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

Birçok biyolojik süreç, protein-protein etkileşimlerine bağlıdır. Aslında, birçok proteinin işlevlerini yerine getirmeleri için protein kompleksleri veya oligomerler oluşturması gerekir. Bazen iki veya daha fazla özdeş protein bir kompleks oluşturur:iki özdeş protein zincirinden oluşan bu kinesin dimer gibi.Diğer durumlarda, farklı proteinler veya polipeptitler bir araya gelerek fonksiyonel bir birim oluştururlar. Örneğin, sitoskeletal mikrotübüller alfa ve beta tubulin dimerlerinden oluşur. Alfa ve beta tubulin rezidülerinin bağlanma yüzeyleri tamamlayıcı şekillere sahiptir.Bu eşleşen şekiller, rezidülerin çok sayıda kovalent olmayan etkileşim oluşturmasına olanak sağlar, bunlar da alfa ve beta tubulini bir arada tutar. Bu tip bir arayüz, yüzey-yüzey etkileşiminin bir örneğidir. Ligand bağlanma yerlerine benzer şekilde, protein-protein arayüzündeki etkileşimlerde de kovalent olmayan bağlar ve hidrofobik kuvvetler bulunabilir.Bununla birlikte, her protein yüzeyindeki sistein amino asitleri arasındaki kovalent disülfür bağları da onları bir arada tutma işlevini görebilir. Ancak protein arayüzlerinin bazılarında yüzeyler mükemmel eşleşmeyebilir. Örneğin, buradaki protein kinaz A gibi birçok enzim, bağ ortaklarının polipeptid halkalarını tanıyabilen ve onlara bağlanabilen bir yarık oluşturur.Bu tip arayüz, yüzey-sicim etkileşimi olarak bilinir. Sarmal-sarmal veya sarılmış sarım etkileşimi olarak bilinen başka bir arayüz tipi, iki proteinin sarmalları birbirine sarıldığında oluşur. Bu arayüz, ökaryotik transkripsiyon faktörleri gibi lösin fermuar bölgeleri içeren proteinlerde sıklıkla gözlenir.Sonuç olarak, etkileşime giren parçaların fiziksel yapısı ve kimyasal özellikleri, iki protein arasındaki arayüzün tipini belirler.

<ol>
	<li>Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE. Protein-protein etkileşim ağlarının analizi. Proteom Araştırmaları Dergisi. 2012 Nisan; 11(4):2014-2031.</li>
	<li>Laraia L, McKenzie G, Bahar DR, Venkitaraman AR, Huggins DJ. Protein-protein etkileşimlerini hedefleyen inhibitörlerin geliştirilmesinde kimyasal, biyolojik ve hesaplama zorluklarının üstesinden gelmek. Kimya Biol. 2015; 22(6):689–703.</li>
	<li>De Las Rivas J, Fontanillo C. Protein-protein etkileşimlerinin temelleri: interaktom ağları oluşturmak ve analiz etmek için temel kavramlar. PLoS Comput Biol. 2010; 6(6):E1000807.</li>
	<li>Lalonde S, Ehrhardt DW, Loqué D, Chen J, Rhee SY, Frommer WB. Protein-protein etkileşimlerinin tespiti için moleküler ve hücresel yaklaşımlar: en son teknikler ve güncel sınırlamalar. Bitki J. 2008 Şubat; 53(4):610-35.</li>
	<li>Amos-Binks A, Patulea C, Pitre S, et al. Protein-protein etkileşimleri için bağlanma yeri tahmini ve yeniden oluşan polipeptit dizileri kullanılarak yeni motif keşfi. BMC Biyoinformatik. 2011;12:225. 2 Haziran 2011'de yayınlandı.</li>
</ol>

