Structural Biology - Protein Folding Flashcards

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1
Q

Why is it important to understand protein folding?

A

Predict the 3D structure from the primary sequence
Understand misfolding related to human diseases
Design proteins with a new function

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2
Q

What are intrinsically disordered proteins?

A

Don’t have a defined 3D / globular structure
Because sequences don’t allow for formation of hydrophobic core
Are very flexible
30% of proteins are intrinsically disordered proteins
A small number can aggregate and cause disease
Neurodegenerative diseases (Alzheimer’s - alpha beta, Parkinson’s - alpha synuclein) and Cancer (P53)

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3
Q

Briefly explain the process of protein folding

A

After ribosomal synthesis, most proteins (but not all) fold into a 3D structure
Spontaneous process
Transition from denatured to native state
Each protein structure has its own free energy
Native (folded) state has minimal free energy due to increased native interactions and increased residue contacts

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4
Q

Explain the anfinsen experiment

A

Proved that the native state is the conformation with the minimal free energy
Denature ribonuclease A (has four disulphide bonds) with 8M urea and beta mercaptoethanol (BME) to unfold the protein to a random coil state with no enzymatic activity
Remove BME witch leads to oxidation of sulfhydryl/thiol groups (reforms disulphide bonds)
Remove urea witch leads to scrambled protein with no activity
Add trace amounts of BME which converts scrambled protein to native state
BME is not a catalyst only breaks disulphide bonds which leads to different conformations of the protein
Conclusion: this process is driven by the conformational free energy that is gained by going into the native structure (active conformation)
Formation of N structure is encoded in the sequence of the protein
Thermodynamics is important in protein folding - every conformation has a different energy but lowest free energy is favoured

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5
Q

Explain the chemical stability of protein folding

A

Chemical stability is the ability of maintaining the chemical structure of native states/polypeptide chain under various conditions (ex. temperature, pH, denaturing agents)
Want intact covalent bonds, oxidation states, metal coordination
Deamination of Asn and Gln residues (to Asp and Glu, respectively)
Hydrolysis of the peptide bond of Asp residues at low pH
Oxidation of Met at high temperature to methionine sulfoxide (Sign of aging in proteins)
Elimination of disulfide bonds
Thiol-catalyzed disulfide interchange at neutral pH (oxidation of disulphides, very reactive)
Oxidation of cysteine residues to thyil radicals, Cys-S·

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6
Q

Explain the conformational/thermodynamic stability of protein folding

A

Proteins fold into the Native structure because it is more stable than the denatured state
Conformational stability is the ability to adopt a well defined conformation instead of a random coil
It is given by the difference in free energy between D and N states DeltaG(D-N)
Non-covalent interactions
Psi and phi in backbone of protein rotate which allow polypeptide to assume various conformations
Tells us about flexibility of secondary structure (alpha helices/beta strands) and how these adapt (compress/elongate) to allow formation of 3D structure
Some conformations are disallowed
Glycine has the greatest accessibility

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7
Q

Explain proteins folding in terms of the free energy change

A

Free energy change upon folding, depends on enthalpy and entropy
Unfavourable entropy change by folding a flexible polypeptide
Favourable enthalpy change from intra molecular side chain interactions (Hydrophobic interactions, Hydrogen bonds, Disulphide bonds)
Favourable entropy change from burying hydrophobic groups in the molecule (Release of water molecules from hydrophobic side chains - strongest force that drives protein folding)
In total net negative delta G

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8
Q

Explain the different parameters which influence protein folding

A

Delta G varies with: pH, Temperature, Pressure, ionic strength, molecular crowding, hydrophobic effect, H-bonds, van Der Waals, disulphide bonds
Example proteins have optimal activity at a specific temperature
Crowding: thick, dense solution like polysaccharides (dextran) gives a more stable protein

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9
Q

How does protein stability affect their function?

A

Average stability (free energy) of a small protein is only 5-15kcal/mol
To fold a protein, need to break interactions in denatured state and from interactions in the native state
Balance between them is very small
So, proteins are not very stable which is important because it allows them to be dynamic to be able to perform a function and allows cells to recycle proteins

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10
Q

Explain how covalent interactions (disulphide bonds) determine protein folding

A

Oxidation forms disulphide bond, reduction breaks it
Process is reversible
Oxidation process can be intramolecular (in same protein) or inter-molecular (with different proteins ex. antibody light and heavy chains)
Cellular enzymes (protein disulphide isomerases) help form disulphide bonds

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11
Q

Explain how compaction determines protein folding

A

Proteins are compact
Compactness = amount of surface area of an object relative to a perfect sphere of comparable volume (perfect sphere = 1 but other object will have <1)
Alpha helices and beta sheets are very compact
Folding is directed by internal residues
Hydrophobic effect drives folding (hydrophobic amino acids cluster together in core of protein to minimise exposure to water)
Interactions between amino acids drive folding (ionic, vdw, disulphide)
Need a good balance between compactness and flexibility to allow function

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12
Q

Explain the hierarchical pattern of protein folding

A

Folding follows a hierarchical pattern (step-wise)
Subdomains form spontaneously
Domains are stable, independent folding units
Large proteins can contain several domains
Tertiary structure forms when these pack together

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13
Q

Explain the adaptability of proteins when folding

A

Proteins are adaptable
ex. rigid hydrophobic core/packing of non-polar side chains
Large mutations don’t affect backbone of protein
Example: Phenylalanine (aromatic) to alanine mutation in T4 lysozyme showed that a benzene was occupying position of side chain and structure was preserved after mutation

