Protein Folding and Intrinsically Disordered Proteins

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Questions and Answers

What is the primary role of protein disulfide isomerase (PDI) during protein folding?

To enhance the stability of quaternary structures

To facilitate disulfide bond formation and rearrangement (correct)

To promote hydrophobic collapse of proteins

To catalyze the formation of peptide bonds

In the energy-entropy diagram known as the folding funnel, what happens to a polypeptide as it folds?

It moves from a high-energy, high-entropy state to a low-energy, low-entropy state (correct)

It transitions from a low-energy, high-entropy state to a high-energy, low-entropy state

It folds without any energy changes

It remains at a high-energy, low-entropy state throughout folding

What structural characteristic is associated with amyloid fibrils in prion diseases?

They form rigid, insoluble structures that are resistant to proteolysis (correct)

They exhibit a high degree of flexibility and disorder

They are composed entirely of globular proteins

They are primarily composed of nucleic acids

How do intrinsically disordered proteins like CREB differ when they are free in solution compared to when they interact with other molecules?

They adopt an ordered conformation upon binding to partners Signup and view all the answers

What is the 'molten globule' state in protein folding?

An intermediate state with partial secondary structure Signup and view all the answers

Which characteristic best describes the concept of 'hydrophobic collapse' in protein folding?

It drives the collapse of the polypeptide into a more ordered structure Signup and view all the answers

What can be inferred about the trajectory of protein folding as indicated by the folding funnel model?

Proteins can have multiple folding pathways originating from various unfolded conformations Signup and view all the answers

What role do intrinsic disorder characteristics in proteins like CREB play in cellular functions?

They allow for flexible interactions with multiple partners Signup and view all the answers

What is a key feature that distinguishes the structure of PrP^Sc^ from normal PrP?

The formation of a high β sheet content Signup and view all the answers

Which characteristic of amyloid fibrils is supported by spectroscopic analysis?

Fibrils are rich in β structure Signup and view all the answers

In the context of prion diseases, what is the significance of the N-terminal region of PrP^C^?

It contributes to the aggregation of PrP^Sc^. Signup and view all the answers

Which of the following best describes the role of the disulfide bond in PrP^C^?

It stabilizes the three α helices within the protein. Signup and view all the answers

What structural characteristic of PrP^Sc^ aids in its ability to form amyloid fibrils?

A longer disordered N-terminal region Signup and view all the answers

Which interaction contributes the least to the stability of a native protein?

Electrostatic attractions Signup and view all the answers

What is the main role of disulfide bonds in proteins?

To lock in a particular folding pattern Signup and view all the answers

Which of the following conditions can lead to protein denaturation?

Changes in temperature Signup and view all the answers

What does the Christian Anfinsen experiment demonstrate about RNase A?

Proteins can spontaneously fold back to their native state Signup and view all the answers

In zinc finger motifs, which side chains are typically coordinated to Zn^2+ ions?

Cys, His, Asp Signup and view all the answers

What is suggested about protein structures based on molecular dynamics simulations?

They could consist of rapidly interconverting conformations. Signup and view all the answers

Which type of agents is known to cause protein denaturation?

Detergents Signup and view all the answers

How does oxygen exposure at pH 8 affect RNase A during renaturation?

It assists in the formation of disulfide bonds. Signup and view all the answers

What characteristic structure do zinc fingers typically form?

Compact folded structures around metal ions Signup and view all the answers

What is NOT a method of denaturation for proteins?

Protein synthesis Signup and view all the answers

What is the primary reason that protein misfolding leads to diseases such as amyloidosis?

It results in insoluble fibrous aggregates of normally soluble proteins. Signup and view all the answers

Which characteristic is typical of amyloid fibrils associated with Alzheimer's disease?

Formed by the aggregation of Aβ protein fragments. Signup and view all the answers

What role does protein disulfide isomerase (PDI) play in protein folding?

It catalyzes the formation of native disulfide bonds in polypeptides. Signup and view all the answers

Which of the following diseases is NOT classified as a transmissible spongiform encephalopathy (TSE)?

Alzheimer's disease Signup and view all the answers

What is the primary component of the amyloid plaques found in the brains of Alzheimer's patients?

Aβ protein Signup and view all the answers

How are prion diseases caused?

By the accumulation of misfolded prion proteins. Signup and view all the answers

In protein folding, what does the term 'mixed disulfide' refer to?

A disulfide bond that includes both PDI and the polypeptide. Signup and view all the answers

What is a common feature of amyloidosis-related diseases?

They involve the accumulation of insoluble proteins. Signup and view all the answers

What typically happens in the brains of individuals suffering from prion diseases?

