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

Многие биологические процессы зависят от белок-белковых взаимодействий. На самом деле, большое количество белков необходимо для формирования белковых комплексов, или олигомеров, которые выполняли бы свои функции. Иногда два или более идентичных белка формируют комплекс, такой, как этот димер кинезина, который состоит из двух идентичных белковых цепочек.В других случаях, другие белки или полипептиды объединиться, чтобы сформировать функциональный блок. Например, цитоскелетные микротрубочки состоят из альфа и бета димеров тубулина. Связывающие поверхности альфа и бета мономероы тубулина имеют дополняющие друг друга формы.Эти подходящие формы позволяют мономерам формировать большое количество нековалентных взаимодействий, которые затем держат альфа и бета-тубулин вместе. Этот тип интерфейса является примером взаимодействия типа поверхность-поверхность. Аналогично сайтам привязки лиганд, взаимодействия на белок-белковом интерфейсе могут включать нековалентные связи и гидрофобные силы.Однако, ковалентные дисульфидные связи между цистеиновыми аминокислотами на поверхности каждого белка могут также сыграть свою роль в удержании их вместе. Но не все интерфесы между белками имеют совпадающие поверхности. Например, многие ферменты, таие, как эта протеинкиназа А, формируют расщелину, которая может распознавать и связывать полипептидные петли своих партнеров по связыванию.Такой тип интерфейса известен как взаимодействие типа поверхность-нить. Известен и другой тип интерфейса спираль-спираль или спиральная катушка, который формируется, когда спирали двух белков оборачивают друг друга. Это интерфейс часто наблюдается в белках, содержащих домены лейциновой молнии, например, эукариотические факторы транскрипции.В заключение, физическая структура и химические свойства взаимодействующих частей определяют тип интерфейса между двумя белками.

<ol>
	<li>Кох Г.К., Поррас., Аранда Б., Хермякоб Х., Орчард С.Э. Анализ сетей белок-белковых взаимодействий. Журнал исследований протеома. 2012 апрель; 11(4):2014-2031.</li>
	<li>Ларайя Л., Маккензи Г., Спринг Д.Р., Венкитараман А.Р., Хаггинс Д.Дж. Преодоление химических, биологических и вычислительных проблем при разработке ингибиторов, нацеленных на белок-белковые взаимодействия. Хим Биол. 2015; 22(6):689–703.</li>
	<li>Де Лас Ривас Дж., Фонтанильо К. Основы белок-белковых взаимодействий: ключевые концепции построения и анализа интерактомных сетей. PLoS Comput Biol. 2010; 6(6):e1000807.</li>
	<li>Лалонд С., Эрхардт Д.В., Локе Д., Чен Дж., Ри С.И., Фроммер В.Б. Молекулярные и клеточные подходы к обнаружению белок-белковых взаимодействий: новейшие методы и современные ограничения. Plant J. 2008 февраль; 53(4):610-35.</li>
	<li>Амос-Бинкс А., Патулеа С., Питре С. и др. Прогнозирование сайтов связывания для белок-белковых взаимодействий и открытие новых мотивов с использованием повторяющихся полипептидных последовательностей. Биоинформатика BMC. 2011;12:225. Опубликовано 2 июня 2011 года.</li>
</ol>

Интерфейсы белок-белок

Многие белки образуют комплексы для выполнения своих функций, что делает белок-белковые взаимодействия (PPI) необходимыми для выживания организма. Большинство ИПП стабилизируются многочисленными слабыми нековалентными химическими силами. Физическая форма интерфейсов определяет способ взаимодействия двух белков. Многие глобулярные белки имеют на своей поверхности близко совпадающие формы, образующие большое количество слабых связей. Кроме того, многие ИПП возникают между двумя спиралями или между поверхностной щелью и полипептидной цепью или нитью. Для изучения интерфейсов белков используются различные вычислительные и биохимические методы. Лабораторные методы, такие как аффинная очистка, масс-спектрометрия и белковые микроматрицы, могут использоваться для выявления новых взаимодействий. Коиммунопреципитация белков и скрининг двухгибридов дрожжей широко используются для получения доказательств того, взаимодействуют ли два белка in vitro. Компьютерные программы могут прогнозировать ИПП на основе аналогичных взаимодействий, обнаруженных в других белках, путем сравнения белковых последовательностей и трехмерных структур. Другие вычислительные подходы, такие как филогенетическое профилирование, прогнозируют ИПП на основе коэволюции партнеров по связыванию. Кроме того, анализ слияния генов используется для прогнозирования партнеров по взаимодействию путем поиска пар белков, слитых в геноме других организмов. Белки обычно взаимодействуют с несколькими партнерами одновременно или в разное время и могут содержать более одного интерфейса взаимодействия. Многие белки образуют большие комплексы, выполняющие специфические функции, которые может выполнять только полный комплекс. В некоторых случаях эти белковые взаимодействия регулируются; то есть белок может взаимодействовать с разными партнерами в зависимости от клеточных потребностей. Дальнейший вычислительный и статистический анализ сортирует такие взаимодействия в сети, которые хранятся в онлайн-базах данных интерактомов. Эти базы данных с возможностью поиска позволяют пользователям изучать конкретные взаимодействия белков, а также разрабатывать лекарства, которые могут усиливать или разрушать взаимодействия на границе раздела.