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14
Q

Explain the sequence versatility of proteins (conservation of sequence and folding)

A

20% sequence identity (80% difference) between 2 proteins = can have the same fold/structure
But can also have the opposite: 88% identity and a different structure
Only some residues are important in determining the unique structure

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15
Q

List different techniques to measure protein stability

A

Absorbance ex. trp, tyr, chromophoric probes (but only gives small signal)
Fluorescence ex. trp, fluorophoric probes, aromatic residues (big signal)
CD
NMR
Differential scanning calorimetry (DSC) to determine delta H of unfolding
Catalytic activity

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16
Q

Explain the protein denaturation curve

A

Denaturation: loss of native structure integrity and loss of activity
Proteins can be denatured by: Heat or cold, pH extremes, organic solvents, chaotropic agents (urea, guanidinium hydrochloride)
Denaturation curve is sigmoidal
Tm = melting point, when protein is 50% denatured and 50% folded
D50% = denaturing concentration at which 50% is denatured and 50% is folded
Denaturation leads to a decrease in fluorescence intensity and increase in wavelength maxima
Ex. Scan for different concentrations of urea and take each point at which difference is the largest to form a sigmoidal curve

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17
Q

Explain how circular dichroism (CD) works

A

CD measures the differential absorption of left and right circularly polarised light by optically active media
De = eL – eR (e=molar absorbance)
Chiral molecules (handedness) are either L or R and are optically active
Circularly polarised light can be clockwise or anticlockwise
Polarised light interacts with chiral molecules, there is differential absorption
Chiral molecules absorb circularly polarised light in only one direction
Light is absorbed at diff wavelengths by the protein
Molar ellipticity (difference in absorption between left handed and right handed circularly polarised light)
If light is absorbed equally in both directions (eL=eR) get linearly (plane) polarised light, molar ellipticity=0
If light is absorbed more in one direction than the other (eL<eR), get elliptically polarised light
CD spectrum gives secondary structure information
Different secondary structure (alpha helix, beta sheet, random coils) have different CD signatures
CD spectrum shows molar absorption difference (of left and right handedness) vs wavelength

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18
Q

Explain the background of circularly polarised light

A

Light (electromagnetic radiation) is an oscillating wave of E-fields (electric) and B-fields (magnetic)
Focusing only on E-field
Oscillations can be Planar (horizontal and vertical components in phase, only in one plane) or Circular (horizonal and vertical out of phase, in 2 planes) or Elliptic (a mix)
Circular polarized light is 2 waves in different planes and one has a 90 degree phase shift
The phase shift can be -90 degrees or +90 degrees
Circular polarised light is chiral (handedness)
Left circularly polarized light = counter clockwise
Right = clockwise

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19
Q

Pros and cons of CD spectra

A

Pros:
CD spectrum recorded in the far-UV (190-240nm)
3D fold of secondary structure gives a particular CD signature
Allows monitoring of folding and unfolding
It can be used to monitor protein folding but also biological activity
Cons:
Lack of structural resolution (Only shows secondary structure, not at amino acid level)
Often over interpreted so need to combine with other techniques

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20
Q

Explain what the levinthal paradox is

A

Assume 3 conformations per amino acid in the denatured state (psi and phi angle allowed conformations)
For 100 amino acid protein there are 3^100 potential conformations
If the chain can sample 1x10^12 (trillion) conformations/sec it will take 2x10^28 years to reach the native state
There are too many different possible conformations for a protein to fold by a random search of conformations
A protein folds by following defined pathways
Most single domain proteins fold in milliseconds to seconds

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21
Q

Explain what makes a protein fold so fast and how intermediates can be trapped

A

A series of conformations are encoded in the protein sequence
Search for minimum energy conformation is not random
Direction towards native structure is a funnelled energy landscape
Free energy decreases down the diagram
At bottom (lowest free energy) is the native state
Energy landscape has local minima
Partially folded proteins (intermediates) can be trapped
This will slow down/inhibit folding
If hydrophobic groups are exposed, protein will aggregate or stick to other proteins

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22
Q

Explain how FRET works and when it is used

A

FRET (fluorescence resonance energy transfer) measures two state folding (no intermediate species D<–>N, single domain proteins)
Two fluorophores are labelled on molecules of interest
One fluorophore is the donor, one is the acceptor
Donor absorbs light at a specific wavelength and emits it at a longer wavelength in the visible spectrum
Acceptor has absorption spectrum that overlaps with emission spectrum of donor
Excite donor with specific absorption wavelength
Donor can transfer energy to acceptor when they are in close proximity (1-10nm)
Acceptor fluorophore is exited and emits light at its characteristic wavelength
EXAMPLE
Red fluorescent protein absorbs yellow light and emits red light (that has lower energy) - Acceptor
Green fluorescent protein absorbs blue and emits green - Donor
When close together, green donor will pass energy to acceptor chromophore and will emit in red

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23
Q

How is FRET used to determine protein folding?

A

FRET used for two state folding
In D state: separation between dyes is larger and transfer efficiency is small
In N state: separation is smaller and transfer efficiency is large
At equilibrium, still movement between D and N states (protein is folding and unfolding)
At D50 protein will be 50% denatured and 50% native
Denaturation is reversible, corresponds to jumps in FRET
No intermediate steps in FRET
Process is highly comparative

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24
Q

How is FRET measured with a device and what is the result of it in graphical form?

