Protein Misfolding / IDPs

Question 1

Alzheimer’s

Answer 1

• brain tissue contains amyloid plaques forming neurofibrillary tangles surrounded by dead and dying neurons
• plaques of amyloid B-peptide derived from amyloid B precursor protein by proteolysis
• injection of the peptide into old monkeys induces disease : evidence that plaques are the cause
• but is it infectious?

Question 2

Tau protein

Answer 2

• normal form is part of microtubule
• also features in the tangles
• tau accumulation correlated with disease progression and severity

Question 3

Parkinson’s

Answer 3

• aggregation of a-synuclein
• abundant in terminal of neuronal cells helping neurotransmitter communication
• membrane bound synuclein can ofrm amyloid fibirils and Lewy bodies
• Lewy bodies are the inclusion bodies – abnormal aggregations of protein – that develop inside nerve cells

Question 4

a-synuclein

Answer 4

• normal protein functions in vesicle docking, redoxi shuttle reducing membranes, influences mithocondrial morphology, etc
• toxic protein breaks membranes causing ion influx, breaks mitochondria, causes oligomeric intermediates and aggregation

Question 5

Prion Diseases

Answer 5

• infectious protein disease

- protein misfolds into amyloid and goes into a new cell where it acts as a template for new amyloids

Question 6

Prion Protein

Answer 6

• Prp
• membrane anchored with no known function
• mouse knockouts normal
• 2 conformational states: PrpC and PrpSC (misfolded)
• PrP is insoluble, more B-sheet, and protease resistant

Question 7

Amyloid Pathway

Answer 7

1. native state
2. amyloidogenic intermediate
3. oligomers
4. protofibrils
5. amyloid fibrils

Question 8

Amyloidogenic precursors

Answer 8

• transient and elusive
• therapeutic targets
• nontoxic

Question 9

Amyloid Fibrils

Answer 9

• stable and highly resistant

- not most toxic but cause neural death

Question 10

Pre-fibrilar oligomers

Answer 10

• most toxic species
• bind and disrupt membranes
• small enough to move around and interact with cellular species

Question 11

Cross B-spine

Answer 11

• common amyloid feature
• tightly packed B sheets
• fiber propogate into octogonal strang to strand association
• cross B conformation with respect to fiber axis

Question 12

Steric Zipper

Answer 12

• tight dry interface between 2 sheets
• double beta sheet with each sheet formed from parallel segments stacked in register
• side chains form dry self complementing steric zipper
• common amyloid motif

Question 13

Intrinsically Disordered Proteins

Answer 13

• functions complementing ordered proteins
• disordered to different degrees
• intermolecular interactions
• remarkable binding promiscuity
• ‘hubs’ for protein protein interactions because of their tendency to interact and ability to bind many things

Question 14

IDP Energy Landscape

Answer 14

• multiple minima with no dominant global minimum

- can jump between meta stable conformations

Question 15

Types of Protein States

Answer 15

1. ordered
2. molten globule (individual elements structured with collective disorder)
3. pre molten globule (primarily disordered some secondary structure)
4. random coil (completely disordered)
   - distinguished via SEC as more disorder = larger size

Question 16

Sequence of IDPs

Answer 16

• low hydrophobic residues to prevent aggregation
• charged and polar residues present for solvent interactions/electrostatic repulsion
• needed for the absence of compact structure : low driving force

Question 17

Structural Approaches

Answer 17

• crystallography: IDP impossible to crystallize/many potential conformations
• NMR: measure observables but still limited

Question 18

Residual Secondary Structure

Answer 18

• a helices
• extended B sheets
• poly prolines (consecutive proline residues - type of structure without a pattern forming)

Question 19

IDP Nature of the Prion Protein

Answer 19

• both folded and unfolded segments

- clearly seen in graphs displaying secondary structure elements

Question 20

Protein-Protein Interactions

Answer 20

• binding promiscuity makes them hubs
• can form ultrahigh affinity complexes without need for defined protein protein interface
• two proteins remain disordered with stable interaction
• study with FRET or NMR to map residues

Question 21

Fuzzy Complexes

Answer 21

• Fuzzy complexes are protein complexes, where structural ambiguity or multiplicity exists and is required for biological function
• Structural multiplicity usually underlies functional multiplicity of protein complexes

Question 22

Protein-Membrane interactions

Answer 22

• a synuclein
• regulating synaptic vesicle trafficking as a chaperone of SNARE complex assembly
• soluble protein becomes molten globule binding to membrane

Question 23

Spider Silk

Answer 23

• disorder to order transition
• silk protein stored as higher oligomeric assemblies
• exposure to shear/salting out promotes partial unfolding and controlled fiber assembly
• exposes hydrphobic surface encouraging aggregation and alignment of elements
• repetitive sequence becomes ordered into silk
• conformation change to amyloid like fiber