L13 Protein-protein Flashcards
(39 cards)
What are the diverse functions of proteins?
- Molecular motors
- Reaction catalysis (enzymes)
- Signal transduction
- Ion channels
- Transcription and translation
- Protein synthesis and degradation
- Cell adhesion
- Immune response
- Viral entry into cells/viral capsid formation
Proteins play critical roles in various biological processes, acting as catalysts, structural components, and signaling molecules.
What is the role of molecular motors in proteins?
They convert chemical energy into mechanical work, enabling movement within cells.
Examples include transporting cargo, contracting muscles, and dividing cells.
What is signal transduction in the context of proteins?
It involves proteins like G-protein coupled receptors transmitting signals from outside the cell to inside by activating G-proteins.
This process triggers various cellular responses.
What is the function of ion channels in proteins?
They regulate the flow of ions across cell membranes, controlling electrical signals and maintaining cellular homeostasis.
An example is the sodium channel in nerve cells.
What does transcription involve in protein function?
Proteins like RNA polymerase help synthesize RNA from DNA.
Translation involves ribosomal proteins and rRNA assembling amino acids into proteins.
What is ubiquitination in protein synthesis and degradation?
It is the process where proteins attach ubiquitin to target proteins, marking them for degradation.
This controls protein levels and quality in cells.
What is the significance of protein-protein interactions?
They mediate the functions of proteins by allowing direct contact and communication between them.
Understanding these interactions helps explain biochemical pathways and functional genomics.
What factors can influence protein-protein interactions?
- pH
- Ion concentration
- Phosphorylation
- Interaction with ligands or other proteins
These factors can alter the binding and activity of proteins.
What is surface complementarity in protein-protein interactions?
It refers to the fitting together of shape and chemical properties of interacting protein surfaces facilitating binding.
This is crucial for effective protein interactions.
What are ‘hot spots’ in protein-protein interactions?
They are specific regions on the protein surface that contribute disproportionately to the binding energy of the interaction.
Hot spots stabilize interactions through non-covalent bonds.
What is cooperative binding in the context of protein interactions?
It’s when the binding of one molecule to a protein enhances the binding of additional molecules.
This process is important for effective transport mechanisms in cells.
What are the advantages of using ELISA for evaluating protein-protein interactions?
- Sensitive
- Specific
- Can quantify bound proteins
ELISA is widely used in various biological samples.
What is the principle behind fluorescence polarization assays?
It measures the change in polarized light emitted from a fluorescently labeled molecule based on its rotation in solution.
Small proteins rotate quickly, leading to less polarization, while larger proteins rotate slowly, resulting in higher polarization.
What does FRET stand for and how does it work?
FRET stands for fluorescence resonance energy transfer, occurring when two fluorophores are close (<10 nm) and energy is transferred between them.
This is used to determine if two proteins interact based on fluorescence emission changes.
Fill in the blank: The process of _______ involves using peptide libraries to identify important amino acids for blocking protein interactions.
[peptide and peptidomimetric molecules]
True or False: Antibodies can block protein-protein interactions by binding to the binding site.
True
What is the role of thioredoxin in protein-protein interactions?
It helps maintain cellular redox balance and can covalently modify NF-kB peptide, influencing its activity and stability.
Thioredoxin regulates gene expression in response to stress.
What are the limitations of ELISA?
- Antibody availability
- Many washing steps that can’t always be automated
These limitations can affect the efficiency and reliability of the assay.
What is the significance of using small molecules in the inhibition of protein-protein interactions?
They can be screened as inhibitors to refine structures for better inhibition.
Computer-based modeling can help in the design of these small molecules.
What are α-helix mimetics used for?
They are inhibitors of the p53-mdm2 interaction.
This approach is part of mimicking protein secondary structures to target protein-protein interactions.
What is the purpose of hit identification in evaluating protein-protein interactions?
To determine potential inhibitors using various techniques like ELISA and fluorescence-based assays.
This step is crucial for validating the effectiveness of potential inhibitors.
What does FRET efficiency indicate?
The proximity of two fluorophores, indicating protein interactions
FRET stands for Förster Resonance Energy Transfer, which is a technique to study molecular interactions.
How do inhibitors affect FRET?
They disrupt protein-protein interactions, reducing FRET
Inhibitors can interfere with the binding of proteins, which is essential for FRET to occur.
List advantages of TR-FRET.
- Sensitive and reproducible
- Large difference between excitation and emission wavelengths reduces interference
- Uses long-lifetime donor fluorophore (lanthanide chelate)
Examples of lanthanides include europium and terbium.