A

Stopped flow device:
Syringe with denatured and non-denatured protein
Are mixed together to initiate refolding or unfolding
Quartz cell and pass through fluorescence detector
Measure difference in signal between N and D state
Get single exponential relaxation curve for 2 state process (look at notes)
Can measure folding and unfolding rate to get delta G of protein
DeltaG=-RT(kfolding/kunfolding)

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25
Q

How do absorbance/fluorescence vs time curves for D to N states look like for 2 state and 3 state folding?

A

For 2-state (D-N): Single exponential curve
Subtract experimental data from theoretical exponential curve to get a straight line
If points are close to the X-axis fit is good
For 3 or 4 state proteins: add up multiple exponentials
Formation of intermediates occurs at different speeds
Fit data to double exponential curve (D-I-N) or fit curve to triple exponential curve (D-I-I-N) to see which one gives a straight line
Formation of intermediate occurs very quickly (4ms)
Formation of N state takes longer (400ms)
Clear separation of formation of intermediate and N state

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26
Q

Explain the principle of the F value analysis, what it is used for and assumptions

A

Experimental method to study the structure of the TS at residue level
Specific probes are used to distinguish between D and N state (CD, fluorescence, NMR)
Series of conservative deletion mutations that deletes sections of protein one by one
Removal of methyl groups
T to S, I to V (1methyl) V to A (2 methyl) I/L to A, F to L, X to A (3 methyl, more aggressive)
Any mutation should end up with alanine and not glycine as it has no side chain which affects conformation of the backbone
Compare differences in thermodynamics and folding rates between Wild type and mutant
Measure F values at different time points to make kinetic profiles
Assumptions: Assume that mutations don’t affect the structure of the N state and don’t create new interactions during folding

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26
Q

Explain transition state theory and folding rate

A

Occurs for all chemical reactions
Used to analyse two state folding
Free energy (G) vs reaction coordinate
N state has lower free energy than D state
Energy barrier from D to TS
Structure of TS tells us what interactions need to form to make the N state
TS has high energy: very short lived and unstable so can’t be characterised structurally
Folding rate is proportional to the exponential of the negative activation free energy (energy difference between TS and D state)
k =exp(-DeltaG(TS–D))
Use mutational analysis to determine two-state folding kinetics (and structure of TS)

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27
Q

How is F value analysis used for a 2-state folding process and how is the F value interpreted?

A

Mutations change the thermodynamic stability of N state
DeltaDeltaG(D-N) = DG(D-N(mut)) - DG(D-N(wt))
Folding rate (k) is related to activation free energy (energy diff between TS and D)
k = exp(-DeltaG(TS–D))
The faster the folding rate, the less stable
Some mutations can change the folding rates (k)
Measure folding rate of mutant and wild type and get difference in delta G
DDG(TS–D) = -RT ln (kwt /kmut)
The F value is the fraction of protein that achieved the native conformation at a specific folding intermediate during the folding process
Ratio between delta delta G TS-D and N-D
When F=1, mutated residue is native, that region is the folding nucleus of the protein (affects kinetic and thermodynamic stability), structured in TS
When F=0, mutated residue is non-native, unstructured in TS, is only formed in N state but not in TS (didn’t affect folding rate)

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28
Q

Explain the 2 competing folding pathways of D1pPDZ and how the F value is used for structural refinement of TSE?

A

PDZ domains are small domains
Adopt a six stranded beta sandwich fold with two alpha helices (bbbabbab)
D1pPDZ =PDZ domain of the D1 C terminal processing protease (D1p)
Has kinetic competition between 2 folding pathways: to native and to misfolding to off pathway metastable intermediate
Analysed by circularly permutated protein: change location of N and C termini
When mutants were produced, only got stable I state
N state is unstable so no advantage in forming it
Misfolded intermediate has alternative packing of N terminal of beta hairpin
TSE = transitional state ensemble, a protein that forms a stable non native intermediate (intermediate that doesn’t lead to formation of N state)

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29
Q

What Is the average protein concentration in a human?

A

Average MW of proteins in human cell = 50kDa
Average protein concentration = 20-30% (very high)
Average protein concentration (molar) = 4-6mM (varies with cell type)
But many will not reach more than 0-5mM

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30
Q

What different factors affect protein folding in vivo?

A

Protein is surrounded my many other proteins, lipids, polysaccharides in vivo
Crowding
Protein aggregation
Cellular components
Compartments

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31
Q

What are chaperones and what are the different types?

A

Proteins that (mostly) use ATP to bind unfolded or misfolded proteins and set them on the folding pathway again
Bacterial trigger factor: no ATP needed, ribosome associated, acts early
HSP70: requires ATP, eukaryotes, bacterial homologue/name in E. coli is DnaK, reverses denaturation/aggregation, works with HSP40 (DnaJ in E. coli)
Chaperonins (HSP60): have bacterial and eukaryotic homologues, large, multi-subunit, cage-like (Type I for bacteria, mitochondria, chloroplasts, Type II for archaea/eukaryotes)
HSP90 (eukaryotic): facilitates late stage folding of signalling proteins, unique regulatory role and induces active conformation
Nucleoplasmins: decameric, acidic, nuclear (mostly in nucleus), assembles nucleosomes
Protein disulphide isomerase (PDI)
Peptidyl-prolyl isomerase (PPI)
HSP70 and HSP60 are needed by E.coli to survive above 30 degrees

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32
Q

What is the structure of the ribosome and what does S mean?

