Name: measuring protein-ligand binding strength
Uploaded: 2020-11-23T11:47:34.000Z
Duration: 2 min 18 s
Channel: JoVE

K12 Standards

Tennessee Academic Standards

High School

Biology

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

BIO1.LS1.3

the-equilibrium-binding-constant-and-binding-strength

The Equilibrium Binding Constant and Binding Strength

細胞内では、タンパク質は他のタンパク質、核酸、低分子リガンドなどの他の分子とランダムに衝突します。
結合が非特異的である場合、分子間の非共有結合相互作用はほとんどなく、短い会合を生じます。
特定のリガンドがタンパク質に結合すると、相補的な表面に沿って広範な非共有結合性相互作用が形成されます。そのような複合体は安定しており、解離する前に長期間結合したままである。
結合相互作用の強度は、その平衡定数K b(結合定数または会合定数とも呼ばれる)の観点から報告されます。 
Kbは、平衡状態で見出される未結合タンパク質およびリガンドの濃度に対するタンパク質-リガンド複合体の濃度の比から計算できます。 
結合による自由エネルギー変化との関係を考えると、Kbが大きいとデルタGが大幅に減少し、タンパク質とリガンドの親和性が強いことを示しています。
タンパク質-リガンド結合には、タンパク質とリガンドの会合による複合体の形成と、複合体の反応物への解離という2つの競合するプロセスが重要です。
関連定数konは、タンパク質とそのリガンドとの間の1秒あたりの結合イベントの数を示す尺度であり、特定の濃度でのタンパク質へのリガンド結合速度を計算するために使用できる。 
逆に、koff は解離イベントの数を示す尺度であり、複合体がどれだけ早く崩壊するかを計算するために使用できます。
会合速度が解離速度と等しい場合、平衡に達し、生成物と反応物の正味濃度は一定のままです。
したがって、平衡状態では、タンパク質とリガンドの平衡濃度の積のk倍は、タンパク質-リガンド複合体の平衡濃度のk倍に等しくなります。
この式を並べ替えると、kon と koff の比率が平衡状態で Kb に等しいことも示しています。

<ol>
	<li>ポラード、トーマスD.「シンプルで有益な結合アッセイのガイド」 細胞の分子生物学 21、第23号(2010):4061-4067。</li>
	<li>「平衡状態のリガンド結合アッセイ:検証と解釈」 British journal of pharmacology 161, no. 6 (2010): 1219-1237.</li>
	<li>Medina-Franco, José L., Oscar Méndez-Lucio, and Karina Martinez-Mayorga. "The interplay between molecular modeling and chemoinformatics to characterize protein-ligand and protein-protein interactions landscapes for drug discovery." in Advances in protein chemistry and structural biology, vol. 96, pp. 1-37.アカデミックプレス、2014年。</li>
</ol>

平衡結合定数と結合強度

平衡結合定数(K_b)は、タンパク質とリガンドの相互作用の強さを定量化します。反応が平衡にある場合、K_bは次のように計算できます。

<img alt="Eq1" src="/files/ftp_upload/11513/Equation 1.png" style="text-align: center; width: 650px;" />

ここで、PとLはそれぞれ未結合のタンパク質とリガンド、PLはタンパク質-リガンド複合体です。

結合したリガンドの量はリガンドの結合速度にも関連するため、実験では、次の比率を使用してタンパク質とリガンドの会合(k_on)と解離(k_off)の速度を調べることによってK_bを決定することもできます。

<img alt="Eq1" src="/files/ftp_upload/11513/Equation 2.png" style="text-align: center; width: 650px;" />

したがって、平衡結合定数を決定するには、平衡濃度を測定するものと反応速度を測定するものの 2 つのカテゴリーの結合アッセイが使用されます。測定を行う際、反応が平衡状態であることが求められる場合があります。