protein-protein arayüzleri

Birçok protein, işlevini yerine getirmek için kompleksler oluşturarak, bir organizmanın hayatta kalması için protein-protein etkileşimlerini (PPI'ler) gerekli hale getirir. Çoğu PPI, çok sayıda zayıf kovalent olmayan kimyasal kuvvetle stabilize edilir. Arayüzlerin fiziksel şekli, iki proteinin etkileşim şeklini belirler. Birçok küresel proteinin yüzeyleri birbirine çok benzeyen şekillere sahiptir ve bu da çok sayıda zayıf bağ oluşturur. Ek olarak, birçok PPI iki sarmal arasında veya bir yüzey yarığı ile bir polipeptit zinciri veya dizisi arasında meydana gelir. Protein arayüzlerini incelemek için çeşitli sayısal ve biyokimyasal yöntemler kullanılır. Afinite saflaştırması, kütle spektrometresi ve protein mikrodizileri gibi laboratuvar yöntemleri yeni etkileşimleri tanımlamak için kullanılabilir. Proteinlerin birlikte immünopresipitasyonu ve maya iki hibrit taraması, iki proteinin in vitro etkileşime girip girmediğine dair kanıt sağlamak için yaygın olarak kullanılır. Bilgisayar programları, protein dizilerini ve üç boyutlu yapıları karşılaştırarak diğer proteinlerde bulunan benzer etkileşimlere dayanarak PPI'lari tahmin edebilir. Filogenetik profil oluşturma gibi diğer sayısal yaklaşımlar, bağlayıcı ortakların birlikte evrimine dayanarak PPI'lari tahmin eder. Ek olarak gen füzyon analizi, diğer organizmaların genomunda kaynaşmış protein çiftlerini bularak etkileşim ortaklarını tahmin etmek için kullanılır. Proteinler tipik olarak birden fazla partnerle aynı anda veya farklı zamanlarda etkileşime girer ve birden fazla etkileşim arayüzü içerebilirler. Birçok protein, yalnızca kompleksin tamamı tarafından gerçekleştirilebilecek spesifik işlevleri yerine getiren büyük kompleksler oluşturur. Bazı durumlarda bu protein etkileşimleri ayarlanır; yani bir protein, hücresel ihtiyaçlara bağlı olarak farklı partnerlerle etkileşime girebilir. Daha ileri sayısal ve istatistiksel analizler, bu tür etkileşimleri çevrimiçi interaktom veritabanlarında seçilen ağlara göre sıralar. Bu aranabilir veritabanları, kullanıcıların belirli protein etkileşimlerini incelemesine ve ayrıca arayüzdeki etkileşimleri artırabilecek veya bozabilecek ilaçlar tasarlamasına olanak tanır.

Protein-Protein Arayüzleri

Birçok protein, işlevlerini yerine getirmek için kompleksler oluşturur ve bir organizmanın hayatta kalması için protein-protein etkileşimlerini (PPI'ler) gerekli kılar. Çoğu ÜFE ...

Education

JoVE Core

Cell Biology

Hücre Biyolojisi

Unit 1

Ünite 1

Protein Function

Protein Fonksiyonu

KEY TERMS AND CONCEPTS

TEMEL TERİMLER VE KAVRAMLAR

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 Hücre Biyolojisi, anlaşılması kolay ancak kapsamlı animasyonlu video derslerde karmaşık hücresel süreçleri gösterir. Bu koleksiyon, organeller ve zarlar, hücresel taşıma ve hücre enerjileri dahil olmak üzere hücrelerin temel bileşenlerine ve işlevlerine odaklanır. Gerçek dünya araştırma deneylerinde hücre biyolojisinin uygulanmasını gösteren bilim insanı eylem videoları ile tamamlanmaktadır.

Characteristics of Life

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Cell Structure

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Cytoplasm

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Proteins: From Genes to Degradation

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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

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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Overview

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The Parasympathetic Nervous System

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The Sympathetic Nervous System

Overview

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Oogenesis

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An Introduction to the Zebrafish: Danio rerio

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Physiology of the Circulatory System

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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What Are Osmoregulation and Excretion?

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Blood Withdrawal I

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Blood Withdrawal II

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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.]

HS-LS1-2

What is Homeostasis?

Maintaining homeostasis requires that the body continuously maintain its internal conditions. Each physiological condition has a particular set point, ...

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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