A

E. coli ribosome is 25 nm diameter, 2.52 MDa (2,520kDa) in mass
Two unequal subunits that dissociate at < 1mM Mg2+
S is a unit to describe the speed at which a molecule migrates under significant force
Bigger molecules travel faster under significant force
50S = travels 50 micro metres per second under a force of 1 million G
30S subunit is 0.93 MDa with 21 proteins and a 16S rRNA
50S subunit is 1.59 MDa with 31 proteins and two rRNAs: 5S and 23S
Ribosomes are 60% RNA
20,000 ribosomes in a cell, 20% of cell’s mass

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33
Q

What are the three phases of protein synthesis?

A

Initiation: binding of mRNA and initiator aminoacyl-tRNA to small subunit, initiation factors bind, then large subunit binds
Elongation: synthesis of all peptide bonds, tRNA binds acceptor (A) and peptidyl sites (P)
Termination: termination tRNA recognizes stop codon

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34
Q

What is the trigger factor and why is it important in protein synthesis?

A

Newly synthesized proteins leave the ribosome through a narrow tunnel in the large subunit (peptidyl transferase centre, PTC)
When synthesis is still ongoing, nascent protein chains may form misfolded intermediates
These are dangerous to the cell: exposes hydrophobic regions leading to aggregation OR can be substrates for proteolysis
Trigger factor is an ATP dependent chaperone (in bacteria) + displays PPIase activity
It binds to ribosomal protein L23 and receives the synthesized protein
Allows protein to fold by ex. recognizing hydrophobic regions
If protein is very long more than one Trigger Factor binds to the protein

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35
Q

What is the structure of the trigger factor and individual domains?

A

N-terminal domain: Has some chaperone activity, L23 ribosome binding
Linker: links N and P domain
P domain: Peptidyl-prolyl activity, Auxiliary (some) chaperone activity
C-terminal domain: Main chaperone activity
Protein is constitutively expressed, but increased expression at low temperatures (when cell is cold shocked) - it is NOT a heat shock protein
Domains are flexible (rotation) and each domain is flexible on the inside (local flexibility)
Allows protein to bind substrates with other conformations

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36
Q

What are heat shock proteins?

A

Heat shock proteins are one of the biggest families of chaperones
Are expressed at low levels normally in the cell
Are overexpressed when the cells are under high temperatures
Prevent aggregation and misfolding
Bind to nascent polypeptides to prevent premature folding
Facilitate membrane translocation/import by preventing folding prior to membrane translocation
Facilitate assembly/disassembly of multiprotein complexes (ex. nucleosome)

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37
Q

Explain how trigger factor, DNaK and GroEL work together in a chaperone network

A

In bacteria
Protein is synthesized and bound by trigger factor
Then chaperone DnaK (Hsp70) in bacteria binds protein from trigger factor and allows it to fold
If DnaK fails it is bound by chaperone GroEL

38
Q

Explain the cycle of how HSP70 and J-domain proteins interact

A

HSP70 is an ATP binding protein
N terminal nucleotide binding domain (NBD) that binds ATP
C-terminal substrate binding domain (SBD) beta and alpha
Alpha and beta are not allowed to interact when protein is in the ATP form
low affinity for substrates in ATP form (like open spring)
Hsp40 (J-domain proteins)
More than 40 J-proteins in the human genome
Modulates ATPase activity of Hsp70
Turns ATP to ADP in Hsp70
Hsp70 in ADP form traps binds the ligand/substrate with high affinity (like spring closing)
Hsp70 only binds a small region of the protein
Hsp70 is the most abundant chaperone and contains many orthologues
Allows protein to fold
Nucleotide exchange factor ex. GrpE
Exchanges ADP for ATP
Release of the substrate in the folded form
Cycle restarts

39
Q

What is the structure of GroEL/GroES?

A

Multiple heptameric rings
Each monomer in heptameric ring is 60kDa
Except top ring, has monomers of 10kDa
2 monomeric rings form an internal chamber that binds the ligand
This isolates protein from crowded medium of the cell and allows the protein to refold
GroEL: active state (middle ring). Cis monomer so it is near GroES. Elongated to form a bigger chamber
GroEL: resting state (bottom ring). Trans monomer - it is far from GroES
GroES: top ring/cap, smaller
look at image in notes

40
Q

What is the mitochondrial form of GroEL/GroES?

A

GroEL/GroES: prokaryotic
HSP60/HSP10: mitochondria/chloroplast

41
Q

Explain the mechanism of the active and inactive states of GroES/GroEL

A

Inactive state (trans) without GroES:
Small chamber
Exposed hydrophobic patches: allows unfolded protein to bind to at least 2 hydrophobic patches

Active state (cis) with GroES:
Hydrophobic patches are hidden in GroEL –> large, hydrophilic cavity
Allows protein to fold on its own
Can fold proteins up to 60kDa

42
Q

What is the GroEL/GroES cycle?

A

Anti cooperative binding of ATP (fast)
Only one of the two heptamers of GroEL will bind ATP at a time
Mis/unfolded polypeptide binds (slow)
GroES binds (very slow) and pushes unfolded protein into the chamber
Then other heptametic ring binds ATP in trans
ATP –> ADP to relase 7Pi
Improperly folded protein binds to the other chamber
Then folded protein + GroES + 7ADP are released
Turn 180 degrees and cycle starts again
GroES can only bind one GroEL
Look at diagram in notes

43
Q

How does GroEL/GroES work on E. coli proteins?

