Protein misfolding and disease Flashcards
What did Pauling: structure of key structural modules tell us?
What did Anfinsen and the refolding of pancreatic ribonuclease tell us?
What is levinthal’s paradox?
What is Bryngelson and Wolynes principle of minimal frustration?
Say about proteins and peptides?
Pauling said that secondary structures are sufficient to bring about the final three dimensional conformation.
Anfinsen slowly removed the denaturant and the ribonuclease refolded. That means all the information for folding is stored in the peptide.
Levinthal’s Paradox: If protein folding shifted through all possible conformations, it would take the age of the universe. THat means only a subset of possible pathways are sampled to get the final structure
Minimal frustration: individual amino acids are positioned where they are through evolution to maximize correct folding events and minimize structural barriers.
What does not a linear drop in energy refer to in protein folding.
From the unfolded to folded, the free energy level undergoes pertubations. There are local minima in the curve. So there are small energy barriers within the folding process. This is where we would need assistance (chaperones)
What is regulated vs impromptu degradation?
Regulated: Some proteins need to be degraded all the time (specific proteins become no longer needed)
Impromptu degradation: stress causes damage to proteins and they need to be destroyed.
Degradation requires ATP. (proteosome)
Describe chaperone’s role as a match maker, protein synthesis, quality control, and secretion.
Complex assembly: bring each subunit to the right position for the large complexes. Example: Ump1 and the proteosome.
Secretion: when a protein crosses the membrane barrier into the ER, it needs to be unfolded to go through the hydrophobic membrane. Then when in the ER
What is the key feature of a chaperone?
It may or may not need energy (repair needs energy), it can reversibly bidn to the substrate.
it does not increase the reaction rate, it does not stay bound to the native protein.
What are the important determinants for protein folding?
Hydrophobic core collapse, disulfide bond, Van der Waals, electrostatic interactions, metal coordination (stabilizing, co-factor)
What is the molten globule
The molten globule refers to the protein that is almost in its final form and it drifts through similar structures. The problem is it has not driven out all of the water yet. The driving forces are therefore water exclusion and hydrophobic core collapse.
How is the proteosome assembled? WHat are the structures of the proteosome and chaperone?
Chaperone is self assembly. A-E and E-A. With an inner ring of 7 ATPases on both sides. Proteosome requires the assistance of UMP1 chaperone. Alpha beta rings self assembly and then the chaperone brings the two pairs together. 3 beta subunits on each half are zymogens. When brought close together, peptides on the zymogens are cleaved off, activating the hydrolytic activity. This compartmentalizes the protease activity. UMP1 is the first digested substrate.
What are the three models of folding initiation.
Hydrophobic collapse, the molten globule forms as a result of tertiary hydrophobic interactions that result in secondary structure maturation and the tertiary structure.
Hierarchical: secondary structures form first which promotes the assembly of the final tertiary structure. Secondary structures are only stable if the tertiary structure is formed.
Nucleation-Condensation: local sites of folding propagates throughout the peptide which results in the final native structure.
What are factors that promote protein unfolding
temperature, pH, pressure, urea, guanidine, organic solvents (stabilizes hydrophobic residues.
Describe the structure of ubiqutin
It is a highly conserved singular protein that interacts with around 1000 proteins. Its carboxyl termini (Arg-Gly-Gly COO). They feature hydrophobic patches. And 7 lysine residues on the surface which can ligate to additional Ub’s and form different chains depending on the function. For example one chain promotes translocation to the lysosome rather than proteosome, or for repair. Glycine 76 is what binds to lysine residues on substrates and lysines on the other ubiquitins. The isopeptide bond is stable and reversible. Gly76 then forms thioester bonds to E1, E2, and E3 enzymes.
Proteins involved in proteolysis have two key features…
Compartmentalization so it doesn’t react with anything else. Like the lysosome.
Their precursors are expressed as inactive zymogens
Regulators of proteolysis, proenzymes (hormones, it could be a tag on the proteosome and once removed will fold correctly and be active), pH, compartmentalization,
Describe the two types of proteolysis.
Specific degradation: always eliminates the same target in the cycle, like an assassin. Requires energy.
Nonspecific degradation: digests everything that comes by. Like stomach enzymes. The environment,aids in the unfolding.
Ubiquitin is always expressed as a fusion protein. Implications on disease and the enzyme.
UchL1 is what cleaves the fusion protein and exposes the reactive carboxy end. Mutation causes PD. Not enough ubiquitin so proteins remain unfolded and proteins can aggregate.
Describe the E1, E2, and E3 enzymes.
E1: activates Ubiquitin, uses ATP to attach ubiquitin to AMP. (Charges the Ubiquitin) And makes a thioester bond. (only ATP step) Charged ubiquitin can jump onto the enzyme and make phosphodiester bond.
E2: transfers ubiqutin to E3 or Substrate
E3: ubiqutin protein ligase: attaches UB to the substrate via an isopeptide bond. Parkin is an E3 enzyme that when mutated is connected to parkinson. Makes sense, tags can’t be added onto the proteins.
