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

Un singolo organismo può contenere migliaia di proteine differenti, e la maggior parte di queste proteine deve interagiscono con altre proteine per svolgere le loro funzioni. Molte proteine hanno partner leganti multipli, ciò risulta in una rete complessa di interazioni proteiche. Varie tecniche di laboratorio, tra cui la biochimica e metodi computazionali, aiutano gli scienziati a comprendere queste complesse reti proteiche.Il tag di affinità è un metodo spesso usato per isolare una proteina da una qualsiasi altra molecola interagente. Un tag di affinità è un modello amminoacidico che è geneticamente aggiunto alla proteina di interesse. Questo tag può essere utilizzato per isolare la proteina bersaglio e per altre proteine ad essa associate.Le proteine che interagiscono con la proteina marcata possono essere analizzate per determinare la loro identità e nuove interazioni;un metodo di analisi di queste interazioni proteiche sconosciute consiste nel suddividere le proteine in segmenti brevi e analizzarle con uno spettrometro di massa per determinare le sequenze amminoacidiche. Queste sequenze possono essere confrontate con le sequenze proteiche esistenti per identificare le proteine associate sconosciute. Inoltre, database liberamente disponibili, come IntAct, hanno dati di interazione proteina-proteina raccolti da ricercatori in tutto il mondo e disponibili per il confronto.Altre banche dati, unite ad un numero crescente di strumenti bioinformatici avanzati, possono essere usate per predire le interazioni molecolari di una proteina sconosciuta. Le mappe della rete di interazione proteina-proteina sono usate per visualizzare queste interazioni tra le proteine in una cellula. I cerchi sono nodi che rappresentano una particolare proteina e le linee sono bordi che collegano una proteina alle altre proteine interagenti.L'esame delle mappe di interazione proteica può aiutare a prevedere le funzioni proteiche. Se il modello di interazione di una proteina sconosciuta ai bordi di connessione è simile a quello di un altro nodo noto, questi due nodi possono agire in modo simile. Alcuni nodi appariranno come hub altamente connessi, lo studio dei quali può portare alla scoperta di meccanismi fondamentali per il mantenimento della salute della cellula, contribuendo così nello sviluppo di nuovi farmaci.

<ol>
	<li>Alberts et al., 6a edizione; pagine 166-169</li>
	<li>Morris, J. H., Knudsen, G. M., Verschueren, E., Johnson, J. R., Cimermancic, P., Greninger, A. L., & Pico, A. R. (2014). Purificazione per affinità: spettrometria di massa e analisi di rete per comprendere le interazioni proteina-proteina. Protocolli sulla natura, 9(11), 2539.</li>
	<li>Ottman, C. (2013). Interazioni proteina-proteina: una panoramica. Interazioni proteina-proteina nella scoperta di farmaci.</li>
	<li>Jordán, F., Nguyen, T. P., & Liu, W. C. (2012). Studio delle reti di interazione proteina-proteina: una visione sistemica delle malattie. Briefing in genomica funzionale, 11(6), 497-504.</li>
	<li>Berggård, T., Linse, S., & James, P. (2007). Metodi per la rilevazione e l'analisi delle interazioni proteina-proteina. Proteomica, 7(16), 2833-2842.</li>
	<li>Gingras, A. C., Gstaiger, M., Raught, B., & Aebersold, R. (2007). Analisi di complessi proteici mediante spettrometria di massa. Recensioni sulla natura Biologia cellulare molecolare, 8(8), 645.</li>
</ol>

reti proteiche

Un organismo può avere migliaia di proteine diverse e queste proteine devono cooperare per garantire la salute di un organismo. Le proteine si legano ad altre proteine e formano complessi per svolgere le loro funzioni. Molte proteine interagiscono con molteplici altre proteine creando una complessa rete di interazioni proteiche.

Queste interazioni possono essere rappresentate attraverso mappe che descrivono reti di interazione proteina-proteina, rappresentate come nodi e bordi. I nodi sono cerchi rappresentativi di una proteina e i bordi sono linee che collegano due proteine interagenti. Queste reti forniscono un modo per visualizzare la complessità delle interazioni proteina-proteina in un sistema. Queste mappe possono includere sia interazioni stabili, come quelle formate nei complessi proteici, sia interazioni transitorie. Le interazioni proteiche che si verificano in una cellula, in un organismo o in uno specifico contesto biologico possono essere collettivamente chiamate interattoma.

Le reti proteiche possono essere studiate utilizzando vari metodi biochimici e computazionali. Uno dei primi passi nello studio delle interazioni proteiche è isolare una proteina di interesse insieme alle altre proteine associate. Ciò può essere effettuato marcando la proteina di interesse con un tag di affinità, come un tag di istidina. Questo tag può quindi essere utilizzato per separare la proteina insieme alle altre proteine utilizzando la cromatografia di affinità. Le proteine isolate vengono quindi digerite con una proteasi, come la tripsina, e quindi analizzate utilizzando la cromatografia liquida-spettrometria di massa (LC-MS). La massa peptidica può quindi essere confrontata con un database con sequenze proteiche note per determinarne l'identità.

Dal punto di vista computazionale, le interazioni proteina-proteina possono essere analizzate utilizzando database e strumenti di previsione. Esistono vari database, come IntAct gestito da EMBL-EBI, che consistono in interazioni proteiche convalidate e previste sperimentalmente. Altri strumenti come STRING dell'Istituto svizzero di bioinformatica possono essere utilizzati per prevedere queste reti di interazione.

Lo studio delle reti proteiche può portare a scoperte scientifiche, come la determinazione della funzione di una proteina sconosciuta. L’esame dei cambiamenti in queste reti può aiutare a chiarire le differenze tra cellule sane e malate. Queste informazioni possono essere utilizzate anche per applicazioni cruciali come la progettazione di farmaci per il trattamento di malattie. L’analisi delle reti proteiche può identificare nodi altamente connessi che potrebbero essere cruciali per la sopravvivenza cellulare, che possono essere presi di mira nel cancro e nelle malattie in cui si desidera la morte cellulare ma che non sarebbero adatti per la maggior parte delle malattie. D’altra parte, i nodi meno connessi che interagiscono solo con pochi percorsi specifici possono essere presi di mira se una specifica funzione cellulare è influenzata, e la progettazione di farmaci che interagiscono con questi nodi meno connessi può portare a minori effetti collaterali.

Reti proteiche

Un organismo può avere migliaia di proteine diverse e queste proteine devono cooperare per garantire la salute di un organismo. Le proteine si legano ad altri ...

Education

Didattica

JoVE Core

Cell Biology

Biologia cellulare

Unit 1

Unità 1

Protein Function

Funzione proteica

KEY TERMS AND CONCEPTS

TERMINI E CONCETTI CHIAVE

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 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 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.

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GTPases and their Regulation

Covalently Linked Protein Regulators

Protein Complexes with Interchangeable Parts

Mechanical Protein Function

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

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Blood Withdrawal II

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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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Homeostatic Imbalance

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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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