A

85 cytosolic proteins are are strictly dependent on GroEL/ES to fold
These proteins usually have more complex tolpologies
Many are alpa/beta proteins
some are a/b barrels that are stabilised by long-range interactions

44
Q

What is Hsp90?

A

Hsp90 is an abundant, very flexible, highly dynamic protein
Binding of substrates is very transient and requires many factors
Acts mainly at late stages of substrate folding
Stably dimerizes via its C term domain
Dimerises transiently via its N term ATPase domain - when ATP is bound
Different co-chaperones help binding to different ligands
Hydrolysis of ATP to release folded ligand
PTMs (e. g. phosphorylation, acetylation) affect its functional state
Details of substrate binding (and mechanism) still under study

45
Q

What is protein disulphide isomerase (PDI) and how does it function?

A

PDI catalyses formation and exchange of disulfide bonds
Shuffles disulfide bonds and allows protein to explore different conformations before it forms the native disulfide bonds (similar to anfinsen experiment)
Binds exposed hydrophobic regions
Allows protein to find most thermodynamically stable pairs
Has broad substrate specificity - diverse disulphide containing proteins
Reduced PDI (thiol) generated by oxidised glutathione GSH breaks misfolded disulfide and leads to formation of oxidsed PDI (which is regenerated by reduced glutathione GSSG)
Breaking of disulfie allows protein to form a different disulfide
Cysteines in conserved motif (CxxxC)
Broad hydrophobic cleft: peptide binding and chaperone activity

46
Q

What is peptide propyl isomers (PPI)?

A

In proline, cis trans isomerization is rate limiting in the folding of proteins (need to have correct conformation)
PPI binds to X-proline bond and accelerates cis-trans isomerisation by 300-fold
Twists the peptide bond so that backbone C, O, N atoms are no longer planar

Use HSQC spectrum to determine if protein is correctly folded
Amino acids that are next to proline can have more than one conformation

47
Q

Give examples of proteins that are degraded in the cell and their half-life

A

In the cell, proteins are degraded at different rates
Rate depends on the stability and function of protein
Ornithine decarboxylase: half life of 11 minutes
Produces antioxidants: polyamines, important for DNA stability, cell division
Produces compounds that increase cell growth and reduce apoptosis
Can be dangerous to the cell so protein is very tightly controlled
P53 had half life of 5-20minutes
Can cause cell cycle arrest/apoptosis
Albumin half life of 3 weeks
Osmotic pressure in serum cells
Carrier of metabolites
Haemoglobin lasts as long as red blood cell (a month)
Structural proteins
Inert, non catalytic
In structures that protect them from degradation
Ex. gamma crystallin in eye lens (70 years), collagen (110 years)
Degradation by CHAPERONES

48
Q

What is protein turnover and what are the different systems that are responsible for it?

A

Protein turnover is the balance between synthesis and degradation
Ubiquitin proteasome system (UPS) degrades cytoplasmic and nuclear proteins
Lysosome endosome system degrades ER proteins, extracellular, cell surface
Aggresome
Catabolism: synthesis < degradation
Anabolism: synthesis > degradation

49
Q

What is the structure of ubiquitin and how does it attach to substrates?

A

Ubiquitination: Most important mechanism to regulate protein degradation
Ubiquitin: small protein of 76 amino acids, used to tag proteins for degradation in proteasome pathway
Degrades cytoplasmic and nuclear proteins
Ubiquitin attaches to substrate via C-terminal glycine 76
Proteins are linked to ubiquitin via isopeptide bond between
carboxyl of C-terminal glycine 76 and amine side chain of lysine in substrate

50
Q

What are the different functions of the ubiquitin lysines? How are polyubiquitin chains formed?

A

Ubiquitin has 7 lysines that are responsible for different cellular functions
G76 binds substrate
K48 polymerises Ub
Lysine 48 Ub1 binds to C-terminal G76 of Ub 2 to form polymer
Chain of 4 Ub = signal for protein to be degraded
Polyubiquitin chains: Can form linear or branched patterns

51
Q

What is the mechanism of attaching a ubiquitin to a target molecule?

A

Ubiquitination at the C-terminal of Gly76
E1 (ubiquitin activating enzyme) uses ATP to adenylate Ubiquitin, release of Ppi
E1 forms thioester bond with ubiquitin, release of AMP
Ubiqutin transferred form E1 to E2 (ubiquitin conjugating enzyme)
Complex is recognized by E3 (ubiquitin protein ligase)
E3 complex binds the target
E3 ligases have specificity for certain motifs that allows it to bind the target
A protein tagged with a single Ub molecule becomes a substrate for other ligases to attach additional Ub molecules

52
Q

Give examples of diseases that use E3 ligases

A

More than 600 E3 ligases in the human genome
Parkin: E3 ligase, involved in destruction of alpha-synuclein (aS)
Knockout of parkin = accumulation of aS leads to Parkinsons disease
HPV: produces E3 protein that targets p53 in the host
90% of cervical cancers are related to this
E3 ligases are important drug targets

53
Q

Explain the ubiquitin-proteasome system (UPS)

A

DNA –> RNA –> Ribosome –> Folding –> Native protein –> Denaturation/damage –> Misfolded –> Hsp40/Hsp70 assist folding
If chaperones are not successful in refolding the protein: Chip (E3 ligase) binds to chaperone-protein complex and ubiquitinates it
Ubiquitination is recognized by region of proteasome
Cleaves ubiquitin
Misfolded protein into chamber where it is degraded

54
Q

What is the function of the proteasome?