Многие белки образуют комплексы для выполнения своих функций, что делает белок-белковые взаимодействия (ИПП) необходимыми для выживания организма. Большинство ИЦП...

Education

JoVE Core

Cell Biology

Клеточная биология

Unit 1

Раздел 1

Protein Function

Функции белков

KEY TERMS AND CONCEPTS

ОСНОВНЫЕ ТЕРМИНЫ И ПОНЯТИЯ

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.

Characteristics of Life

Biology is a natural science that studies life and living organisms, including their structure, function, development, interactions, evolution, ...

https://cloudfront.jove.com/files/media/science-education/science-education-thumbs/10647.jpg

Cell Structure

Background
Cells represent the most basic biological units of all organisms, whether it be simple, single-celled organisms like bacteria, or large, ...

Visualizing Onion and Cheek Cells
ExpandImmediately before the experiment, wash and peel onion bulbs for the class.
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Visualizing Onion and Human Cells
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What are Cells?

Cell Diversity

The concept of a cell started with microscopic observations of dead cork tissue by Robert Hooke in 1665. Hooke coined the term &#34;cell&#34; based on the ...

Cytoplasm

The cytoplasm consists of organelles and a framework of protein scaffolds called the cytoskeleton suspended in an aqueous solution, the cytosol. The ...

The Nucleus

The nucleus is a membrane-bound organelle that acts as a control center in a eukaryotic cell. It contains chromosomal DNA, which controls gene expression ...

The Central Dogma

The DNA Helix

Nucleic Acids

DNA as a Genetic Template

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the ...

Chromosome Structure

Base-pairing and DNA Repair

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RNA Structure

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Protein Families

Types of RNA

Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse ...

Conservation of Protein Domains

Transcription

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. ...

Globular and Fibrous Proteins

Translation

Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes ...

Intrinsically Disordered Proteins

Ribosomes

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Protein Complex Assembly

Protein and Protein Structures

Conjugated Proteins

Proteins: From Genes to Degradation

Amyloid Fibrils

What are Proteins?

Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino ...

Ligand Binding Sites

Protein Organization

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Protein Folding

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Conserved Binding Sites

Cofactors and Coenzymes

Enzymes are proteins made of amino acids. The functional group of each constituent amino acid catalyzes a wide variety of chemical reactions via ionic ...

Cooperative Allosteric Transitions

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.]

Levels of Organization

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Animal and Plant Cell Structure

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

Structural Organization of the Human Body: An Overview

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Overview of Human Digestion

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Anatomy of the Intestines

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Accessory Organs

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Protein Digestion

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Carbohydrate Digestion

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What is a Nervous System?

Overview

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The Parasympathetic Nervous System

Overview

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The Sympathetic Nervous System

Overview

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Oogenesis

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Fertilization

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What is the Skeletal System?

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an-introduction-to-the-zebrafish-danio-rerio

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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Measuring Blood Pressure
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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

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
Blood collection is a common requirement for ...

Kidney Structure

The kidneys are two large bean-shaped organs located in the upper abdomen. They filter the blood several times a day to remove toxins and rebalance water ...

Blood Withdrawal II

Source: Kay Stewart, RVT, RLATG, CMAR; Valerie A. Schroeder, RVT, RLATG. University of Notre Dame, IN
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What is the Immune System?

Overview

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Bone Remodeling

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Spermatogenesis

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Bone Structure

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Breathing

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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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Negative and Positive Feedback

Homeostatic Imbalance

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pH Homeostasis

Acid-base homeostasis is essential for maintaining normal physiological activities in humans. The pH of various body fluids is strictly regulated because ...

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

Description

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