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

Wiele procesów biologicznych zależy od interakcji białko-białko. W rzeczywistości duża liczba białek musi tworzyć kompleksy białkowe lub oligomery, aby pełnić swoje funkcje.
Czasami dwa lub więcej identycznych białek tworzy kompleks, taki jak dimer kinezyny. W innych przypadkach różne białka lub polipeptydy łączą się, tworząc jednostkę funkcjonalną. 
Na przykład mikrotubule cytoszkieletu składają się z dimerów alfa- i beta-tubuliny. Powierzchnie wiążące monomerów alfa- i beta-tubuliny mają komplementarne kształty. 
Te pasujące kształty umożliwiają monomerom tworzenie ze sobą dużej liczby wiązań niekowalencyjnych, które następnie utrzymują razem alfa- i beta-tubulinę. Ten typ interfejsu jest przykładem interakcji powierzchnia-powierzchnia.
Podobnie jak w przypadku miejsc wiązania ligandów, interakcje na granicy faz białko-białko mogą obejmować wiązania niekowalencyjne i siły hydrofobowe. Jednak kowalencyjne wiązania dwusiarczkowe między aminokwasami cysteiny na każdej powierzchni białka mogą również odgrywać rolę w utrzymywaniu ich razem.
Jednak nie wszystkie interfejsy białkowe obejmują ściśle dopasowane powierzchnie. Na przykład wiele enzymów, takich jak kinaza białkowa A, tworzy szczelinę, która może rozpoznawać i wiązać pętle polipeptydowe swoich partnerów wiążących. Ten typ interfejsu jest znany jako interakcja powierzchnia-ciąg.
Inny rodzaj interfejsu, znany jako oddziaływanie helisa-helisa lub oddziaływanie zwinięte-cewka, powstaje, gdy helisy dwóch białek owijają się wokół siebie. Ten interfejs jest często obserwowany w białkach, które zawierają domeny zamka błyskawicznego leucyny, takie jak eukariotyczne czynniki transkrypcyjne.
Podsumowując, struktura fizyczna i właściwości chemiczne oddziałujących części określają rodzaj interfejsu między dwoma białkami.

<ol>
	<li>Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Analiza sieci interakcji białko-białko. Dziennik Badań nad Proteomem. 2012 kwiecień; 11(4):2014-2031.</li>
	<li>Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Pokonywanie wyzwań chemicznych, biologicznych i obliczeniowych związanych z opracowywaniem inhibitorów ukierunkowanych na interakcje białko-białko. Chem Biol. 2015; 22(6):689–703.</li>
	<li>De Las Rivas J, Fontanillo C. Podstawy interakcji białko-białko: kluczowe koncepcje budowania i analizowania sieci interaktomowych. PLoS Comput Biol. 2010; 6(6):E1000807.</li>
	<li>Lalonde S, Ehrhardt DW, Loqué D, Chen J, Rhee SY, Frommer WB. Molekularne i komórkowe podejścia do wykrywania interakcji białko-białko: najnowsze techniki i obecne ograniczenia. Zakład J. 2008 Luty; 53(4):610-35.</li>
	<li>Amos-Binks A, Patulea C, Pitre S, et al. Przewidywanie miejsca wiązania dla interakcji białko-białko i odkrywanie nowych motywów przy użyciu ponownie występujących sekwencji polipeptydowych. BMC Bioinformatyka. 2011;12:225. Opublikowano 2011 cze 2.</li>
</ol>

interfejsy białko-białko

Wiele białek tworzy kompleksy, aby spełniać swoje funkcje, dzięki czemu interakcje białko-białko (PPI) są niezbędne dla przetrwania organizmu. Większość PPI jest stabilizowana przez liczne słabe niekowalencyjne siły chemiczne. Fizyczny kształt połączeń determinuje sposób, w jaki dwa białka oddziałują na siebie. Wiele białek kulistych ma na powierzchni ściśle dopasowane kształty, które tworzą dużą liczbę słabych wiązań. Ponadto wiele PPI występuje pomiędzy dwiema helisami lub pomiędzy szczeliną powierzchniową a łańcuchem lub struną polipeptydową. Do badania interfejsów białkowych stosuje się różne metody obliczeniowe i biochemiczne. Do identyfikacji nowych interakcji można zastosować metody laboratoryjne, takie jak oczyszczanie przez powinowactwo, spektrometria mas i mikromacierze białkowe. Koimmunoprecypitacja białek i badania przesiewowe dwuhybrydowe drożdży są szeroko stosowane w celu dostarczenia dowodów na to, czy dwa białka oddziałują in vitro. Programy komputerowe potrafią przewidzieć PPI na podstawie podobnych interakcji występujących w innych białkach, porównując sekwencje białek i struktury trójwymiarowe. Inne podejścia obliczeniowe, takie jak profilowanie filogenetyczne, przewidują PPI w oparciu o koewolucję partnerów wiążących. Ponadto analizę fuzji genów wykorzystuje się do przewidywania partnerów interakcji poprzez znajdowanie par białek, które ulegają fuzji w genomie innych organizmów. Białka zazwyczaj oddziałują z wieloma partnerami w tym samym lub różnym czasie i mogą zawierać więcej niż jeden interfejs interakcji. Wiele białek tworzy duże kompleksy, które pełnią określone funkcje, które może spełnić jedynie kompletny kompleks. W niektórych przypadkach te interakcje białek są regulowane; oznacza to, że białko może oddziaływać z różnymi partnerami w zależności od potrzeb komórkowych. Dalsze analizy obliczeniowe i statystyczne sortują takie interakcje w sieci, które są gromadzone w internetowych bazach danych interakcji. Te bazy danych umożliwiają użytkownikom badanie konkretnych interakcji białek, a także projektowanie leków, które mogą wzmacniać lub zakłócać interakcje na styku.

Interfejsy białko-białko

Wiele białek tworzy kompleksy, które pełnią swoje funkcje, co sprawia, że interakcje białko-białko (IPP) są niezbędne do przetrwania organizmu. Większość IPP ...

Education

JoVE Core

Cell Biology

Biologia komórki

Unit 1

Jednostka 1

Protein Function

Funkcja białka

KEY TERMS AND CONCEPTS

Kluczowe terminy i pojęcia

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 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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Protein Folding

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GTPases and their Regulation

Covalently Linked Protein Regulators

Protein Complexes with Interchangeable Parts

Mechanical Protein Function

Structural Protein Function

Protein Networks

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The Parasympathetic Nervous System

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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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Homeostatic Imbalance

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HS-LS1-3

Protein Binding Surfaces and Contacts

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