平衡濃度を決定する方法は、必要な感度とシグナル検出の容易さによって異なります。これらの理由から、分光学的アッセイが最も広く使用されています。これらの実験では、反応により特定の波長で反応物または生成物の吸光度変化が生じ、紫外可視分光光度計で検出できます。あるいは、反応物または生成物は蛍光プローブでタグ付けすることも、固有の蛍光団を含むこともできます。 そして、蛍光の変化から反応の進行状況を測定することができます。これらのアッセイは、実験の残りの部分を一定に保ちながら、1 つの反応物の濃度を変化させることによって実行されます。結果はグラフ化され、さまざまな曲線近似法を使用して分析できます。

タンパク質とリガンド間の相互作用も、さまざまな生化学的および分光学的手法を使用して研究されています。 X 線結晶構造解析と NMR 分光法を使用した構造解析は、分子シミュレーションによるタンパク質とリガンドの相互作用の予測に役立ちます。タンパク質とリガンドのドッキング研究などの理論的および計算的アプローチは、薬剤候補を含む小分子リガンドの位置と相互作用を特徴付けるために広く使用されています。コンピュータ支援による医薬品設計は、従来の試行錯誤による医薬品試験のペースを加速する、迅速かつコスト効率の高い代替手段です。

平衡結合定数(Kb)は、タンパク質-リガンド相互作用の強度を定量化します。Kbは、反応が...

Education

JoVE Core

Molecular Biology

分子生物学

Unit 1

ユニット1

Protein Function

タンパク質の機能

KEY TERMS AND CONCEPTS

主要用語と概念

measuring protein-ligand binding strength

Protein-ligand binding strength can be measured with the equilibrium binding constant, Kb. This value describes how strongly a protein binds a ligand when the reaction has reached equilibrium. In a bound complex, the protein and ligand are joined as PL, while P and L are the unbound forms.

Kb can be determined in two main ways. One approach uses equilibrium concentrations. The other uses reaction kinetics, which are the rates of binding and unbinding. Kb can also be related to the binding rate constant, kon, and the dissociation rate constant, koff, by taking their ratio.

When scientists measure equilibrium concentrations, the reaction must already be at equilibrium. The best method depends on how sensitive the assay needs to be and how easy it is to detect the signal. For this reason, spectroscopic assays are used most often. These assays track absorbance changes in a reactant or product with a UV-Vis spectrophotometer.

Fluorescence can also be used to follow binding. A reactant or product may be tagged with a fluorescent probe, or it may already have an intrinsic fluorophore. In that case, the progress of the reaction is measured by changes in fluorescence. These experiments usually change the concentration of one reactant while the other parts of the setup stay constant, and the results are then graphed and fit to curves.

Protein-ligand interactions are also studied with other biochemical and spectroscopic methods. X-ray crystallography and NMR spectroscopy can provide structural information that helps predict how a protein and ligand may interact through molecular simulations. Protein-ligand docking studies are also used to place small molecule ligands, including drug candidates, and to examine their interactions. These computer-aided methods offer a fast and low-cost way to support drug design.

Measuring Protein-Ligand Binding Strength

measuring-protein-ligand-binding-strength

ligand binding sites

How Ligands Attach to Proteins

Ligands attach to proteins at specific binding sites on the protein surface. These sites let proteins interact with other molecules or ions and help them carry out important cell functions. Although many possible ligands may be nearby, only a matching ligand can bind to a given protein. A ligand-binding site has a shape and chemical pattern that fit its ligand. This fit comes from the protein’s amino acid chain, which gives the site its structure and reactivity. The ligand stays in place...

protein-protein interfaces

How Proteins Connect to Form Complexes

Proteins connect with other proteins to form complexes that carry out cell functions. These protein-protein interactions, or PPIs, are important for an organism's survival. Most PPIs are held together by many weak, noncovalent chemical forces rather than one strong bond. The shape of the interaction surface helps determine how two proteins fit together. Many globular proteins have surface shapes that match closely and can form many weak bonds. Other PPIs happen between two helices or between a...