A

Large proteolytic complexes in eukaryotes, archaea, bacteria
In eukaryotes: are found in nucleus and cytoplasm
Degradation process gives peptides 7-8 amino acids long

55
Q

What is the structure of the proteasome?

A

Cylindrical complex
Core particle (blue): 20S, 4 stacked heptameric rings (abba) forming pore/chamber
Regulatory particle (red): 19S, regulates entry to destruction chamber, recognizes ubiquitin, sometimes uses ATP
Each ring has 7 domains/proteins

56
Q

What is the proteasome mechanism in eukaryotes?

A

7 beta subunits/isoforms
beta 1, beta 2, beta 5 contain N-terminal catalytic threonines, 6 active sites
Before CP autocatalytic maturation of precursor, these are protected by pro-peptides
Threonine in active site are in different conformations/environment so have different substrate specificities
3 proteolytic activities: chymotrypsin like, trypsin like, peptidyl glutamyl peptide hydrolysing like
Regulatory particle (RP) caps 20S CP: recognizes and unfolds ubiquitinated proteins before degradation
RP removes Ub from substrates to recycle
Some RP’s use ATP hydrolysis to provide energy for protein unfolding

57
Q

What is the proteasome mechanism in bacteria?

A

All 14 beta subunits (same isoform) have proteolytic activity
Bacteria don’t have ubiquitin so simpler structure
Not all bacteria have proteosomes
Mycobacteria have ubiquitin like protein (Pup): binds so proteasome substrates, is essential for degradation
Inner two rings of seven beta subunits
Seven protease (x2) active sites
Protein enters central pore for degradation
Outer two rings contain seven alpha subunits
A gate through which proteins enter the barrel
Are controlled by binding to cap structures or regulatory particles - recognize protein substrates and initiate degradation process

58
Q

What external factors can affect protein quality?

A

Oxidants in the air, ozone, nitric oxide, carbon monoxide
Radiation like UV
Ionizing radiation

59
Q

How do reactive species affect protein quality/induce misfolding?

A

Reactive species can modify amino acids within proteins, damage prosthetic groups or oxidise key transition metal centres
Introduces extra charges/changes charges = increases local hydrophilicity
Ex. in hydrophobic core or surface
Two of the same charges next to each other = unfolding
Can modify other amino acids leading to partial unfolding and exposure of hydrophobic regions leading to degradation
E3 ligases recognise degrons (degradation motifs)

60
Q

What internal factor can affect protein quality?

A

Oxygen is the final acceptor in the ETC (respiration) to form water
Oxygen reacts with leaked electrons from respiration to form superoxide radicals (O2-)
Superoxide radicals react with/reduce Iron or Copper ions in the cell (Fe3+ –> Fe2+)
Superoxide radicals interacts with protons to form hydrogen peroxide, H2O2
H2O2 reacts with Fe2+ and Cu+ to form highly reactive hydroxyl radicals (OH)

61
Q

Explain the two step response of cells to oxidative stress/protein damage

A

Cells are often exposed to low level of oxidative stress/protein damage
A large stress leads to accumulation of damaged proteins (bad for the cell)
Cells have a two-step transient response
0.5 - 5h after oxidative stress exposure: capacity to degrade oxidised proteins increases (protein synthesis independent) and reduction in ATP dependent proteolytic capacity (broad response)
5h - 48h after: protein synthesis dependent increase in proteolytic capacity and ATP stimulated proteolytic capacity (more specific response)

62
Q

How does dissociation of the proteasome allow response to protein damage?

A

Dissociation/disassembly of 26S proteasome into free 19S regulators and 20S core proteasomes
20S proteosome without RP allows for indiscriminate protease activity in first 5 hours
3-5h after: 26S proteasome re-forms from free 19S regulator and 20S core proteasome
Chaperones are involved in process: Hsp70 stabilises 19S regulator after dissociation from 20S and reassembles functional 26S
In yeast: Ecm29 binds 19S regulator after dissociation, required to degrade proteins

63
Q

What is the related autophagy pathway?

A

Different pathway to degraded proteins
Basal/micro autophagy: non-selective, bulk clearance of misfolded proteins
Defective organelles or proteins are recognized by lysosome and degraded
Ex. Starvation induced
Vs aggresome-autophagy pathway is specialised

64
Q

What is the aggresome-autophagy pathway?

A

Specialized, selective clearance of misfolded or aggregated proteins
Small amount of misfolded proteins –> refolded by chaperones OR tagged with Lys48 linked polyubiquitin chains –> degradation by proteosome
If chaperone and proteosome systems are overwhelmed –> aggregated protein–> cytotoxicity
If amount of aggregated protein is too high –> PD linked E3 ligase parkin + E2 enzyme –>protein ubiquitinated using K63 (instead of K48) –> recognized by HDAC6 –> binds dynein motor complex –> transport towards MTOC to form aggresome
Binding to p62 –> aggregate is surrounded by autophagic membranes to form autophagosome –> fuse with lysosome for degradation

65
Q

What is chaperone mediated autophagy in lysosomes?

A

Lysosomes have low pH (pH 5.5) and contain different proteolytic enzymes (serine proteases, aspartic proteases)
Substrate containing specific motif (KFERQ) is recognized by a homologue of Hsp70 (Hcp70)
Substrate is recognized by receptor on surface of lysosome
Another chaperone (lysosomal Hsp70) pulls the substrate into the lysosome where it is degraded
Only happens to proteins that contain specific motif

66
Q

How do misfolded proteins lead to diseases via the formation of off-pathway intermediates?

