Name: how equilibrium binding constant affects binding
Uploaded: 2023-04-30T18:28:41.000Z
Duration: 2 min 18 s
Channel: JoVE

<ol>
	<li>Pollard, Thomas D. "Una guida a saggi di legame semplici e informativi". Biologia molecolare della cellula 21, n. 23 (2010): 4061-4067.</li>
	<li>Hulme, Edward C. e Mike A. Trevethick. "Saggi di legame del ligando all'equilibrio: convalida e interpretazione". British Journal of Pharmacology 161, n. 6 (2010): 1219-1237.</li>
	<li>Medina-Franco, José L., Oscar Méndez-Lucio e Karina Martinez-Mayorga. "L'interazione tra modellazione molecolare e chemioinformatica per caratterizzare i paesaggi di interazioni proteina-ligando e proteina-proteina per la scoperta di farmaci". In Advances in protein chemistry and structural biology, vol. 96, pp. 1-37. Stampa accademica, 2014.</li>
</ol>

la costante di legame all'equilibrio e la forza di legame

The Equilibrium Binding Constant and Binding Strength

La costante di legame ad equilibrio (Kb) quantifica la forza di un'interazione proteina-ligando. Kb può essere calcolato come segue quando la reazione è ad equilibrio:

<img alt="Eq1" src="/files/ftp_upload/11513/Equation 1.png" style="text-align: center; width: 650px;" />

dove P e L sono rispettivamente la proteina e il ligando non legati e PL è il complesso proteina-ligando.

Poiché la quantità di ligando legato è correlata anche alla sua velocità di legame, gli esperimenti possono anche determinare Kb esaminando i tassi di associazione proteina-ligando (kon) e di dissociazione (koff) utilizzando il seguente rapporto:

<img alt="Eq1" src="/files/ftp_upload/11513/Equation 2.png" style="text-align: center;width: 650px;" />

Pertanto, per determinare la costante di legame ad equilibrio vengono utilizzate due categorie di test di legame: quelli che misurano le concentrazioni di equilibrio e quelli che misurano la cinetica di una reazione. In tal caso, la reazione dev’essere all'equilibrio al momento della misurazione.

Il metodo per determinare le concentrazioni ad equilibrio dipende dalla sensibilità desiderata e dalla facilità di rilevamento del segnale. Per questi motivi, i test spettroscopici sono quelli più utilizzati. In questi esperimenti, la reazione produce una variazione di assorbanza di un reagente o di un prodotto ad una determinata lunghezza d'onda, rilevabile da uno spettrofotometro UV-Vis. In alternativa, il reagente o il prodotto può essere marcato con una sonda fluorescente o può contenere un fluoroforo intrinseco. Quindi, il progresso della reazione può essere misurato dalla variazione della fluorescenza. Questi test vengono eseguiti variando le concentrazioni di un reagente, mentre il resto dell'esperimento viene mantenuto costante. I risultati possono quindi essere rappresentati graficamente e analizzati con vari metodi di adattamento della curva.

Le interazioni tra proteine e ligandi vengono studiate anche utilizzando una varietà di tecniche biochimiche e spettroscopiche. L'analisi strutturale, eseguita tramite cristallografia a raggi X e spettroscopia NMR, aiuta a prevedere le interazioni proteina-ligando attraverso simulazioni molecolari. Approcci teorici e computazionali, come gli studi di docking proteina-ligando, sono ampiamente utilizzati per caratterizzare la posizione e le interazioni dei ligandi di piccole molecole, compresi i candidati farmaci. La progettazione di farmaci assistita da computer è un'alternativa rapida ed economica per accelerare il ritmo dei test convenzionali sui farmaci per tentativi ed errori.

La costante di legame all'equilibrio e la forza di legame

La costante di legame all'equilibrio (Kb) quantifica la forza di un'interazione proteina-ligando. Kb può essere calcolato come segue quando la reazione è a ...

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

Education

Didattica

JoVE Core

Cell Biology

Biologia cellulare

Unit 1

Unità 1

Energy and Catalysis

Energia e Catalisi

KEY TERMS AND CONCEPTS

TERMINI E CONCETTI CHIAVE

how equilibrium binding constant affects binding

The equilibrium binding constant describes how strongly two molecules bind at equilibrium. It is a useful way to compare binding strength in molecular interactions.

This topic focuses on how binding is measured and what the equilibrium binding constant means. A higher value indicates stronger binding, while a lower value indicates weaker binding. Understanding this constant helps explain how tightly molecules stay together under equilibrium conditions.

The page also connects the binding constant to real binding strength. It shows why this value matters when comparing different molecular pairs. For high school students, it provides a clear link between a chemistry concept and molecular behavior.