conserved binding sites

Predicting Protein Ligand-Binding Pockets

Protein ligand-binding pockets help explain how proteins work. A ligand is a small molecule that binds to a specific spot on a protein. These sites are often conserved in related proteins because they are important for function. When the exact site on a protein surface is not known, it can be predicted. One approach is the energetic method. It examines how amino acid residues interact with the ligand and looks for positions where the binding energy is lowest. Those low-energy regions are...

the equilibrium binding constant and binding strength

Protein-ligand binding strength can be measured with the equilibrium binding constant, Kb. This value describes how strongly a protein binds a ligand when the reaction has reached equilibrium. In a bound complex, the protein and ligand are joined as PL, while P and L are the unbound forms. Kb can be determined in two main ways. One approach uses equilibrium concentrations. The other uses reaction kinetics, which are the rates of binding and unbinding. Kb can also be related to the binding rate...

cofactors and coenzymes

Protein Helpers: Cofactors and Coenzymes

Cofactors and coenzymes help enzymes work. Many enzymes need these helper molecules to carry out chemical reactions. Without them, the enzyme may not function properly. A cofactor is a helper molecule that can be either an inorganic ion or an organic molecule. Coenzymes are organic cofactors. They often move between enzymes and help transfer chemical groups or electrons during a reaction. Some cofactors are vitamins or come from vitamins. These molecules are important because they support...

allosteric regulation

How Allosteric Control Changes Enzymes

Allosteric control changes how enzymes work by using a site other than the active site. A small molecule binds to this separate allosteric site and changes the enzyme’s shape. That shape change can alter how well the enzyme binds its substrate and how fast the reaction runs. Many enzymes use this kind of regulation to turn activity up or down when the cell needs it. In some cases, the allosteric molecule acts as an activator and improves enzyme function. In other cases, it acts as an inhibitor...

ligand binding and linkage

Allosteric Proteins: Positive and Negative Effects

Allosteric proteins have more than one ligand binding site. A ligand is a molecule that binds to a protein. When a ligand binds at one site, it can affect binding at the other sites. These sites are called coupled or linked because they influence one another. In enzymes, the site that binds the substrate is the active site. The other site is the regulatory site. When a ligand binds to the regulatory site, it can change the protein’s shape. This conformational change can then alter how the...

cooperative allosteric transitions

Allosteric Switching in Multimeric Proteins

Allosteric switching in multimeric proteins helps explain how ligand binding at one site can change the behavior of the whole protein. In these proteins, each subunit has its own ligand-binding site. When a ligand binds to one subunit, it can cause a shape change that affects the other subunits and their binding sites. This change in shape comes from the protein’s structure, which includes both flexible and stable segments. A molecule that causes the shift is called a modulator. Because the...

phosphorylation

Phosphorylation in Cell Signaling

Phosphorylation is a key step in cell signaling. It changes how a molecule behaves by adding a phosphate group. In many cells, this modification helps control activity, shape, and interactions with other molecules. Phosphorylation is carried out by enzymes called kinases. These enzymes transfer a phosphate group to a target molecule. A phosphatase can remove that phosphate group and reverse the change. Together, kinases and phosphatases help cells turn signals on and off in a controlled way. <br...

protein kinases and phosphatases

Phosphorylation Switches in Protein Control

Protein control often depends on chemical changes that alter a protein’s charge, shape, and conformation. These changes can include phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis. In cells, these modifications are usually driven by enzymes. Phosphorylation is one of the most important protein modifications. It adds a phosphate group to a protein and often changes how that protein works. A family of enzymes called kinases...

gtpases and their regulation

GTPase Signaling Switches in Cells

GTPases are cell proteins that act as signaling switches. They help control cell signaling, vesicle transport, cell shape, and cell movement. When these proteins change or stop working properly, disease can result. There are about 40,000 known G-proteins. They are usually grouped into two main types. Small G-proteins have one domain, while large G-proteins have multiple domains. Large G-proteins are also called heterotrimeric G-proteins. They have three subunits: alpha, beta, and gamma. The...

