Module 3. Protein Structure

T or F: alpha helices and beta sheets have repeating psi and phi angles

T

alpha helix characteristics

- right handed (clockwise)

- core tightly packed

- 3.6 AA/turn

what stabilizes secondary structures

hydrogen bonds

2 main classes of beta sheets

1. parallel

2. anti-parallel

parallel beta sheets

both n-termini are on the same side

antiparallel beta sheets

align in opposite directions

- on one side, one strand's terminus is N while the other is C

how many residues are involved in a beta turn

in a beta turn, ____ residues are involved and the backbone bends by nearly ______ degrees

4, 180

why are beta turns important

contributes to the globularity of proteins

what residues are preferred for a beta turn

proline and glycine

irregular structure

structure with no psi , phi angle pattern

random coil

no structure, denatured

circular dichroism (CD)

determines protein secondary structure

motifs

short, recurring patterns of AA sequences or 3D structures

-based on the secondary structure

βαβ motif

helix that connects 2 PARALLEL strands of a beta sheet

β hairpin

antiparallel strands of β sheet connected by a tight turn

β barrels

β strands in a sheet roll up to form a barrel

what IMF bonds AA side chains with each other and AA side chains with peptide backbones

hydrogen bonds

where are disulfide bonds common in

extracellular proteins

- interior usually has reducing conditions

what contributes to protein stability

hydrophobic effects

- required to have 2 layers of structure

protein domains

single polypeptide chain that has separate units

what 2 ways determine protein structures

1. xray crystallography

2. NMR

X-ray crystallography

results in an electron density map

- determines the structure of a crystal

- very static picture of protein

- you can't see any flexible regions of the protein

NMR

- purified protein is placed in solution

- no crystals needed

- shows flexibility of protein

The _________ the angstrom (minimum distance), the better the resolution

lower

alphafold

theoretical way to determine protein structure through AI

-input protein sequence and it'll make predictions of the protein's structure

denaturation

loss of structure sufficient to cause loss of function

what does an s-shaped curve (sigmoidal) mean for protein folding

cooperative = all or none

- 50% folded, 50% unfolded

- loss of structure in one part makes other parts more likely to lose structure

common denaturants

1. chaotropic agents

- guanidium and urea

2. organic solvents

- acetone, MeOH, EtOH

3. increased temp

4. detergent

Anfinsen's experiment

he used BME and urea to denature a small single domain protein (pure RNase) then renatured it by removing the urea and oxidizing it

- >90% of the protein were active

key implications of anfinsen's experiment

all the info that required for folding is found in the primary structure (AA sequence)

- primary structure dictates tertiary structure

levinthal's paradox

It is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest-energy one is found

- there must be folding pathways

chaperones

proteins that help other proteins achieve correctly folded structures

- prevent aggregation

- protect exposed hydrophobic regions

- provides right environment for folding, by isolation

2 types of chaperones

clamp type chaperones and chamber type chaperones

protein disulfide isomerase (PDI)

catalyzes interchange of incorrectly formed disulfide bonds unticl the correct ones are formed

peptide prolyl cis-trans isomerase (PPI)

catalyzes conversions of cis/trans isomers of prolines

intrinsically disordered proteins (IDP) or intrinsically disordered regions (IDR)

- very dynamic and flexible

- does not have a set form until it binds to specific partners

- important in cell signaling

- implicated in diseases like diabetes, cancer, and neurodegenerative diseases

1st known protein folding disease

sickle cell anemia

sickle cell anemia

HBB E6V mutation that favors polymerization if the Hb into rigid fibers instead of globular proteins

where does the cystic fibrosis mutation take place

the cystic fibrosis transmembrane conductance regulator (CFTR), ΔF508

cystic fibrosis effect

normally maintains salt/water balance, but CF thickens mucus (mainly in the lungs) to build up and weaken the immune system

most common mutation for cystic fibrosis

ΔF508 (deletion of Phe at position 508)