How Equilibrium Binding Constant Affects Binding

how-equilibrium-binding-constant-affects-binding

the first law of thermodynamics

Energy Changes in Cells and Matter

The first law of thermodynamics describes how energy changes form in the universe. The total amount of energy stays constant. Energy can move from one place to another or change into a different form, but it cannot be created or destroyed. These energy changes happen in everyday life. A light bulb changes electrical energy into light energy. A gas stove changes chemical energy in natural gas into heat energy. Plants also carry out a major energy transformation when they convert sunlight energy...

the second law of thermodynamics

Entropy and Spontaneous Change

Entropy helps predict whether a process will happen on its own. Entropy is a measure of randomness or disorder in a system. High entropy means high disorder and low energy. A student’s bedroom is a simple example. If no work is done, the room becomes messy over time. That messy state is highly disordered and has high entropy. To make the room clean again, energy must be added as the student puts things away. That organized state has low entropy. Processes that increase the entropy of the...

enthalpy within the cell

Cellular Enthalpy and Energy Changes

Cellular enthalpy describes how heat and energy change during chemical and physical processes. Enthalpy is written as H and is defined as the sum of a system’s internal energy, U, and the product of pressure and volume, PV. It is a state function, which means its value depends on the state of the system, not the path taken. Scientists cannot measure the enthalpy of a single substance directly. They can determine enthalpy changes, or ΔH, for a process instead. For reactions or changes that...

entropy within the cell

Cell Energy Loss and Entropy

Cell energy loss and entropy explain why living things need constant energy input. Cells obtain energy, transform it, and use it to do work, but these transfers are never completely efficient. In each transfer, some energy is lost in a form that cannot be used. In many cases, that lost energy is heat energy.

an introduction to free energy

Gibbs Free Energy and Reaction Work

Gibbs free energy describes the usable energy in a chemical reaction. It helps scientists compare how much energy different reactions release. This measurement is called Gibbs free energy, or G, after Josiah Willard Gibbs. The second law of thermodynamics explains why not all energy stays available for work. Some energy is lost in an unusable form, such as heat, and this loss increases entropy. Gibbs free energy is the energy left after that entropy loss is taken into account. Every chemical...

endergonic and exergonic reactions in the cell

endergonic-and-exergonic-reactions-in-the-cell

Cell Reactions That Release or Store Energy

Cell reactions can either release energy or store it for later use. In chemistry, this difference is described by the value of ΔG, or free energy change. When energy is released during a reaction, ΔG is negative. The products then have less free energy than the reactants because some free energy has been given off. Reactions with a negative ΔG are called exergonic reactions. Exergonic means energy is leaving the system. These reactions are also called spontaneous reactions because they can...

the equilibrium binding constant and binding strength

The equilibrium binding constant describes how strongly two molecules bind at equilibrium. It is a useful way to compare binding strength in molecular interactions. This topic focuses on how binding is measured and what the equilibrium binding constant means. A higher value indicates stronger binding, while a lower value indicates weaker binding. Understanding this constant helps explain how tightly molecules stay together under equilibrium conditions. The page also connects the binding...

free energy and equilibrium

Free Energy and Reaction Direction

Free energy and reaction direction are linked in chemical equilibrium. A free energy change, ΔG, shows the driving force for a process. When ΔG is negative, the process is driven forward. When ΔG is positive, the reverse direction is favored. When ΔG is zero, the forward and reverse driving forces are equal, and the system is at equilibrium. The reaction quotient, Q, helps show how close a system is to equilibrium. Q is the numerical value of the mass action expression for the system. It can...

non-equilibrium in the cell

Cells Stay Out of Equilibrium

Cells stay out of chemical equilibrium by constantly using energy and moving materials in and out. Chemical reactions in metabolism are often reversible. They can go in both directions. In one direction, they release energy to the surroundings. In the reverse direction, they absorb energy. The same idea applies to reactions that build and break down cell molecules. Proteins, for example, can be broken into individual amino acids, and amino acids can be used to build proteins again. In a closed...

oxidation and reduction of organic molecules

oxidation-and-reduction-of-organic-molecules

Electron Carriers in Cell Energy Transfer

Cell energy production depends on redox reactions, which are oxidation and reduction reactions that happen together. In oxidation, an electron is removed from an atom in a compound. In reduction, that same electron is added to another compound. Because these reactions usually occur as a pair, they are called redox reactions. When a molecule loses an electron, its potential energy goes down. The electron does not stay free in the cytoplasm. Instead, it moves to a second compound and reduces...

introduction to enzymes

Enzyme Function, Cofactors, and Inhibitors

Enzymes are proteins that speed up biochemical reactions without being used up. Humans have used enzymes since about 7000 BCE, when they fermented sugars to make alcohol without knowing the reaction was enzyme-catalyzed. The word enzyme was coined by Wilhelm Kuhne in 1877. It comes from the Greek words en, meaning “in” or “within,” and zyme, meaning “yeast.” Enzymes work through active sites, which are regions that bind substrates and help convert them into products. Many enzymes also have...

enzymes and activation energy

How Enzymes Lower Reaction Energy

Enzymes lower the energy needed for a chemical reaction to begin. That starting energy is called activation energy, or free energy of activation, and it is often written as Ea. During a reaction, bonds break and new bonds form. In glucose breakdown, for example, bonds between carbon atoms break and release energy because they are energy-storing bonds. Before a reaction can move forward, reactant molecules must reach a high-energy, unstable shape called the transition state. To get there, the...

