Name: allosteric switching in multimeric proteins
Uploaded: 2020-11-23T11:47:34.000Z
Duration: 1 min 58 s
Channel: JoVE

K12 Standards

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Biology

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

From Molecules to Organisms: Structures and Processes

BIO1.LS1.3

Cooperative Allosteric Transitions

Wiele białek ma wiele podjednostek, z których każda zawiera oddzielne miejsce wiązania liganda.
Kiedy cząsteczka, znana jako modulator, wiąże się z jedną z podjednostek, wyzwala zmianę konformacyjną w miejscach wiązania innych podjednostek, zmieniając ich powinowactwo do odpowiednich ligandów. Nazywa się to kooperatywnym przejściem allosterycznym i można je wyjaśnić za pomocą kilku modeli teoretycznych.
Model uzgodniony lub "wszystko albo nic" zakłada, że wszystkie podjednostki istnieją razem w konformacji "wyłączonej" lub "włączonej".
Wiązanie może wystąpić w dowolnej formie, jednak stan "włączony" ma większe powinowactwo do liganda niż stan "wyłączony". Kiedy ligand wiąże się w którejkolwiek z podjednostek, sprzyja jednoczesnej transformacji wszystkich miejsc wiązania do formy o wysokim powinowactwie.
Kooperatywność można również wyjaśnić za pomocą modelu sekwencyjnego, który zakłada, że każda podjednostka może istnieć niezależnie w stanie wysokiego lub niskiego powinowactwa, ale bardziej prawdopodobne jest, że będzie w stanie wysokiego powinowactwa, gdy ligand jest związany z którąkolwiek z podjednostek. 
Miejsca wiązania białek allosterycznych są zwykle mieszanką elastycznych i stałych segmentów łańcucha aminokwasowego. Kiedy ligand się wiąże, te niestabilne części są stabilizowane w określonej konformacji, a to wpływa na kształt miejsc wiązania na innych podjednostkach. 
Hemoglobina jest przykładem białka tetramerycznego, które ulega kooperatywnemu przejściu allosterycznym, gdy wiąże się tlen.
Każda podjednostka hemoglobiny ma pojedyncze miejsce wiązania. Kiedy jedna cząsteczka tlenu wiąże się z pojedynczą podjednostką, kooperatywność zwiększa powinowactwo do tlenu w pozostałych miejscach wiązania, ułatwiając tlenowi wiązanie się z cząsteczką hemoglobiny, która jest już związana z tlenem.

<ol>
	<li>Cornish-Bowden, A. (2014), Zrozumienie interakcji allosterycznych i kooperacyjnych w enzymach. LUTY J, 281: 621-632. doi:10.1111/febs.12469</li>
	<li>Alberts et al., wydanie 6; strony 152-153</li>
	<li>Lehninger Zasady biochemii, wydanie 5, strony 162,165</li>
</ol>

przejście allosteryczne

Przejście allosteryczne może zachodzić w białkach multimerycznych, gdzie każda podjednostka białka ma swoje własne miejsce wiązania liganda. Kiedy ligand wiąże się z którąkolwiek z tych podjednostek, wyzwala zmianę allosteryczną, która wpływa na miejsca wiązania w innych podjednostkach; może to zmienić powinowactwo innych miejsc dla ich odpowiednich ligandów. Zdolność białka do zmiany kształtu miejsca wiązania przypisuje się obecności w strukturze mieszanki elastycznych i stabilnych segmentów. Cząsteczka, która wyzwala tę zmianę, nazywana jest modulatorem. Do wyjaśnienia kooperatywności białek multimerycznych często stosuje się dwa modele: model skoncentrowany i model sekwencyjny. Model skoncentrowany, znany również jako model „wszystko albo nic”, zakłada, że wszystkie podjednostki multimerycznego białka przełączają się jednocześnie między konformacją „włączoną” i „wyłączoną”. W formie „włączonej” miejsca wiązania mają wysokie powinowactwo do odpowiednich ligandów, a w formie „wyłączonej” miejsca wiązania mają niskie powinowactwo. Kiedy ligand wiąże się z którąkolwiek z podjednostek, sprzyja konwersji do postaci o wysokim powinowactwie, jednocześnie zmieniając konformację wszystkich innych miejsc wiązania białka. Chociaż ligand może wiązać się z dowolną formą, łatwiej jest mu się związać, gdy jest w formie o wysokim powinowactwie. Model sekwencyjny zakłada, że każda podjednostka multimerycznego białka może istnieć niezależnie w konformacji „włączonej” lub „wyłączonej”, czyli w formie o niskim lub wysokim powinowactwie, niezależnie od stanu pozostałych podjednostek. Wiązanie ligandu z podjednostką zmienia równowagę pomiędzy formami o niskim i wysokim powinowactwie, tak że jest bardziej prawdopodobne, że podjednostka będzie w postaci o wysokim powinowactwie. Dodatkowo wiązanie ligandu z jedną podjednostką przesuwa równowagę pozostałych podjednostek białka. Zwiększa to prawdopodobieństwo, że po związaniu jednego liganda inny ligand zwiąże się z inną podjednostką. Ta kooperatywność zwiększa wrażliwość białka na stężenie ligandu. Wiązanie ligandu w jednym miejscu może zmienić powinowactwo całej cząsteczki białka, umożliwiając w ten sposób szybką reakcję przy niskich stężeniach.

Przejście allosteryczne

Kooperacyjne przejścia allosteryczne mogą zachodzić w białkach multimerycznych, w których każda podjednostka białka ma swoje własne miejsce wiązania ligandu. Kiedy ligand ...

Education

JoVE Core

Molecular Biology

Biologia molekularna

Unit 1

Jednostka 1

Protein Function

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KEY TERMS AND CONCEPTS

Kluczowe terminy i pojęcia

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 binding sites can change shape, the protein can alter the affinity of other sites for their ligands.

Two common models describe this cooperativity in multimeric proteins. The concerted model, also called the all-or-none model, says that all subunits switch together between an “on” state and an “off” state. In the on state, the sites have high affinity. In the off state, they have low affinity. A ligand can bind to either form, but binding is easier in the high-affinity form.

The sequential model takes a different view. It assumes that each subunit can be in an on or off conformation on its own, no matter what the other subunits are doing. When a ligand binds to one subunit, it shifts the balance toward the high-affinity form in that subunit and makes it more likely for other subunits to follow.

This cooperativity makes the protein more sensitive to ligand concentration. After one ligand binds, another ligand is more likely to bind at a different subunit. As a result, a single binding event can change the affinity of the entire protein and support a rapid response even at low ligand levels.

Allosteric Switching in Multimeric Proteins

allosteric-switching-in-multimeric-proteins

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

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

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...

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 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 ligand binding can switch multimeric proteins between low- and high-affinity states through concerted and sequential cooperativity models.

Allosteric Switching in Multimeric Proteins | JoVE K12

molecular biology

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Characteristics of Life

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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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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

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

Karyotyping

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Replication in Eukaryotes

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Mutations

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Lesson: Translation
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MicroRNAs

siRNA - Small Interfering RNAs

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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

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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

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Globular ...

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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 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

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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 ...

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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.
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Allosteric Switching in Multimeric Proteins

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