Large vacuoles develop, giving tissue a spongy appearance. Signup and view all the answers

What mechanism do molecular chaperones impede during protein folding?

Improper association of exposed hydrophobic segments. Signup and view all the answers

What is the primary factor responsible for stabilizing proteins in their native structure?

Hydrophobic effect Signup and view all the answers

Which type of symmetry is exhibited by oligomeric proteins?

Rotational symmetry Signup and view all the answers

Which term describes the arrangement of subunits in a protein's quaternary structure?

Subunit geometry Signup and view all the answers

What does a large positive hydropathic index indicate about a polypeptide chain?

It indicates a hydrophobic region Signup and view all the answers

What defines an ion pair or salt bridge in proteins?

The association of two oppositely charged groups Signup and view all the answers

What percentage of charged residues in proteins are typically found in ion pairs?

75% Signup and view all the answers

How can hydropathies be utilized in protein analysis?

To identify internal and external protein regions Signup and view all the answers

Which forces play a minor role in the stabilization of proteins compared to the hydrophobic effect?

Electrostatic interactions Signup and view all the answers

What does the term 'hydropathy scale' refer to?

Hydrophobic and hydrophilic tendencies of amino acids Signup and view all the answers

What structural information is typically derived from X-ray crystallography in proteins?

Interior and exterior regions of proteins Signup and view all the answers

Study Notes

Intrinsically Disordered Proteins

Intrinsically disordered proteins may adopt a particular secondary or tertiary structure when they bind to other molecules like ions, organic molecules, proteins or nucleic acids
An example of an intrinsically disordered protein is the cyclic AMP response element-binding protein (CREB)
The CREB protein is disordered when free in solution but folds to an ordered conformation when it interacts with the CREB-binding protein.

Protein Folding Pathways

Proteins follow specific folding pathways.
Folding begins with formation of secondary structures, and the process happens quickly.
The driving force of folding is termed hydrophobic collapse.
The collapsed state is known as molten globule.
Over the next 5 to 1000 milliseconds, the secondary structure is stabilized, and tertiary structure begins to form, forming subdomains and domains.
Slight conformational adjustments produce the native tertiary and quaternary structure.

Energy-Entropy Diagram: Protein Folding Funnel

A folding protein must proceed from a high-energy, high entropy state to a low-energy, low entropy state.
The energy-entropy relationship is known as the folding funnel.
The surface of the folding funnel represents all possible conformations that the polypeptide can assume.
The height of each point corresponds to the conformation's energy, and the funnel width at that energy is indicative of the polypeptide's entropy (number of different conformations it can assume with that energy).
The unfolded polypeptide proceeds from a high-energy, high-entropy (wide), disordered state to a low energy, low-entropy native conformation.
Folding can occur via multiple trajectories.

Protein Disulfide Isomerase Catalyzes Disulfide Interchange

Protein disulfide isomerase (PDI) plays a role during protein folding.
PDI reacts with a disulfide group on the polypeptide to form a mixed disulfide and a Cys-SH group on the polypeptide.
Another sulfide group on the polypeptide is brought into proximity by the spontaneous folding of the polypeptide and is attacked by the Cys-SH group.
This process repeats, ultimately yielding a polypeptide containing native disulfide bonds along with regenerated PDI.
Oxidized (disulfide containing) PDI also catalyzes the initial formation of a polypeptide's disulfide bonds by a similar mechanism.
Molecular chaperones are essential proteins that bind to unfolded and partially folded polypeptide chains to disrupt the improper association of exposed hydrophobic segments that would otherwise lead to non-native folding as well as polypeptide aggregation and precipitation.

Protein Folding & Disease

Many diseases are caused by protein misfolding.
At least 35 different human diseases are associated with the extracellular deposition of normally soluble proteins in certain tissues in the form of insoluble fibrous aggregates.
These aggregates are known as amyloids.
The diseases are known as amyloidosis and are often rare inherited diseases in which a mutant form of normally occurring proteins (lysozyme, fibrinogen) accumulate in various tissues as amyloids.
Alzheimer's disease is a neurodegenerative condition that affects mainly the elderly.
Alzheimer's is characterized by brain tissue containing abundant amyloid plaques (deposits) surrounded by dead and dying neurons.
The plaques consist of amyloid deposits of Aβ protein surrounded by halo neurites (axon and dendrites) from dead and dying neurons.
Aβ protein are fibrils of 40 to 42 residue protein.
Aβ is a fragment of Aβ precursor protein (AAP), and it is excised from AAP by actions of enzymes ϐ and γ secretases.
Prion diseases are infectious.
Prion diseases are caused by prions (proteinaceous infectious particles).
In prion diseases, neurons develop large vacuoles that give brain tissue a spongelike microscopic appearance.
The associated diseases are called transmissible spongiform encephalopathies (TSEs), which include bovine spongiform encephalopathy, kuru, Creutzfeldt-Jakob disease (CJK) and Scrapie.
Despite the strong electrostatic attraction between the oppositely charged members of an ion pair, these interactions contribute little to the stability of a native protein.