introduction to enzyme kinetics

Graphing Enzyme Kinetics Data

Enzyme kinetics uses graphs to show how fast a biochemical reaction happens. Scientists measure the initial reaction rate, or velocity (Vo), at different substrate concentrations ([S]). They may also run trials with inhibitors or other molecules that change the reaction rate. The results are often plotted as Vo against [S]. For many single-substrate reactions, the data fits the Michaelis-Menten equation. This equation, named after Leonor Michaelis and Maud Menten, helps estimate the maximum...

turnover number and catalytic efficiency

How Fast Enzymes Work in Digestion

Enzymes can work at very different speeds, and their turnover number shows how fast they convert substrate molecules into products. Turnover number is the maximum number of substrate molecules an enzyme can transform per unit time. For most enzymes, this value is between 1 and 1000 molecules per second. Some enzymes are especially fast. Catalase has the highest known turnover number and can convert up to 2.8×10^6 molecules of hydrogen peroxide into water and oxygen each second. Lysozyme has...

catalytically perfect enzymes

Diffusion-Controlled Enzymes and Reaction Speed

Catalytically perfect enzymes are enzymes that speed up biochemical reactions at very high rates. The idea was first proposed by W. J. Albery and J. R. Knowles in 1976. These enzymes have catalytic efficiency values of about 10^8 to 10^9 M^-1 s^-1 and are also called diffusion-controlled enzymes because diffusion of the substrate into the active site is the only rate-limiting step. Examples of catalytically perfect enzymes include triose phosphate isomerase, fumarase, and superoxide dismutase.

introduction to mechanisms of enzyme catalysis

introduction-to-mechanisms-of-enzyme-catalysis

How Enzymes Change Shape to Catalyze

Enzyme catalysis depends on how enzymes bind substrates and how the active site responds during the reaction. Scientists once described this process with a simple lock-and-key model, where the enzyme and substrate fit together in one instant. Research now supports induced fit, a more dynamic model in which binding causes a small change in the enzyme’s shape. That shift helps create an ideal match between the enzyme and the substrate’s transition state, which improves catalysis. The active site...

ligand binding and linkage

Ligand Binding and Allosteric Effects

Ligand binding and linkage describe how one molecule can affect another when it binds to a protein. In this topic, the focus is on how binding at one site can influence activity at a different site on the same protein. This idea is important for understanding protein function in high school biology. It helps explain why some proteins respond more strongly after a ligand attaches. The transcript centers on the connection between ligand binding and linkage, which is a key concept in molecular...

cooperative allosteric transitions

How Proteins Shift Shape Together

Proteins can change shape in a coordinated way during allosteric transitions. In a cooperative transition, one part of the protein affects another part, so the change spreads through the molecule. These shape changes help proteins switch between different states. The shift can influence how the protein works and how it responds to other molecules. Cooperative allosteric transitions are an important idea in protein function. They explain how a small change at one site can lead to a larger...

ribozymes

Catalytic RNA: Ribozymes in Action

Ribozymes are RNA molecules that can act as enzymes. They help speed up specific chemical reactions without being protein enzymes. This makes them an important example of RNA with more than one job in the cell. Some ribozymes can cut RNA molecules, and others can join them together. This shows that RNA can do catalytic work as well as carry genetic information. Ribozymes are a key part of how scientists think about the many roles of RNA in biology. One well-known ribozyme is ribonuclease P,...

atp energy storage and release

ATP Powers Cellular Transport and Reactions

ATP powers cellular transport and many reactions by transferring energy through phosphorylation. ATP is a highly unstable molecule. If it is not used quickly, it breaks down into ADP and inorganic phosphate, and the released energy is lost as heat. Cells use ATP through energy coupling. This means the exergonic reaction of ATP hydrolysis is linked to an endergonic reaction so the reaction can move forward. One major example is the sodium-potassium pump, a transmembrane ion pump that is vital...

atp and macromolecule synthesis

ATP in Building Cell Macromolecules

ATP helps cells build biological macromolecules. These organic compounds are mainly made of carbon atoms bonded to hydrogen, oxygen, nitrogen, and small amounts of other elements. The four major classes of biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids. Most macromolecules start as small subunits called monomers. Cells join monomers with covalent bonds to make larger molecules called polymers. This building process needs energy, so cells depend on ATP, the...

coupled reactions

ATP Powers Cellular Work

ATP powers many kinds of cellular work by coupling energy-releasing reactions to energy-requiring ones. Some reactions happen on their own and release energy. Others need an energy input to move forward. Cells link these reactions so important processes can still occur. Adenosine triphosphate, or ATP, stores energy that cells can use quickly. ATP hydrolysis is the breaking of ATP, and it releases energy. Cells often use that released energy to drive endergonic reactions, which are reactions...

key terms and concepts

Learn how the equilibrium binding constant reflects binding strength and why higher or lower values matter in molecular interactions at equilibrium.

How Equilibrium Binding Constant Affects Binding | 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.

How Equilibrium Binding Constant Affects Binding

Description

Transcript

Tags