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

Muchos procesos biológicos dependen de las interacciones proteína-proteína. De hecho, un gran número de proteínas necesitan formar complejos proteicos u oligómeros para llevar a cabo sus funciones.
A veces, dos o más proteínas idénticas forman un complejo, como este dímero de kinesina, y en otros casos, diferentes proteínas o polipéptidos se unen para formar una unidad funcional. 
Por ejemplo, los microtúbulos del citoesqueleto están formados por dímeros de alfa y beta-tubulina. Las superficies de unión de los monómeros de alfa y beta-tubulina tienen formas complementarias. 
Estas formas coincidentes permiten que los monómeros formen un gran número de enlaces no covalentes entre sí, que luego mantienen unidas la tubulina alfa y beta. Este tipo de interfaz es un ejemplo de interacción superficie-superficie.
Al igual que los sitios de unión de ligandos, las interacciones en una interfaz proteína-proteína pueden involucrar enlaces no covalentes y fuerzas hidrofóbicas. Sin embargo, los enlaces disulfuro covalentes entre los aminoácidos de cisteína en cada superficie de proteína también pueden desempeñar un papel para mantenerlos unidos.
Sin embargo, no todas las interfaces de proteínas implican superficies muy coincidentes. Por ejemplo, muchas enzimas, como la proteína quinasa A aquí, forman una hendidura que puede reconocer y unirse a los bucles polipeptídicos de sus socios de unión. Este tipo de interfaz se conoce como interacción superficie-cadena.
Otro tipo de interfaz, conocida como hélice-hélice, o interacción bobinada-enrollada, se forma cuando las hélices de dos proteínas se envuelven entre sí. Esta interfaz se observa con frecuencia en proteínas que contienen dominios cremallera de leucina, como los factores de transcripción eucariotas.
En conclusión, la estructura física y las propiedades químicas de las partes que interactúan determinan el tipo de interfaz entre dos proteínas.

<ol>
	<li>Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Análisis de redes de interacción proteína-proteína. Revista de Investigación del Proteoma. Abril de 2012; 11(4):2014-2031.</li>
	<li>Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Superar desafíos químicos, biológicos y computacionales en el desarrollo de inhibidores dirigidos a las interacciones proteína-proteína. Chem Biol. 2015; 22(6):689–703.</li>
	<li>De Las Rivas J, Fontanillo C. Fundamentos de las interacciones proteína-proteína: conceptos clave para construir y analizar redes de interactoma. PLoS Comput Biol. 2010; 6(6):E1000807.</li>
	<li>Lalonde S, Ehrhardt DW, Loqué D, Chen J, Rhee SY, Frommer WB. Aproximaciones moleculares y celulares para la detección de interacciones proteína-proteína: últimas técnicas y limitaciones actuales. Planta J. febrero de 2008; 53(4):610-35.</li>
	<li>Amos-Binks A, Patulea C, Pitre S, et al. Predicción del sitio de unión para las interacciones proteína-proteína y descubrimiento de nuevos motivos utilizando secuencias polipeptídicas recurrentes. BMC Bioinformática. 2011;12:225. Publicado el 2 de junio de 2011.</li>
</ol>

interfaces proteína-proteína

Muchas proteínas forman complejos para llevar a cabo sus funciones, lo que hace que las interacciones proteína-proteína (IBP) sean esenciales para la supervivencia de un organismo. La mayoría de los IBP se estabilizan mediante numerosas fuerzas químicas no covalentes débiles. La forma física de las interfaces determina la forma en que interactúan dos proteínas. Muchas proteínas globulares tienen formas muy parecidas en sus superficies, que forman una gran cantidad de enlaces débiles. Además, muchos PPI se producen entre dos hélices o entre una hendidura superficial y una cadena o hilo polipeptídico.

Se utilizan varios métodos computacionales y bioquímicos para estudiar las interfaces de proteínas. Se pueden utilizar métodos de laboratorio, como la purificación por afinidad, la espectrometría de masas y los microarrays de proteínas, para identificar nuevas interacciones. La co-inmunoprecipitación de proteínas y la detección de dos híbridos de levadura se utilizan ampliamente para proporcionar evidencia sobre si dos proteínas interactúan in vitro. Los programas informáticos pueden predecir los PPI basándose en interacciones similares encontradas en otras proteínas comparando secuencias de proteínas y estructuras tridimensionales. Otros enfoques computacionales, como los perfiles filogenéticos, predicen los PPI basándose en la coevolución de los socios vinculantes. Además, el análisis de fusión de genes se utiliza para predecir parejas de interacción al encontrar pares de proteínas que están fusionadas en el genoma de otros organismos.

Las proteínas suelen interactuar con múltiples socios al mismo tiempo o en momentos diferentes, y pueden contener más de una interfaz de interacción. Muchas proteínas forman grandes complejos que realizan funciones específicas que sólo pueden ser realizadas por el complejo completo. En algunos casos, estas interacciones proteicas están reguladas; es decir, una proteína puede interactuar con diferentes socios según las necesidades celulares. Análisis computacionales y estadísticos adicionales clasifican dichas interacciones en redes, que se almacenan en bases de datos de interactomas en línea. Estas bases de datos con capacidad de búsqueda permiten a los usuarios estudiar interacciones de proteínas específicas, así como diseñar medicamentos que puedan mejorar o alterar las interacciones en la interfaz.

Interfaces proteína-proteína

Muchas proteínas forman complejos para llevar a cabo sus funciones, lo que hace que las interacciones proteína-proteína (IBP) sean esenciales para la supervivencia de un organismo. La mayoría de los IBP ...

Education

Educación

JoVE Core

Cell Biology

Biología Celular

Unit 1

Unidad 1

Protein Function

Función proteica

KEY TERMS AND CONCEPTS

TÉRMINOS Y CONCEPTOS CLAVE

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 Biología Celular ilustra procesos celulares complejos mediante completos vídeos animados fáciles de entender. Esta colección se centra en los componentes esenciales de las células y su funcionamiento, incluyendo los orgánulos y las membranas, el transporte celular y el metabolismo energético celular. Todo este material se complementa con los vídeos de científicos en acción, que muestran la aplicación de la biología celular en experimentos reales de investigación.

Characteristics of Life

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Cell Structure

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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. ...

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Proteins: From Genes to Degradation

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Protein Folding

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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

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

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Overview of Human Digestion

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An Introduction to the Zebrafish: Danio rerio

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Homeostasis
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Anatomy of the Circulatory System

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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

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Overview

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Bone Structure

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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.]

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What is Homeostasis?

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Negative and Positive Feedback

Homeostatic Imbalance

Homeostasis is the maintenance of a stable internal environment within the body, which is crucial for the proper functioning of cells, tissues, organs, ...

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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