covalently linked protein regulators

How Protein Tags Change Cell Signaling

Proteins can be changed after they are made by adding small chemical tags or small proteins. These post-translational modifications help control protein function and stability when the cell environment changes. Common covalent regulators include methyl, acetyl, and phosphate groups, as well as small proteins such as ubiquitin. About 200 types of covalent regulators have been identified. These tags attach to specific amino acids in a protein. Phosphate groups can attach only to serine,...

protein complexes with interchangeable parts

protein-complexes-with-interchangeable-parts

SCF Ubiquitin Ligase and F-Box Variants

The SCF ubiquitin ligase is a protein complex that uses an F-box protein to help choose which target proteins get marked for destruction. This complex is made of five separate proteins, and each one has a different job. Together, they attach ubiquitin to target proteins so the cell can send those proteins to be degraded. The F-box protein is the part that binds the substrate, or target protein. That binding step lets the ubiquitin-conjugating enzyme reach the target and attach ubiquitin. In...

mechanical protein functions

Protein Force: Cell Movement and Support

Proteins can create and respond to mechanical force in cells. Some proteins generate force, while others are pulled or stretched by it. Proteins such as keratin provide structural support and are subjected to mechanical force. Proteins such as ion pumps help move molecules across cell membranes and can generate mechanical force. Cell movement and muscle contraction depend on turning chemical energy into motion. This often happens through conformational change, which is a shift in a protein’s...

structural protein function

Collagen and the Cell Skeleton

Structural proteins give cells and tissues shape, support, and strength. They help build bones, cartilage, hair, and muscles. Important examples include collagen, actin, myosin, and keratin. Collagen is the most abundant protein in mammals. It is found throughout the body. In skin, ligaments, and tendons, collagen adds tensile strength and elasticity. In bones and teeth, it helps form hard, load-bearing tissue through mineralization. Collagen also does more than provide support. It can...

protein networks

Mapping Protein Interactions

Mapping protein interactions shows how proteins work together in a cell. Many proteins must connect with other proteins to carry out their jobs and keep an organism healthy. These connections can be shown as protein-protein interaction networks, also called protein maps. In these maps, proteins are shown as nodes, or circles. Lines called edges connect two proteins that interact. The network can include stable interactions, such as those in protein complexes, and transient interactions that...

allosteric proteins-atcase

ATCase Feedback Inhibition in Pyrimidine Synthesis

ATCase is a key enzyme in pyrimidine synthesis. It is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl-L-aspartate. This reaction starts the pathway that makes pyrimidines. ATCase is regulated by feedback inhibition. The end products UTP and CTP bind to the enzyme and reduce its activity when pyrimidine levels are high compared with purines in the cell. This binding at one site affects the linked catalytic site, which helps keep...

key terms and concepts

Learn how the equilibrium binding constant, Kb, is measured using equilibrium concentrations, kinetics, absorbance, fluorescence, and docking methods.

Measuring Protein-Ligand Binding Strength | JoVE K12

molecular biology

JoVE Core 分子生物学は、明確で簡潔なアニメーション ビデオ レッスンを通じて細胞の分子プロセスを紹介します。さらに、科学者の実際のビデオでは、これらの概念の応用が現代の研究室での実際の実験を通じて実証されています。

Arizona Science Standards

Life Science

HS+B.L1

HS+B.L1U1.5

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

Levels of Organization

Biological organization is the classification of biological structures, ranging from atoms at the bottom of the hierarchy to the Earth&#x27;s biosphere. ...

the-tree-of-life-bacteria-archaea-and-eukaryotes

The Tree of Life - Bacteria, Archaea, and Eukaryotes

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains &#8212; Archaea and Bacteria. Bacteria include many common microorganisms, such as ...