Disulfide Bonds

Disulfide bonds within and between polypeptide chains form as a protein folds into its native conformation.
Disulfide bonds are important for locking in a particular backbone folding pattern as the protein proceeds from its fully extended state to its mature form.

Metal Ion Stabilized Zinc Finger

Metal ions stabilize some small domains.
Metal ions may function to internally cross-link proteins.
At least 10 motifs collectively known as zinc fingers have been described in nucleic acid binding proteins.
These structures contain about 25 to 60 residues arranged around one or two Zn^2+^ ions that are tetrahedrally coordinated by the side chains of Cys, His, and occasionally Asp and Glu.

Protein Denaturation

Proteins can be denatured by:
- Heating
- pH variations
- Detergents
- Chaotropic agents (guanidium ion and urea)

Denaturation and Renaturation of RNase A

Proteins can be renatured (denatured protein regains its native, functional three-dimensional structure after the removal of the denaturing agent)
Christian Anfinsen's experiment on Ribonuclease A (RNase A) showed that proteins can be denatured reversibly.
RNase A is a 124-residue single chain protein
RNase A unfolded and the four disulfide bonds were reductively cleaved in an 8M urea solution containing 2-mercaptoethanol.
Dialyzing away the urea and reductant and exposing the resulting solution to O2 at pH 8 (which oxidizes the SH group to form disulfides) yields a protein that is 100% enzymatically active and physically indistinguishable from native RNase A.
Anfinsen's work demonstrated that a protein can fold spontaneously into its native conformation and that the protein's primary structure indicates its 3D structure.

Molecular Dynamics of Myoglobin: Proteins "Breathing"

Calculations by Martin Karplus indicated that a protein's native structure probably consists of a large collection of rapidly interconverting conformations that have essentially equal stabilities.
Conformational flexibility, also known as "breathing," with structural displacement of up to 2 A◦ allows small molecules to diffuse in and out of the interior of certain proteins.

4º Structure of Hemoglobin

Most proteins, particularly those with molecular masses >100 kD, consist of more than one polypeptide chain/subunits (oligomers) that associate with specific geometry.
The spatial arrangement of these subunits is known as a protein's quaternary structure.
Subunit construction of enzymes provides a structural basis for regulating their activities.
Multisubunit proteins have subunit composition like α2β2.

Symmetries of Oligomeric Proteins

Subunits are symmetrically arranged.
Proteins can have only rotational symmetry.

Protein Stability

Proteins are stabilized by several forces.
The hydrophobic effect, which causes nonpolar substances to minimize their contact with water, is the major determinant of native protein structure.
The hydrophobic effect has the greatest influence on protein stability.
The combined hydrophobic and hydrophilic tendencies of individual amino acid residues in protein can be expressed as hydropathies.

Hydropathy Plot: Bovine Chymotrypsinogen

Hydropathies are good predictors of which portions of a polypeptide chain are inside a protein (out of contact with aqueous solvent) and which portions are outside.
A large positive hydropathic index indicates a hydrophobic region of the polypeptide, whereas a large negative value indicates a hydrophilic region.

Ion Pairs in Myoglobin

Electrostatic interactions (also known as ion pairs or salt bridges) contribute to protein stability.
The association of two ionic protein groups of opposite charge (e.g., Lys and Asp) is known as an ion pair or a salt bridge.
About 75% of charged residues in protein are members of ion pairs that are mostly located on the protein surface.
The Scrapie prion (PrP) consists mostly of hydrophobic residues.
The hydrophobicity causes partially proteolyzed PrP to aggregate.
Human PrP^C^ (normal cellular PrP) consists of a disordered 98 residue N terminal tail and a 110 residue C terminal domain containing three α helices and a short two-stranded antiparallel β sheet.
Scrapie form of PrP^Sc^ is identical to normal PrP in sequence but differs in secondary and tertiary structure.

Amyloid Fibril Model

Spectroscopic analysis of amyloid fibrils indicates that they are rich in ϐ structure, with individual β strands oriented perpendicular to the fiber axis.

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Description

Explore the fascinating mechanisms of protein folding and the role of intrinsically disordered proteins. Understand how proteins transition from disordered states into structured forms upon binding with other molecules. This quiz delves into the nuances of folding pathways and specific examples like the CREB protein.