Module 3 - hierarchy of protein structure and folding Flashcards
Why can proteins change shape so easily?
they are held together by weak interactions
What are the 4 hierarchial levels of protein structure?
primary - amino acid sequence
secondary - a helices, b strands, or b turns
tertiary - arrangement of all atoms in the polypeptide chain
quaternary - arrangement of subunits
How are alpha helices stabilized?
intrastrand hydrogen bonding between the carbonyl oxygen of one amino acid and the hydrogen of the amide four residues away
How do the amino acid dipoles affect the dipole of the overall alpha helice?
they all add together in the same direction to create a net dipole with partial charges on both ends (positive at the N terminus, negative at the C terminus)
Describe amphipathic alpha helices
amino acids with hydrophilic or hydrophobic properties are positioned every 3-4 residues so when the helix forms they are one their own respective faces
- located on the outside of globular proteins, with a hydrophobic face facing into the protein (ex: apolipoprotein)
- also located as transmembrane proteins, with the hydrophobic face pointing out toward the membrane and hydrophilic residues pointing in (rhodopsin)
- helical wheels can be used to predict the presence of amphipathic alpha-helices based on the spacing of hydrophilic and hydrophobic amino acids
How do parallel and antiparallel beta sheets form? Which is more stable?
parallel: when peptides are stacked on top of each other, the carboxyl groups and amino groups line up vertically, so H bonds form diagonally between them
antiparallel: when peptides are stacked on top of each other, the carboxyl groups are directly in line with the amino groups, so H bonds form vertically
antiparallel are more stable than parallel, and they are also more common in proteins (called B pleated sheets)
What is a beta turn vs a loop?
turn: small 3-4 amino acid turns
loop: on protein surfaces, more amino acids in length
Where are the general areas for alpha helices, beta turns, parallel beta sheets, and antiparallel beta sheets on a Ramachandran plot?
alpha helices around the middle, beta turns at the top center, both beta-sheets at the top left but antiparallel are slightly higher and to the left
How is a Ramachandran plot developed?
from measuring phi and psi angles of existing structures
What is the difference between tertiary structures that are a/B and a+B?
a/B - both mixed together in the same domain
a+B - different domains (half protein is a, half is B)
What domains are present in the structure of pyruvate kinase?
all 4 types - short helical, a/B, B, and a+B
What are the 4 special types of tertiary structures?
four-helix bundle, greek key fold, Rossmann fold, and TIM Barrel fold
What is the four helix bundle?
normal “squiggly line” formation with alpha helices on the straight lines
What is the greek key fold?
beta strands that resemble the greek key
up, left, down, left, up, way right, down
What is the Rossmann fold?
alternating alpha helices and beta strands, two regions
up, right, down, right, up, right, down, right, up
WAY left, down, left, up, left, down, left, up, left, down, left, up
What is the TIM Barrel fold?
alternating alpha helix/beta strand fold
just a squiggly line, but alternating a/B
How can tertiary structures be stabilized?
disulfide bonds between cysteines or by metal ions like zinc fingers
Describe the quaternary structure of keratin
homodimer of two helical polypeptides that form a coiled-coil held together by disulfide bridges
Describe the quaternary structure of collagen
three helical subunits held together by cross-links of hydroxylated lysines
Describe the quaternary structure of G protein
heterotrimeric quaternary complex with three distinct polypeptides (a1b1g1)
Describe the quaternary structure of hemoglobin
Heterotetrameric complex containing two copies each of an a and b subunit, giving rise to an a2b2 heterotetramer. Each subunit contains an oxygen-binding heme.
Describe the quaternary structure of immunoglobulins
aka antibodies, two copies each of related protein subunits (two heavy chains and two light chains) with antigen binding sites at the end of the light chains
the variable and constant domains are all-b structures called Ig folds
Protein unfolding is a —– ——-.
cooperative process
Describe the Anfinsen experiments and what was learned from them.
- urea and BME were added to fully unfold a protein
- when both were removed at the same time, the protein refolded with the correct disulfide bonds
- when BME was removed first, it refolded incorrectly.
Why?
- BME reduces sulfurs and breaks disulfide bonds (tertiary structure)
- urea denatures hydrogen bonds (secondary structure)
- removing BME first causes wrong disulfide bonds to form because the correct hydrogen bonds were not in place first
What was learned?
- primary amino acid sequences contain all structural information required for protein function using ribonuclease A (RNaseA)
Before alpha helices form completely, they are partially formed early on as part of structures called…
molten globules
What is the hydrophobic collapse model?
suggests that the clustering of hydrophobic side chains drives the formation of a hydrophobic core which facilitates secondary and tertiary structure formation
What does the folding funnel visually illustrate?
there is not a single starting point or single path taken to achieve the final folded state of a protein
What are the two examples of chaperone proteins?
GroEL/GroES protein complex and the Hsp70 (heat shock protein 70)
How does the GroEL/GroES protein complex function?
ATP opens top and unfolded protein enters, closes and folds, conformational change releases a protein that was previously folded in the bottom and ATP causes and new unfolded protein to enter the bottom, conformational change opens the top and the folded protein is released, etc.
How does the Hsp70 chaperone protein work?
- when bound to ATP, the Hsp70 undergoes a conformational change to reveal hydrophobic groups that bind to an unfolded protein
- ATP is hydrolyzed and Hsp70 closes on the protein to help it fold
- ADP is released, and Hsp70 opens again to release the partially refolded protein (can be repeated until folding is complete)
Some diseases are caused by proteins that misfold (but have no amino acid changes). What are some examples, and the differences between them?
Cystic fibrosis - misfolded proteins degrade and cause loss of function
Huntington’s disease - misfolded proteins aggregate and cause a gain of function
Creutzfeld-Jakob disease - a different protein conformation aggregates and causes gain of function
