenden Teile die Art der Grenzfläche zwischen zwei Proteinen bestimmen.

<ol>
	<li>Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyse von Protein-Protein-Interaktionsnetzwerken. Zeitschrift für Proteomforschung. 2012 April; 11(4):2014-2031.</li>
	<li>Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Überwindung chemischer, biologischer und rechnerischer Herausforderungen bei der Entwicklung von Inhibitoren, die auf Protein-Protein-Wechselwirkungen abzielen. Chem Biol. 2015; 22(6):689–703.</li>
	<li>De Las Rivas J, Fontanillo C. Grundlagen von Protein-Protein-Wechselwirkungen: Schlüsselkonzepte zum Aufbau und zur Analyse von Interaktomnetzwerken. PLoS Comput Biol. 2010; 6(6):e1000807.</li>
	<li>Lalonde S, Ehrhardt DW, Loqué D, Chen J, Rhee SY, Frommer WB. Molekulare und zelluläre Ansätze zum Nachweis von Protein-Protein-Wechselwirkungen: neueste Techniken und aktuelle Grenzen. Pflanze J. 2008 Februar; 53(4):610-35.</li>
	<li>Amos-Binks A, Patulea C, Pitre S, et al. Vorhersage der Bindungsstelle für Protein-Protein-Wechselwirkungen und Entdeckung neuer Motive anhand wiederkehrender Polypeptidsequenzen. BMC Bioinformatik. 2011;12:225. Veröffentlicht 2011 Jun 2.</li>
</ol>

protein-protein-grenzflächen

Viele Proteine bilden Komplexe, um ihre Funktionen auszuführen, wodurch Protein-Protein-Wechselwirkungen (PPIs) für das Überleben eines Organismus unerlässlich sind. Die meisten PPIs werden durch zahlreiche schwache nichtkovalente chemische Kräfte stabilisiert. Die physische Form der Schnittstellen bestimmt die Art und Weise, wie zwei Proteine interagieren. Viele globuläre Proteine haben passende Formen auf ihren Oberflächen, die eine große Anzahl schwacher Bindungen bilden. Zusätzlich treten viele PPIs zwischen zwei Helices oder zwischen einer Oberflächenkerbe und einer Polypeptidkette oder einem Strang auf.

Verschiedene computergestützte und biochemische Methoden werden verwendet, um Protein-Schnittstellen zu untersuchen. Labormethoden wie Affinitätsreinigung, Massenspektrometrie und Protein-Microarrays können zur Identifizierung neuer Wechselwirkungen verwendet werden. Die Co-Immunopräzipitation von Proteinen und das Yeast-Two-Hybrid-Screening werden häufig verwendet, um Hinweise darauf zu liefern, ob zwei Proteine in vitro interagieren. Computerprogramme können PPIs vorhersagen, basierend auf ähnlichen Wechselwirkungen, die in anderen Proteinen gefunden wurden, indem sie Proteinsequenzen und dreidimensionale Strukturen vergleichen. Andere computergestützte Ansätze, wie phylogenetisches Profiling, sagen PPIs basierend auf der Koevolution der Bindungspartner voraus. Zusätzlich wird die Genfusionsanalyse verwendet, um Wechselwirkungspartner vorherzusagen, indem Proteinpaare gefunden werden, die im Genom anderer Organismen fusioniert sind.

Proteine interagieren typischerweise entweder zur gleichen oder zu verschiedenen Zeiten mit mehreren Partnern und können mehr als eine Interaktionsschnittstelle enthalten. Viele Proteine bilden große Komplexe, die spezifische Funktionen ausführen, die nur vom vollständigen Komplex ausgeführt werden können. In einigen Fällen sind diese Protein-Wechselwirkungen reguliert; das heißt, ein Protein kann je nach zellulärem Bedarf mit verschiedenen Partnern interagieren. Weitere computergestützte und statistische Analysen ordnen solche Wechselwirkungen in Netzwerke, die in Online-Interaktom-Datenbanken kuratiert werden. Diese durchsuchbaren Datenbanken ermöglichen es den Nutzern, spezifische Protein-Wechselwirkungen zu studieren sowie Medikamente zu entwickeln, die Wechselwirkungen an der Schnittstelle verstärken oder unterbrechen können.

Protein-Protein-Grenzflächen

Viele Proteine bilden Komplexe, um ihre Funktionen zu erfüllen, so dass Protein-Protein-Wechselwirkungen (PPIs) für das Überleben eines Organismus unerlässlich sind. Die meisten PPIs ...

Education

Lehre

JoVE Core

Cell Biology

Zellbiologie

Unit 1

Einheit 1

Protein Function

Proteinfunktion

KEY TERMS AND CONCEPTS

KERNBEGRIFFE UND KONZEPTE

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 protein complexes form. It also helps scientists understand why some proteins bind strongly while others do not. This knowledge is useful for linking protein structure to protein function.

Protein Binding Surfaces and Contacts

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 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

Enzyme helpers include cofactors and coenzymes. Enzymes are proteins made of amino acids, and the functional groups on those amino acids can drive many chemical reactions through ionic interactions or acid-base reactions. But amino acids alone cannot handle oxidation-reduction and group transfer reactions, so they need non-protein helpers called cofactors. Cofactors are often described as the chemical teeth of an enzyme. They can be metal ions or organic molecules called coenzymes. These...

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

Protein kinases and phosphatases help control how proteins work in cells. Kinases add phosphate groups to proteins. Phosphatases remove those phosphate groups. This phosphorylation and dephosphorylation process can change a protein’s shape and activity. It is one way cells turn protein function on or off at the right time. These changes also help cells respond to signals and manage many cell activities. Together, protein kinases and phosphatases keep cellular signaling balanced. When one adds...

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

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...

key terms and concepts

Learn how protein binding surfaces and contacts let proteins recognize each other, form complexes, and support cell function in a clear high school science format.

Protein Binding Surfaces and Contacts | 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.

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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

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HS-LS1-3

Protein Binding Surfaces and Contacts

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