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

De nombreux processus biologiques dépendent des interactions protéine-protéine. En fait, un grand nombre de protéines ont besoin de former des complexes protéiques, ou oligomères, pour exécuter leurs fonctions. Parfois deux ou plus des protéines identiques forment un complexe, tel que le dimère kinésine, qui se compose de deux chaînes de protéines identiques.Dans d'autres cas, différentes protéines ou polypeptides se réunissent pour former une unité fonctionnelle. Par exemple, les microtubules du cytosquelette se composent de dimères alpha et bêta tubuline. Les surfaces de liaison des monomères alpha et bêta tubuline ont des formes complémentaires.Ces formes correspondantes permettent aux monomères de former un grand nombre d'interactions non-covalentes, qui maintiennent ensuite la tubuline alpha et bêta ensemble. Ce type d'interface est un exemple d'une interaction surface-surface. Similaires aux sites de liaison du ligand, les interactions sur l'interface protéine-protéine peuvent impliquer des liaisons non-covalentes et des forces hydrophobes.Cependant, les liaisons disulfure covalentes entre les acides aminés de cystéine sur chaque surface protéique peuvent également jouer un rôle pour les garder ensemble. Pourtant, toutes les interfaces de protéines ne nécessitent pas de surfaces étroitement correspondantes. Par exemple, de nombreuses enzymes, comme la protéine kinase A ici, forme une fente pouvant reconnaître et lier les boucles polypeptidiques de ses partenaires de liaison.Ce type d'interface est appelé interaction surface-chaîne. Un autre type d'interface, connu sous le nom d'interaction hélice-hélice ou superhélice, se forme quand les hélices de deux protéines s'enveloppent l'une autour de l'autre. Cette interface est fréquemment observée dans les protéines qui contiennent des domaines glissière à leucine, tels que les facteurs de transcription eucaryotes.En conclusion, la structure physique et les propriétés chimiques des pièces en interaction détermine le type d'interface entre deux protéines.

<ol>
	<li>Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Analyse des réseaux d’interaction protéine-protéine. Journal de recherche sur le protéome. avril 2012 ; 11(4) :2014-2031.</li>
	<li>Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Surmonter les défis chimiques, biologiques et informatiques dans le développement d’inhibiteurs ciblant les interactions protéine-protéine. Chem Biol. 2015; 22(6) :689 à 703.</li>
	<li>De Las Rivas J, Fontanillo C. Essentiels des interactions protéine-protéine : concepts clés pour la construction et l’analyse des réseaux d’interactomes. PLoS Comput Biol. 2010 ; 6(6) :e1000807.</li>
	<li>Lalonde S., Ehrhardt D.W., Loqué D., Chen J., Rhee S.Y., Frommer W.W. Approches moléculaires et cellulaires pour la détection des interactions protéine-protéine : dernières techniques et limites actuelles. Plant J. 2008 février ; 53(4) :610 à 35.</li>
	<li>Amos-Binks A, Patulea C, Pitre S, et al. Prédiction du site de liaison pour les interactions protéine-protéine et découverte de nouveaux motifs à l’aide de séquences polypeptidiques récurrentes. Bioinformatique BMC. 2011;12:225. Publié le 2 juin 2011.</li>
</ol>

interfaces protéine-protéine

De nombreuses protéines forment des complexes pour remplir leurs fonctions, ce qui rend les interactions protéine-protéine (IPP) essentielles à la survie d'un organisme. La plupart des IPP sont stabilisées par de nombreuses forces chimiques non covalentes faibles. La forme physique des interfaces détermine la manière dont deux protéines interagissent. De nombreuses protéines globulaires ont des formes très proches sur leur surface, qui forment un grand nombre de liaisons faibles. De plus, de nombreux IPP se produisent entre deux hélices ou entre une fente superficielle et une chaîne ou une chaîne polypeptidique.

Diverses méthodes informatiques et biochimiques sont utilisées pour étudier les interfaces protéiques. Des méthodes de laboratoire, telles que la purification par affinité, la spectrométrie de masse et les puces à protéines, peuvent être utilisées pour identifier de nouvelles interactions. La co-immunoprécipitation de protéines et le criblage de deux hybrides de levure sont largement utilisés pour prouver si deux protéines interagissent in vitro. Les programmes informatiques peuvent prédire les IPP sur la base d'interactions similaires trouvées dans d'autres protéines en comparant les séquences protéiques et les structures tridimensionnelles. D'autres approches informatiques, telles que le profilage phylogénétique, prédisent les IPP sur la base de la coévolution des partenaires de liaison. De plus, l’analyse de la fusion génétique est utilisée pour prédire les partenaires d’interaction en trouvant des paires de protéines fusionnées dans le génome d’autres organismes.

Les protéines interagissent généralement avec plusieurs partenaires au même moment ou à des moments différents, et elles peuvent contenir plusieurs interfaces d'interaction. De nombreuses protéines forment de grands complexes qui remplissent des fonctions spécifiques qui ne peuvent être remplies que par le complexe complet. Dans certains cas, ces interactions protéiques sont régulées, c'est-à-dire qu'une protéine peut interagir avec différents partenaires en fonction des besoins cellulaires. D'autres analyses informatiques et statistiques classent ces interactions en réseaux, qui sont conservés dans des bases de données d'interactomes en ligne. Ces bases de données consultables permettent aux utilisateurs d'étudier des interactions protéiques spécifiques, ainsi que de concevoir des médicaments susceptibles d'améliorer ou de perturber les interactions au niveau de l'interface.

Interfaces protéine-protéine

De nombreuses protéines forment des complexes pour remplir leurs fonctions, ce qui rend les interactions protéine-protéine (IPP) essentielles à la survie d'un organisme. La plupart des IPP ...

Education

Enseignement

JoVE Core

Cell Biology

Biologie cellulaire

Unit 1

Unité 1

Protein Function

Fonction des protéines

KEY TERMS AND CONCEPTS

TERMES ET CONCEPTS CLÉS

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 Biologie cellulaire illustre les processus cellulaires complexes dans des leçons vidéos complètes mais faciles à comprendre. Cette collection se concentre sur les composants et fonctions essentiels de la cellule ; cela inclut les organelles et les membranes ainsi que le transport et le métabolisme énergétique cellulaire. Elle est complétée par nos vidéos de scientifiques à l'action qui démontrent l'application de la biologie cellulaire dans des expériences concrètes.

Characteristics of Life

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Covalently Linked Protein Regulators

Protein Complexes with Interchangeable Parts

Mechanical Protein Function

Structural Protein Function

Protein Networks

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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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

Protein Binding Surfaces and Contacts

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