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

A single organism can contain thousands of different proteins, and most of these proteins must interact with other proteins in order to perform their functions.
Many proteins have multiple binding partners, which results in a complex network of protein interactions.
Various laboratory techniques, including both biochemical and computational methods, help scientists understand these protein networks.
Affinity tagging is a method often used to isolate a protein along with any other interacting molecules. An affinity tag is an amino acid motif that is genetically added to the protein of interest. This tag can be used to isolate the target protein along with other proteins associated with it.&#160;
Proteins interacting with the tagged protein can be analyzed to determine their identity and novel interactions.
One method of analyzing these unknown protein interactions is to break the proteins into short segments and analyze with a mass spectrometer to determine the amino acid sequences. These sequences can be compared to existing protein sequence databases to identify unknown associated proteins.&#160;&#160;
Additionally, freely available databases, such as IntAct, have protein-protein interaction data uploaded by researchers worldwide available for comparison. Other databases coupled with a growing number of advanced bioinformatics tools, can be used to predict the molecular interactions of an unknown protein
Protein-protein interaction network maps are used to visualize these interactions between proteins in a cell.&#160; The circles are nodes, which represent a particular protein, and lines are edges, which connect a protein to the other interacting proteins.&#160;
Examining protein interaction maps can help predict protein functions. If an unknown protein&#39;s interaction pattern of connecting edges is similar to that of another node, these two nodes may act similarly.
Some nodes will appear as highly connected hubs, the study of which may lead to discovering fundamental mechanisms for maintaining the health of the cell thereby aiding in drug development.

protein networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein, and edges are lines that connect two interacting proteins. These networks provide a way to visualize the complexity of the protein-protein interactions in a system. These maps can include both stable interactions, like the ones formed in protein complexes, as well as transient interactions. The protein interactions occurring in a cell, an organism, or a specific biological context can be collectively called an &#8216;interactome&#8217;.
Protein networks can be studied using various biochemical and computational methods. One of the first steps in studying protein interactions is to isolate a protein of interest along with the other associated proteins. This can be carried out by tagging the protein of interest with an affinity tag, such as a histidine tag. This tag can then be used to separate the protein along with the other proteins using affinity chromatography. Isolated proteins are then digested with a protease, such as trypsin,&#160; and then analyzed using liquid chromatography-mass spectrometry (LC-MS). The peptide mass can then be compared to a database with known protein sequences to determined its identity.
Computationally, protein-protein interactions can be analyzed using databases as well as prediction tools. There are various databases, such as IntAct managed by EMBL-EBI, that consist of experimentally validated and predicted protein interactions. Other tools like STRING by the Swiss Institute of Bioinformatics can be used to predict these interaction networks.
The study of protein networks can lead to scientific discoveries, such as determining the function of an unknown protein. Examining the changes in these networks can help elucidate the differences between healthy and diseased cells. This information can also be used for crucial applications such as designing drugs for the treatment of diseases.&#160; Analysis of protein networks can identify highly connected nodes that may be crucial for cellular survival, which can be targeted in cancer and diseases where cell death is desired but would be unsuitable for most diseases. On the other hand, less connected nodes that only interact with a few specific pathways may be targeted if a specific cell function is affected, and designing drugs that interact with these less connected nodes may lead to fewer side effects.

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other ...

Education

JoVE Core

Cell Biology

Unit 1

Protein Function

KEY TERMS AND CONCEPTS

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

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 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 Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics. It is complemented by scientist-in-action videos that demonstrate the application of cell biology in real-world research experiments.

Characteristics of Life

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Protein Folding

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GTPases and their Regulation

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Protein Complexes with Interchangeable Parts

Mechanical Protein Function

Structural Protein Function

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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structural-organization-of-the-human-body-an-overview

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The Parasympathetic Nervous System

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an-introduction-to-the-zebrafish-danio-rerio

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Homeostasis
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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

Mapping Protein Interaction Networks

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