Introduction to Virus

Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic ...

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. ...

Compare and contrast existing models, identify patterns, and use structural and functional evidence to analyze the characteristics of life. Engage in argument about the designation of viruses as non-living based on these characteristics.
EXPLANATION: Students begin to develop patterns of living and non-living organisms in kindergarten and build on detailed characteristics of different classifications of living organisms throughout elementary and middle school. Biology 1 discussions introduce viral particles and viral cycles, building on student understanding of living organisms to engage in an argument regarding the classification of a viral particle as either living or non-living.

BIO1.LS1.1

What are Cells?

Cells are the smallest and basic units of life, whether it is a single cell that forms the entire organism, e.g., in a bacterium, or trillions of them, ...

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry ...

Eukaryotic Evolution

The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the ...

Animal and Plant Cell Structure

Animal and plant cells not only differ in their structure, function, and mode of nutrition but also in how they reproduce, specialize, and organize into ...

Evaluate comparative models of various cell types with a focus on organic molecules that make up cellular structures.
EXPLANATION: Students explicitly discuss the structure and function of major cellular organelles in seventh grade. Building on this understanding, Biology I students should shift their focus to the different types of cells found in organisms and how the role of each cell type relates to its composition and the prevalence of different organelles within that cell. An example might include the absence (or enucleation) of the nucleus in red blood cells in mammals providing for increased levels of oxygen transport in organisms or the lack of centrioles in most neurons. Varying cell types can include both prokaryotic and eukaryotic cell types.

BIO1.LS1.2

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell&#39;s genetic blueprint and carry instructions for its ...

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA ...

DNA Base Pairing

Erwin Chargaff&#x2019;s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff&#x2019;s rules state that in a ...

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between ...

DNA Packaging

Overview

Eukaryotes have large genomes compared to prokaryotes. In order to fit their genomes into a cell, eukaryotes must pack their DNA tightly inside ...

Organization of Genes

Overview

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. ...

Karyotyping

Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by ...

Replication in Prokaryotes

Overview

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to ...

Replication in Eukaryotes

Overview

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high ...

Mutations

Overview

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. ...

Transcription

Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene ...

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following ...

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form ...

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations ...

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or ...

Types of RNA

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

MicroRNAs

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional ...

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while ...

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect ...

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding ...

What are Proteins?

Protein Organization

Protein Folding

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein ...

conservation-of-protein-domains-over-different-proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.&#160; Although these domains are often structurally ...

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular ...

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows ...

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.&#160; Most protein complexes ...

Conjugated Proteins

Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with ...

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein&#39;s function.&#160; For example, enzyme activity is often regulated through a feedback mechanism where the ...

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins.&#160; Under most circumstances, misfolded proteins are either refolded by chaperone proteins or ...

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand ...

Antibody Structure

Phosphorylation

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their ...

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, ...

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism&#39;s survival. Most PPIs ...

GTPases and their Regulation

Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell ...

Conserved Binding Sites

Many proteins&#8217; biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein ...

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an ...

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at ...

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex&#8217;s function. ...

Cofactors and Coenzymes

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical ...

Allosteric Regulation

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures ...

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other ...

Integrate evidence to develop a structural model of a DNA molecule. Using the model, develop and communicate an explanation for how DNA serves as a template for self-replication and encodes biological information.
EXPLANATION: Discussions of DNA in earlier grades have been limited to discussions of genes and the role of genes in the appearance and activities of an organism. Biology 1 represents a student's introduction to a molecular model of a DNA as well as the organization of DNA into genes and genes subsequently into chromosomes. Students should address interactions between genes in proteins which regulate both the shape and reproduction of DNA molecules. It is important to note that not all segments of DNA are transcribed for proteins. Portions of DNA are involved in regulating the expression of genes or affect the structure of the chromosomes (replication origin, centromeres, and telomeres).

Measuring Protein-Ligand Binding Strength

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