1-40 Mutations and Proteins Flashcards
What are “irregular” structures or “random coils”?
Loops that are neither α-helices, β-sheets, or β-turns; generally, they’re only random in the sense that they’re not periodic. Usually, they have a specific structure. Surface loops give proteins their individuality and are crucial to function.
What are protein motifs and domains?
Stretches of secondary structures that often function in molecular recognition. There is no clear difference between motifs and domains, although motifs tend to be smaller and unstable when independent, while domains are stable and semi-independent. Some examples include:
- helix-turn-helix motif
- zinc finger motif
- coiled-coil domain
What is the helix-turn-helix motif?
A common element used by proteins to recognize specific sequences of DNA. It consists of a recognition α-helix (which sits in the major groove and binds to specific NT sequences) and a support α-helix (supports the recognition α-helix along with sidechain-sidechain contacts), joined by a turn. The helices are held together by a small, hydrophobic core.
HTH motifs are found in all kingdoms of life, including in the antennapedia homeodomain, where varying expression can result in bizarre developmental patterns for Drosophila.
What is the zinc finger motif?
A common DNA binding motif, which often alternates an amino acid X with Cys and His. The Zn2+ holds the structure together without an extensive hydrophobic core, though hydrophobic side chains stabilize the helix.
What is the coiled-coil domain?
Stable structures found in fibrous proteins and transcription factors, with a signature heptad repeat. The seven residues are labeled a-g, with characteristic hydrophobic residues at a and d, and opposite charges at e and g.
Coiled-coils are often used for DNA binding, protein-protein recognition, mechanical force transduction (e.g., myosin tails), and viral penetration (influenza haemagglutinin, HA).
What is protein misfolding?
The only functional version of a protein is the folded (native) form. All of the information necessary for folding is contained in the AA sequence. Folding is a complex process, however, and requires the formation of intermediate species that partially folded, partially unfolded. Intermediates are particularly vulnerable to aggregation because they often expose hydrophobic residues that have yet to be buried.
What are chaperones, and what are two heat shock protein classes?
A large family of proteins designed to prevent aggregation during folding. Chaperones are believed to target large, multidomain proteins.
- Hsp70 class: acts locally; binds to proteins (probably co-translationally) when they are in non-native conformations and covers up sticky hydrophobic patches
- Hsp60 class: form a large structure into which misfolded proteins enter. Once sealed in, they are forcibly unfolded and then given time to refold properly
- Hsp100 class: disassembly machines defined by the AAA domain
Hsp60 and Hsp70 expression is upregulated when cells are exposed to high temperature (during a high fever) or in other conditions where aggregation is a concern.
How does Hsp70’s conformation change as it acts to prevent aggregation?
- ADP-bound state: Nucleotide-binding domain (NBD) connected to substrate-binding domain (SBD); SBD can bind to a short AA stretch in a hydrophobic pocket
- ATP-bound state: conformational change in NBD; create binding sites on NBD for linker and lid; lid opens, can exchange substrate rapidly
How do Hsp60 chaperones do their work?
The current model is iterative annealing.
- Assembly: 14 Hsp60 monomers associate to form a large, hollow “double donut” structure
- Seal proteins in: Misfolded proteins enter the cavity, which is sealed by the GroES “cap”
- Unfold/refold: ATP hydrolysis is used to physically unfold the misfolded protein, which can then refold properly while protected inside the cavity
- Cycle: if it doesn’t fold by the time the GroES cap dissociates, the protein is expelled back into the cell and given another chance to fold on its own. It may take several rounds of unfolding/release to fold especially problematic proteins
What is the Hsp100 class of chaperones?
A class that uses energy from ATP hydrolysis to disassemble protein aggregates. It is defined by the AAA (ATPase Associated with various Activities) domain, which is used to unfold proteins in repeated cycles. The unfolded peptide may then be fed into a protease domain to be degraded into small peptides and free AAs.