A

Misfolding and aggregation of proteins are associated with diseases
Ex. neurodegenerative diseases (alzheimers, parkinsons), non-neuropathic diseases (diabetes type II)
Synthesis of a protein by ribosome –> unfolded state –> native state –> can form crystal, fibre or oligomer
Unfolded state –> disordered aggregate –> chaperones help to form directly or lysosome/aggresomal degradation
Off pathway intermediates: unwanted species that lead to formation of amyloid fibrils
Amyloid fibrils are difficult to remove from cells
Cause mechanical damage to cells + cell lysis
Lead to disease

67
Q

What are amyloid fibrils?

A

Amyloid fibrils are insoluble protein aggregates that accumulate in extracellular space
Can be functional: bacteria and fungi use amyloid fibrils to protect surfaces and interact with other species, important in biofilm formation
Or can cause disease: neurodegenerative diseases (Alzheimer’s, Parkinson’s)
Start from different precursor proteins but have same structural features
Not all proteins form fibrils in vivo, some only form aggregates which can lead to neurological (accumulate in brain) or non-neurological diseases

68
Q

Give 3 examples of diseases that involve amyloid fibrils

A

Beta-amyloid: beta amyloid fibrils cause Alzheimer’s disease. Beta amyloid is derived from cleavage of larger amyloid precursor protein
Alpha-synuclein: Forms fibrils in Parkinson’s. Aggregation leads to formation of Lewy bodies
Prions: infectious proteins that can cause normal proteins to misfold and aggregate to amyloid fibrils

69
Q

What is Alzheimer’s disease and what are the 2 main causes (brief)?

A

Associated with aging: 1 in 14 people over age of 65 and 1 in 6 over age 80
Leads to mental deterioration and death
Cause 1: Amyloid beta peptide
Cause 2: Tau protein

70
Q

How does Tau protein lead to Alzheimer’s disease?

A

Tau: tubulin associated unit, important in function of axons, very long
Two conformations: paired helical fibril and straight fibril
More than 100 tau fibrils in different conformations
In Alzheimer’s: Tau is hyperphosphorylated and aggregates to form neurofibrillary tangles

71
Q

How does amyloid beta peptide lead to Alzheimer’s disease?

A

Protein degradation and chaperone mechanisms become less efficient over time –> more protein aggregation
Beta-amyloid is produced by cleavage/proteolysis of larger amyloid precursor protein (770aa) (by beta and gamma secretases)
In Alzheimer’s: imbalance in production/degradation of beta-amyloid. Abnormal processing of APP leads to production of beta-amyloid-42
Beta-amyloid forms insoluble plaques in brain tissue and in spaces between neurons in brain –> neurofibrillary tangles and dead neurons
Are the plaques the cause Injection of Ab Peptide in monkeys induced the disease
Doesn’t seem to be an infectious disease
Treatments: Levanemab and Aducanumab to stop aggregation (Mab’s)

72
Q

How is Parkinson’s disease caused by alpha synuclein?

A

Alpha synuclein function: Release and docking of exocytosis, formation of presynaptic vesicles, Regulating release of neurotransmitters between neurons, Abundant in dendrites in neurons (close to synapses)
Misfolding of alpha synuclein leads to aggregation which is toxic
Forms Lewy bodies (intraneural aggregates)
Inhibits progression of vesicles from ER to Golgi
Lyses mitochondria
Permeabilize membranes
Alpha synuclein aggregate can be secreted + endocytosed so disease can be passed to other cells
Can also aggregate in other organs (heart tissue, blood cells): called alpha-synucleinopathies

Alpha synuclein can bind membranes
Exists in 2 conformations: disordered in cytoplasm OR ordered bound to membrane and forms helices at N-terminal

73
Q

What are prion diseases and give some examples of diseases?

A

Prion diseases cause transmissible spongiform encelopathies (TSEs)
Neurodegenerative disease in humans + animals caused by prion proteins
Don’t contain genetic material (DNA/RNA)
Contain misfolded version of prion protein (PrP)
Examples: Scrapie (sheep), Bovine spongiform encephalopathy (BSE), Creutzfeldt Jakob disease

74
Q

How can prion diseases be transmitted?

A

Transmission of protein between individuals or species
Ex. Eating contaminated meat lead to outbreak of BSE in cattle and CJD in humans

75
Q

What is the structure and function of the normal prion protein (PRPc)?

A

280 aa
Membrane anchored
Widespread protein observed only in mammals
Prion proteins are found in brain
Formation of axons/dendrites, neuronal homeostasis, cell signalling/adhesion/protective role against stress
Soluble
40% alpha helix
3% beta sheet
Protease sensitive

76
Q

What is the structure and effect of the abnormal prion protein (PRPSc)?

A

Misfolded version of prion protein
Forms aggregates and fibrils in the brain
Sc= scrapie, prion disease in sheep
Chemically identical to PrPC (same sequence)
Stable conformational variant of PrPC
Self propagating: can induce conversion of PrPC to PrPSc
Insoluble
30% alpha helix
45% beta sheet (common for fibrils)
Protease resistant (proteolysis removes 67aa at N-terminal to give PrP)

77
Q

How does accumulation of PrPSc lead to tissue damage and what effects does this have?

