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

K12 Standards

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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

W komórce białka losowo zderzają się z innymi cząsteczkami, takimi jak inne białka, kwasy nukleinowe i ligandy drobnocząsteczkowe.
Jeśli wiązanie jest niespecyficzne, kilka niekowalencyjnych oddziaływań między cząsteczkami powoduje krótkie skojarzenie.
Jeśli określony ligand wiąże się z białkiem, tworzy rozległe oddziaływania niekowalencyjne wzdłuż komplementarnych powierzchni. Takie kompleksy są stabilne, pozostają związane przez długi czas, zanim się rozłączą.
Siła oddziaływania wiązania jest podawana w postaci jego stałej równowagi, Kb, zwanej również stałą wiązania lub asocjacji. 
Kb można obliczyć ze stosunku stężenia kompleksu białko-ligand do stężeń białka niezwiązanego i liganda znajdujących się w stanie równowagi. 
Biorąc pod uwagę jego związek ze zmianą energii swobodnej spowodowaną wiązaniem, duże Kb oznacza duży spadek delta G, co wskazuje na silne powinowactwo między białkiem a ligandem.
Dwa konkurencyjne procesy są ważne dla wiązania białka-liganda: asocjacja białka i liganda w celu utworzenia kompleksu oraz dysocjacja kompleksu na reagenty.
Stała asocjacji, kon, jest miarą liczby zdarzeń wiązania na sekundę między białkiem a jego ligandem; może być użyta do obliczenia szybkości wiązania liganda z białkiem przy danym stężeniu. 
I odwrotnie, koff jest miarą liczby zdarzeń dysocjacji; może być użyta do obliczenia, jak szybko kompleks się rozpada.
Gdy szybkość asocjacji jest równa szybkości dysocjacji, osiągana jest równowaga, w której stężenia netto produktów i reagentów pozostają stałe.
Zatem w stanie równowagi krazy iloczyn stężeń równowagowych białka i liganda jest równy k razy stężenie równowagowe kompleksu białko-ligand.
Przegrupowanie tego wyrażenia pokazuje również, że stosunek kon do koff jest równy Kb w stanie równowagi.

<ol>
	<li>Pollard, Thomas D. "Przewodnik po prostych i pouczających testach wiązania". Biologia molekularna komórki 21, nr 23 (2010): 4061-4067.</li>
	<li>Hulme'a, Edwarda C. i Mike'a A. Trevethicka. "Testy wiązania ligandów w stanie równowagi: walidacja i interpretacja". Brytyjski dziennik farmakologiczny 161, nr 6 (2010): 1219-1237.</li>
	<li>Medina-Franco, José L., Oscar Méndez-Lucio i Karina Martinez-Mayorga. "Wzajemne oddziaływanie między modelowaniem molekularnym a chemoinformatyką w celu scharakteryzowania krajobrazów interakcji białko-ligand i białko-białko w celu odkrywania leków". W: Postępy chemii białek i biologii strukturalnej, tom 96, s. 1-37. Wydawnictwo Naukowe, 2014.</li>
</ol>

stała wiązania i siła wiązania

Stała wiązania (kb) określa ilościowo siłę oddziaływania białko-ligand. Gdy reakcja jest w równowadze, kb można obliczyć w następujący sposób:

<img alt="Eq1" src="/files/ftp_upload/11513/Equation 1.png" style="text-align: center;">

gdzie P i L oznaczają odpowiednio niezwiązane białko i ligand, a PL oznacza kompleks białko-ligand.

Ponieważ ilość związanego liganda jest również powiązana z szybkością wiązania ligandu, eksperymenty mogą również określić kb poprzez zbadanie szybkości asocjacji białko-ligand (kon) i dysocjacji (koff) przy użyciu następującego stosunku:

<img alt="Eq1" src="/files/ftp_upload/11513/Equation 2.png" style="text-align: center;">

Zatem do określenia stałej równowagi wiązania stosuje się dwie kategorie testów wiązania – te, które mierzą stężenia równowagowe i te, które mierzą kinetykę reakcji. W takim przypadku reakcja musi być w równowadze w momencie pomiaru.

Metoda wyznaczania stężeń równowagowych zależy od pożądanej czułości i łatwości detekcji sygnału. Z tych powodów najczęściej stosuje się testy spektroskopowe. W tych eksperymentach reakcja powoduje zmianę absorbancji reagenta lub produktu przy danej długości fali, wykrywalną za pomocą spektrofotometru UV-Vis. Alternatywnie, reagent lub produkt można oznaczyć sondą fluorescencyjną lub może zawierać wewnętrzny fluorofor. Następnie postęp reakcji można zmierzyć na podstawie zmiany fluorescencji. Testy te przeprowadza się poprzez zmianę stężeń jednego reagenta, podczas gdy pozostała część eksperymentu pozostaje stała. Wyniki można następnie przedstawić na wykresie i przeanalizować za pomocą różnych metod dopasowywania krzywych.

Interakcje między białkami i ligandami bada się również przy użyciu różnych technik biochemicznych i spektroskopowych. Analiza strukturalna wykorzystująca krystalografię rentgenowską i spektroskopię NMR pomaga w przewidywaniu interakcji białko-ligand za pomocą symulacji molekularnych. Podejścia teoretyczne i obliczeniowe, takie jak badania dokowania białko-ligand, są szeroko stosowane w celu scharakteryzowania pozycji i interakcji ligandów małocząsteczkowych, w tym kandydatów na leki. Wspomagane komputerowo projektowanie leków to szybka i tania alternatywa umożliwiająca przyspieszenie tempa konwencjonalnego testowania leków metodą prób i błędów.

Stała wiązania i siła wiązania

Stała wiązania równowagi (Kb) określa ilościowo siłę oddziaływania białko-ligand. Kb można obliczyć w następujący sposób, gdy reakcja zachodzi w ...

Education

JoVE Core

Molecular Biology

Biologia molekularna

Unit 1

Jednostka 1

Protein Function

Funkcja białka

KEY TERMS AND CONCEPTS

Kluczowe terminy i pojęcia

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

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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

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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

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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

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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.

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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.

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MicroRNAs

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piRNA - Piwi-interacting RNAs

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Measuring Protein-Ligand Binding Strength

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