Lecture 11 - Protein Tertiary Structure Flashcards
What is the tertiary structure?
folded 3-D structure
stabilized by non-covalent interactions between R-groups, and covalent disulfide bonds
How can a protein be denatured/what happens when a protein is denatured
Breaking of bonds responsible for secondary and tertiary structure
Creates unnatural hydrophobic aggregation (insoluble)
1) adding chaotropic agents (urea, guandinium chloride, Beta-mercaptaethanol)
2) extreme pH
3) raise temperature
4) detergents
What is the Anfinsen refolding experiment?
If you remove BME before you remove urea, then native state not achieved. disulfide bonds form
If urea removed first, then tertiary structure forms, then removal of BME allows proper disulfide bonding so correct tertiary structure locked in
Therefore, amino acid sequence dictates folding, cysteines help lock fold into place
What is the Levinthal paradox, and how is it resolved?
Levinthal paradox –> many many possible configurations, but correct native structure found in much less time than required to sample all possible configurations.
Resolved through: 1) limited # secondary structural elements
2) elements form spontaneously through co-translational folding
3) folding landscapes that lead to correct 3-D structure
What is a folding landscape?
show descent in energy levels to native state
go through intermediate minima along the way
What is co-translational folding
After ~30 amino acids (<30=not able to fold) then local secondary structures start to form. These structures interact and stabilize spontaneously to form tertiary structure
What are the thermodynamics of protein folding
Conformational entropy decreases because of increased order, enthalpy is negative so folding favoured due to weak non-covalent interactions, hydrophobic entropy increases because removing need for clathrates b/c less hydrophobic surface area so overall, favourable
How do chaperones work and what is one example
GroEL-GroES complex ( Gro-EL is the bottom)
works by preventing unwanted hydrophobic interactions from occuring
Forms hydrophobic interactions with residues
What is the structure of a domain?
hydrophobic on inside, hydrophilic region on outside
domain= compact. locally folded, stable region
Globular= compact, spherical
Fibrous - elongated, single structure
What are 2 types of post-translational modifications
covalent attachments of new group
(ex. add hydroxyl to proline in collagen to stabilize fibers)
Proeolytic cleavage
cleaved by proteases after synthesis to activate
mechanism to regulate activity