A

Accumulation of PrPSc in brain leads to formation of holes and gives sponge-like appearance
Symptoms are cognitive decline, motor dysfunction
Leads to diseases: Familial CJD, GSS syndrome, Fatal Familial Insomnia
Mutation can increase likelihood of spontaneous conversion, which can convert other proteins

78
Q

Explain the strain specificity and infections in terms of PrPSc proteins

A

Different strains of PrPSc have different pathologies and structures
Infection between species that are close to each other: Mouse PrP can infect hamster (or cows to humans)
Scrapie (from sheep) can’t infect humans

79
Q

What is Creutzfeld-Jakob Disease?

A

CJD is most common prion disease in humans
Variant of CJD (vCJD) from infected meat or blood transfusions
CJD disease is VERY uncommon (2 people per million)
Only 2-5% get vCJD from infections
80% CJD form sporadically

80
Q

Explain the difference between amyloid fibrils, amyloidogenic precursors (monomers) and pre-fibrillar oligomers

A

Amyloid fibrils: stable, resistant to detergents/denaturants, cause cellular and neuronal death
Amyloidogenic precursors: transient, non-toxic, unstable
Pre-fibrillar oligomers: most toxic species, affect mitochondria, plasma membrane, trigger apoptotic mechanisms, very unstable and heterogenous in terms of structure, difficult to isolate/study

81
Q

How do amyloids form a cross-beta sheet?

A

Amyloids form a beta-sheet: hydrogen bonds form between adjacent strands
Form a cross-beta sheet: beta strands are oriented perpendicular (90 degrees) to fibril axis and form cross-sectional pattern
Intersheet distance: 10 angstroms, varies according to sequence
Interstrand distance: Contacts between strands in the same sheet, is constant
Forms stable + ordered structure = insoluble fibrils
look at image in notes

82
Q

Explain the steric zipper model of amyloid fibrils

A

Multiple beta sheets stack on top of each other
Side chains protrude inside the two beta sheets like a self complementing steric zipper between sheets
Forms dry spaces like small hydrophobic cores
Within each beta strand, every segment is bound to two neighbouring segments through stacks of backbone and H-bonds
Stabilizes fibrils

83
Q

Explain the conjectural plot of amyloid fibrils

A

Monomers have certain free energy
Energy is gained in formation of a fibril
Fibrils only form at high monomer concentration as energy barrier is very high
Delta G of dissolution is very high so fibrils are hard to dissolve

84
Q

What are intrinsically disordered proteins (IDPs) and what diseases are they related to?

A

Make up 30% of eukaryotic proteins
Some of them are related to aggregation diseases
Complement function of folded/ordered proteins
Connection to neurodegenerative diseases
Abeta - alzheimers
Alpha-synuclein - parkinsons
Tau - tauopathies
Prion protein - prion diseases
Cancer - p53
Intrinsic disorder can affect different levels of structural organisation
Whole proteins can be disordered
Or certain protein regions can be disordered
Disordered to different degrees
Are in more than one conformation at a time
Structural heterogeneity

85
Q

Explain the energy landscapes of ordered Vs IDPs

A

Ordered: well defined folding landscape
Funnel shape
High energy conformation –> conformation of minimal energy (native/folded state)
IDPS: flat landscape composed of multiple minima
Fluctuating conformations of comparable free energy
Look at image in notes

86
Q

What are the 4 different states of native proteins?

A

Random coil: no native/non native interactions
Pre molten globule: some secondary structure elements but many unstructured elements
Molten globule: expanded form of native state (secondary structure is formed but no tertiary contacts)
Native/folded
Size exclusion chromatography: 4 different states of native proteins will come out of column at different times

87
Q

What are the sequence properties of IDPs?

A

Folded: have large hydrophobic amino acids (found in hydrophobic cores)
IDPs: NO compact structure
Polar/charged amino acids
= low hydrophobicity and low driving force for protein compaction/hydrophobic core formation
= High net charge so electrostatic repulsion
Contain residues that break secondary structure (ex. proline)
Look at diagram in notes

87
Q

What different structural techniques can or can’t be used to analyse IDPs?

A

Crystallography needs crystals IDP’s don’t crystallise
Proteins are too flexible for EM
NMR is used to see behaviour of amino acids in solution

88
Q

What are unfolded Vs misfolded proteins

A

Unfolded: random coil, premolten globule, molten globule
Misfolded: amyloid-like fibrils made out of off-pathway interactions

89
Q

How is the structure of PrP characterised by NMR

A

PrP: Unstructured N-terminal, folded C-terminal
Helical structure is clear
Don’t see N-terminal residual structure (small regions of beta strands and polyproline) in NMR

89
Q

How is NMR used to characterise IDPs?

A

IDP’s can be recognized in a H1-N15 HSQC spectrum
Each peak corresponds to amino acid in a particular chemical environment
Limited dispersion: Amino acids in protein are very flexible and are not in a unique chemical environment
Sharp peaks: long T2 relaxation
NMR can identify residual secondary structure in IDPs
Ex. Polyprolines, residual beta strands, residual alpha helices
Look at image in notes

90
Q

How is CD used to characterise IDPs?

A

Circular dichroism: to measure level of structure of IDP
Specific spectrum for alpha helix, beta sheet and random coil
Plot a double wavelength CD plot
Measure at 200nm (minimum for random coil) and 222nm (minimum for alpha helix)
Separate pure random coil (green) from residual structure (pre molten globule conformation) (purple)
Polyprolines have their own spectrum (similar to RC)

91
Q

Why are IDP interactions difficult to characterise?

A

Form fuzzy complexes
IDPs can bind to more than one place in the protein
So very difficult to characterise interaction
Complex won’t crystallize and no noise in NMR
IDP is swarming around surface of folded protein