Lecture 6 – Folding a Protein Flashcards
What is a supersecondary structure?
Elements of secondary structure - i.e helices and strands are connected by turns or by regions of less ordered structure called loops to coils
What are common motifs of supersecondary structure?
helix-turn-helix, beta hairpin, greek key ad strand-helix-strand
What are examples of helix-turn-helix?
DNA binding proteins and calcium binding proteins
What helix-turn-helix protein has a more complicated turn?
Calcium binding proteins
Are beta hairpins common?
Yes
What is the structure of the beta hairpin?
Antiparallel, length varying.
What happens in a beta hairpin?
A single strand has nothing to bond with but the other strand in the hairpin coming back is able to bond
What are examples of beta hairpins?
Bovine pancreatic trypsin inhibitor and snake venom toxin
What does snake venom toxin have?
2 beta hairpins and one other strand
What is involved in a greek key?
4 antiparallel strands
How are the strands stabilised in strand-helix-strand?
By the side chains of the helix and other strand
What do super secondary structure elements combine to form?
Domains
What are domains?
Independently folded regions that often possess a specific function within a protein
What does a protein domain typically have?
A hydrophobic core and the hydrophilic parts of the protein are arranged on the surface in contact or near solvent
What is very important for protein stability?
Hydrophobic Core
What do small proteins contain?
Usually one domain
What do larger proteins (>250 residues) contain?
May have multiple domains
What are protein families based on?
Tertiary Structure
What are the protein families?
Alpha domain family, alpha/beta family and antiparallel beta family
What is the structure of the alpha domain family?
Mostly helical
What does the alpha domain family include?
4 helix bundles
How are 4 helix bundles arranged?
Slightly tilted to allow side chains to fit tight. The hydrophobic residues are found on the interior and hydrophilic on the exterior causing a hydrophobic core to form
What is amphipathic?
When something is partly hydrophobic and partly hydrophilic
What does the alpha domain also include?
Globin Fold
What is the alpha/beta family?
Mix of alpha and beta structure including strand-helix-strand repeated many times
What does the barrel structure have?
Bottom and middle internal layers of side chains hydrophobic and pointing out is the hydrophilic side chains which commonly form the active site
What is the horseshoe fold?
A 16 strand helix motif repeat where all of the strands are parallel
What is antiparallel beta family?
Mostly anti-parallel beta structure with no helices, just turns
What is an example of antiparallel beta family?
Retinal binding protein
What is the structure of retinal binding protein?
It has a hydrophobic inside of a barrel with the strands wrapping around a molecular held inside.
What does nature do with domain?
Common structural domains are repeated and combined to make different types of proteins
What are common protein domains?
EGF, chymotrypsin, kringle domain and calcium-binding domain
How are proteins synthesised?
As linear, non-branching polymers that have to fold into a 3 dimensional functional structure
Where are proteins made?
At the ribosome and then generally they fold into their active shape spontaneously
Where are the instructions needed for protein folding found?
Embedded in the amino acid sequence
Who proved that the instructions for protein folding were in the amino acid sequence?
Christian Afinsen.
What did Afinsen observe?
Denatured proteins were able to refold themselves
What is protein folding directed largely by?
Its internal hydrophobic residues which form an internal core while hydrophilic residues are solvent exopsed
How is the sequence of protein folding described?
Not random
What is the first step in protein folding?
Formation of short secondary structure segments
What happens after formation of short secondary structure segments?
Subdomains form
What happens after subdomains form?
Subdomains come together to form a partly folded domain; a “molten globule” that can rearrange (tertiary structure still partly disordered)
What happens after a molten globule forms?
Final domain emerges small conformational adjustments to give final compact native structure
How are non covalent bonds individually?
Weak but in proteins, collectively they make a significant contribution to protein conformational stability
What do some proteins have?
Additional covalent bonds (disulphide bonds) which contribute to conformational stability
What is most likely the most important non covalent contributor to protein stability in aqueous solution?
Hydrophobic Core
How do some proteins get assistance in folding?
By chaperones
What are the types of protein folding?
Chaperone independent, chaperone dependent and chaperonin dependent
What is an example of a chaperone?
Hsp70
What is an example of chaperonin?
GroEL-GroES
What % of proteins fold chaperone independent and dependent?
85%
What % of proteins fold chaperonin dependent?
15%
What can weakening of non covalent interactions do?
Lead to unfolding and loss of biological function (denaturation)
What may denaturation result from?
Change in pH, heating, detergents, organic solvents, urea and guanidium HCL
What can proteins in living organisms that are folded normally do?
Sometimes change their shape and become misfolded
What can some misfolded proteins do?
Can cause other proteins to change their shape as well, sometimes with disastrous consequences
What are the proteins that cause the brain disease called?
Prions or “proteins infectious agent”
What transformation occurs due to prions?
alpha to beta
What other diseases are thought to be caused by protein misfiling or aggregation?
Alzheimers and Type 2 diabetes
