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

Een organisme kan duizenden verschillende eiwitten hebben, en deze eiwitten moeten samenwerken om de gezondheid van een organisme te garanderen. Eiwitten binden zich aan andere eiwitten en vormen complexen om hun functies uit te voeren. Veel eiwitten interageren met meerdere andere eiwitten, waardoor een complex netwerk van eiwitinteracties ontstaat.

Deze interacties kunnen worden weergegeven door middel van kaarten die eiwit-eiwitinteractienetwerken weergeven, weergegeven als knooppunten en randen. Knooppunten zijn cirkels die representatief zijn voor een eiwit, en randen zijn lijnen die twee op elkaar inwerkende eiwitten verbinden. Deze netwerken bieden een manier om de complexiteit van de eiwit-eiwitinteracties in een systeem te visualiseren. Deze kaarten kunnen zowel stabiele interacties omvatten, zoals die gevormd in eiwitcomplexen, als tijdelijke interacties. De eiwitinteracties die plaatsvinden in een cel, een organisme of een specifieke biologische context kunnen gezamenlijk een ‘interactoom’ worden genoemd.

Eiwitnetwerken kunnen worden bestudeerd met behulp van verschillende biochemische en computationele methoden. Een van de eerste stappen bij het bestuderen van eiwitinteracties is het isoleren van het beoogde eiwit samen met de andere geassocieerde eiwitten. Dit kan worden uitgevoerd door het beoogde eiwit te markeren met een affiniteitstag, zoals een histidine-tag. Deze tag kan vervolgens worden gebruikt om het eiwit samen met de andere eiwitten te scheiden met behulp van affiniteitschromatografie. Geïsoleerde eiwitten worden vervolgens gedigereerd met een protease, zoals trypsine, en vervolgens geanalyseerd met behulp van vloeistofchromatografie-massaspectrometrie (LC-MS). De peptidemassa kan vervolgens worden vergeleken met een database met bekende eiwitsequenties om de identiteit ervan te bepalen.

Computationeel kunnen eiwit-eiwit-interacties worden geanalyseerd met behulp van databases en voorspellingsinstrumenten. Er zijn verschillende databases, zoals IntAct beheerd door EMBL-EBI, die bestaan uit experimenteel gevalideerde en voorspelde eiwitinteracties. Andere tools zoals STRING van het Zwitserse Instituut voor Bio-informatica kunnen worden gebruikt om deze interactienetwerken te voorspellen.

De studie van eiwitnetwerken kan leiden tot wetenschappelijke ontdekkingen, zoals het bepalen van de functie van een onbekend eiwit. Het onderzoeken van de veranderingen in deze netwerken kan de verschillen tussen gezonde en zieke cellen helpen ophelderen. Deze informatie kan ook worden gebruikt voor cruciale toepassingen, zoals het ontwerpen van medicijnen voor de behandeling van ziekten. Analyse van eiwitnetwerken kan sterk verbonden knooppunten identificeren die cruciaal kunnen zijn voor cellulaire overleving, die het doelwit kunnen zijn bij kanker en ziekten waarbij celdood gewenst is, maar voor de meeste ziekten ongeschikt zou zijn. Aan de andere kant kunnen minder verbonden knooppunten die slechts met een paar specifieke routes interageren, worden aangevallen als een specifieke celfunctie wordt aangetast, en het ontwerpen van medicijnen die interageren met deze minder verbonden knooppunten kan tot minder bijwerkingen leiden.

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

Celbiologie

Unit 1

Eenheid 1

Protein Function

Eiwitfunctie

KEY TERMS AND CONCEPTS

BELANGRIJKE TERMEN EN CONCEPTEN

Eiwitnetwerken

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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https://cloudfront.jove.com/files/media/science-education/science-education-thumbs/10647.jpg

Cell Structure

Background
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Cytoplasm

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Conservation of Protein Domains

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Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. ...

Globular and Fibrous Proteins

Translation

Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes ...

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Ribosomes

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Proteins: From Genes to Degradation

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Ligand Binding Sites

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Protein-Protein Interfaces

Protein Folding

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Conserved Binding Sites

Cofactors and Coenzymes

Enzymes are proteins made of amino acids. The functional group of each constituent amino acid catalyzes a wide variety of chemical reactions via ionic ...

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Protein Kinases and Phosphatases

GTPases and their Regulation

Covalently Linked Protein Regulators

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

Structural Organization of the Human Body: An Overview

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Overview of Human Digestion

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Overview

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The Parasympathetic Nervous System

Overview

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The Sympathetic Nervous System

Overview

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Oogenesis

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Fertilization

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

An Introduction to the Zebrafish: Danio rerio

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Physiology of the Circulatory System

Homeostasis
Conditions in the external environment of an organism can change rapidly and drastically. To survive, organisms must maintain a fairly ...

Anatomy of the Circulatory System

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Measuring Blood Pressure
ExpandTo prepare for the blood pressure exercise, simply place the appropriate number of alcohol swabs, sphygmomanometers, and ...

Anatomy of the Heart

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Measuring Circulatory System Function in Humans
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Blood Flow

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Blood Withdrawal I

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Kidney Structure

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Blood Withdrawal II

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
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Overview

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Bone Remodeling

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Spermatogenesis

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Bone Structure

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Breathing

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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

Homeostatic Imbalance

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pH Homeostasis

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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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