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

许多生物过程 取决于蛋白质 互动。其实很大 蛋白质数量 需要形成蛋白质 复合物或低聚物，履行其职能。有时两个或更多 相同的蛋白质 形成一个复合体 例如这种驱动蛋白 二聚体，由两个 相同的蛋白质链。在其他情况下，不同 蛋白质或多肽 聚在一起形成 功能单元。例如，细胞骨架微管 由alpha和 β微管蛋白二聚体。alpha的绑定表面 和β微管蛋白单体 具有互补的形状。这些匹配的形状 使单体 形成大量 非共价相互作用 然后持有阿尔法 和β微管蛋白在一起。这类介面 是一个例子 表面的 相互作用。类似于配体结合 网站，互动 在蛋白质-蛋白质界面 可能涉及非共价键 和疏水力。但是，共价 二硫键 半胱氨酸氨基酸之间 在每个蛋白质表面上 可能也起作用 让他们在一起。并不是所有的蛋白质 界面紧密相关 匹配的表面。例如，许多酶 例如这里的蛋白激酶A 形成可以识别的裂缝 并结合多肽环 他们有约束力的伙伴。这种类型的接口是已知的 作为表面弦相互作用。另一种类型的接口，已知 作为螺旋螺旋或盘绕螺旋 互动，何时形成 两种蛋白质的螺旋 互相缠绕。该界面是 经常观察 在含有以下成分的蛋白质中 亮氨酸拉链结构域，如真核生物 转录因子。总之，身体 结构与化学 的属性 相互作用的部分 确定类型 两种蛋白质之间的界面。

<ol>
	<li>Koh GC， Porras P， Aranda B， Hermjakob H， Orchard SE. 分析蛋白质-蛋白质相互作用网络。蛋白质组研究杂志。2012 年 4 月;11（4）:2014-2031 年。</li>
	<li>Laraia L、McKenzie G、Spring DR、Venkitaraman AR、Huggins DJ。克服开发靶向蛋白质-蛋白质相互作用的抑制剂中的化学、生物和计算挑战。化学生物学。2015;22（6）:689–703。</li>
	<li>De Las Rivas J， Fontanillo C. 蛋白质-蛋白质相互作用要点:构建和分析相互作用组网络的关键概念。PLoS 计算生物学 2010;6（6）:e1000807。</li>
	<li>Lalonde S， Ehrhardt DW， Loqué D， Chen J， Rhee SY， Frommer WB.检测蛋白质-蛋白质相互作用的分子和细胞方法:最新技术和当前局限性。Plant J. 2008 年 2 月;53（4）:610-35。</li>
	<li>Amos-Binks A， Patulea C， Pitre S， et al. 使用重复出现的多肽序列预测蛋白质-蛋白质相互作用和新基序发现的结合位点。BMC 生物信息学。2011;12:225.2011 年 6 月 2 日发布。</li>
</ol>

蛋白质-蛋白质相互作用界面

许多蛋白质通过形成复合物来执行其功能，使得蛋白质-蛋白质相互作用（PPI）对于生物体的生存至关重要。 大多数质子泵抑制剂通过多种许多弱的非共价化学力来稳定。 界面的物理形状决定了两种蛋白质相互作用的方式。 许多球状蛋白质的表面形状紧密匹配，形成大量弱键。 此外，许多 PPI 发生在两个螺旋之间或表面裂缝与多肽链或串之间。

各种计算和生物化学方法用于研究蛋白质界面的方法多种多样，包括计算和生物化学手段。 亲和纯化、质谱和蛋白质微阵列等实验室方法可用于识别新的相互作用。 蛋白质的免疫共沉淀和酵母双杂交筛选被广泛用于证实提供两种蛋白质是否在体外相互作用的证据。 计算机程序可以通过比较蛋白质序列和三维结构，根据其他蛋白质中发现的类似相互作用来预测 PPI。 其他计算方法，例如系统发育分析，根据结合伴侣伙伴的共同进化来预测 PPI。 此外，基因融合分析通过寻找融合在其他生物体基因组中的蛋白质对来预测相互作用伙伴侣。

蛋白质通常在同一时间或不同时间与多个伙伴相互作用，并且它们可能包含多个相互作用界面。 许多蛋白质形成大型复合物，执行只能由完整复合物执行的特定功能。 在某些情况下，这些蛋白质相互作用受到调节； 也就是说，蛋白质可以根据细胞需求与不同的伙伴侣相互作用。 进一步的计算和统计分析将此类相互作用分类为网络，并在在线相互作用组数据库中进行管理。 这些可搜索的数据库使用户能够研究特定的蛋白质相互作用，以及设计可以增强或破坏界面相互作用的药物。

许多蛋白质通过形成复合物来执行其功能，因此蛋白质-蛋白质相互作用（PPIs）对生物体的生存至关重要。大多数PPIs……

Education

教育

JoVE Core

Cell Biology

细胞生物学

Unit 1

第一单元

Protein Function

蛋白质功能

KEY TERMS AND CONCEPTS

关键术语与概念

蛋白质-蛋白质接口

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

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Cell Structure

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Visualizing Onion and Cheek Cells
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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 ...

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Nucleic Acids

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Chromosome Structure

Base-pairing and DNA Repair

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Protein Families

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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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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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Carbohydrate Digestion

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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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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

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Kidney Structure

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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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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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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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