Protein: Folding, Structure, Function, Disease

Front 1

Protein-misfolding and aggregation diseases

Back 1

1. improper folding

-ALS, cystic fibrosis, Marfans

2. Not stable enough to perform normal function

-cancer

3. Improperly trafficked

-familial hypercholesterolemia, α1-antitrypsin deficiency

4. forms insoluble aggregates

-Alzheimer's, type II diabetes, Parkinson's

Front 2

protein folding equilibrium

Back 2

equilibrium bw/n unfolded and folded

-folded can lead to aggregation → LOF or GOF

-unfolded can also be degraded → LOF

Front 3

Protein Structure

Back 3

-structure → function

-prdict function from 3D structue

-design drugs based on structure

-some natively unfolded (no stable structure in soln) → take on structure of receptor (undergo unfolded → folded transition)

Front 4

number of possible aa arrangements

Back 4

=N^L

N= # aas = 20

L = chain length

→ huge diversity! (even in short peptides)

Front 5

aa structure

Back 5

Cα bound to:

1. COO-

2. NH3+

3. R

4. α-proton

-chiral → all optically active except Gly

-enantiomers: (nonsuperimposable mirror images) L form only in euk proteins → rotates light L

Front 6

NP, aliphatic aas

Back 6

Gly

Ala

Pro

Branched:

Val

Leu

Ile

Front 7

Gly,

Back 7

G

Front 8

Ala,

Back 8

A

Front 9

Pro,

Back 9

P

*secondary amine

Front 10

Val,

Back 10

V

Front 11

Leu,

Back 11

L

Front 12

Ile,

Back 12

I

Front 13

Phe,

Back 13

F

Front 14

Tyr,

Back 14

Y

Front 15

Trp,

Back 15

W

Front 16

Asn,

Back 16

N

Front 17

Gln,

Back 17

Q

Front 18

Ser,

Back 18

S

Front 19

Thr,

Back 19

T

Front 20

Met,

Back 20

M

Front 21

Cys,

Back 21

C

Front 22

Asp,

Back 22

D

Front 23

Glu,

Back 23

E

Front 24

Arg,

Back 24

R

Front 25

Lys,

Back 25

K

Front 26

His,

Back 26

H

Front 27

aromatic aas

Back 27

Phe-NP

Tyr - more polar

Trp - more polar

Front 28

polar uncharged aas

Back 28

Asn

Gln

Ser

Thr

Front 29

sulfur containing aas

Back 29

Met

Cys

Front 30

Charged aas

Back 30

Negative (acidic):

Asp

Glu

Positive (basic):

Arg

Lys

His

Front 31

disulfide bonds

Back 31

2 Cysteine (-SH) ↔ cystine (-S-S-)

reduced ↔ oxidized

Front 32

Asp pKa

Back 32

3.9

Front 33

Glu pKa

Back 33

4.1

Front 34

His pKa

Back 34

6.0

**general acid base in many physio rxns

Front 35

Cys pKa

Back 35

8.4

Front 36

Tyr pKa

Back 36

10.5

(almost always protonated at physio conds)

Front 37

Lys pKa

Back 37

10.5

(almost always protonated at physio conds)

Front 38

Arg pKa

Back 38

12.5

(almost always protonated at physio conds)

Front 39

Structural lassification of proteins

Back 39

1. globular

-compact

-mainly stabilized by -phobic interactions

-Hb, Mb

2. fibrous

-linear

-repeating unit structure

-collagen, elastin

3. transmembrane

-adenylyl cyclase

Front 40

levels of globular protein structure

Back 40

1o-linear aa sequence

2o-regions of polypeptide chain stabilized by repeating patterns of H-bonding

3o-folding of 2o structure into unique 3D shape

4o- 2+ subunits (not all proteins)

-homo or heteromltimers

Front 41

peptide bond formation

Back 41

Front 42

peptide bonds

Back 42

-bond hybridization bw/n major and minor form → planar

-almost always trans (C α1 trans to C α2)- sterics

Front 43

secondary structure

Back 43

1. α-helix

2. ß-sheet

3. ß-turns (reverse turns)

Front 44

α-helix

Back 44

-all residues H-bond:

--carbonyl O and amide H 4 residues down chain

-413 helix → 4 residues in loop, 13 atoms in loop

-R groups project outward

Front 45

ß-sheet

Back 45

-inter-strand H-bonding (C(O) and NH)

-tend to twist into ß-barrel

-R-groups alternate above and below plane perpendicular) → more bulky R groups b/c less sterics

1. antiparallel:

-more stable → H-bonds closer and more linear

2. parallel

Front 46

reverse turn (ß-turn)

Back 46

(turn reverse turn)

-polypeptide changes direction 180o

-short:

--70% <7 residues

--most common= 2 residues

-occur at surface of molecule

-R groups can point in same or opposite directions

Front 47

tertiary structure

Back 47

all noncovalent structure contained in folded protein (and disulfide bonds)

Front 48

globular protein solubility

Back 48

-fold so that -phobi residues are on inside and philic on outside → increased solubility

-(phobic core densely packed)

Front 49

protein-protein interactions

Back 49

-intramolecular → protein folding

-intermolecular → fibrils, aggregation

-widespread (al cellular levels)

-aberrant interations → disease:

atheroscelrosis, diabetes, Alzheimer's. Parkinson's, mad cow, Creutzfeld-Jacob

Front 50

Protein folding

Back 50

-all info for folding in a sequence

-cooperative (too fast to be random)

-chaperone proteins:

--assist in forming appropriate disulfidde bonds, intercovert prolyl cis/trans peptide bonds, protect -phobic groups to prevent aggregation

Front 51

entropy vs hydrophobic effect

Back 51

-entropy of polypeptide chain favors unfolded state

-hydrophobic effect favors folded state → major force responsible for protein folding

--increasing size → decreasing surface to buried residue ratio

--increases entropy of water= major driving force!! (reduces amount of "ice"-like structure of water

Front 52

Native state stabilization

Back 52

balance of:

1. forces that favor folding:

-hydrophobic collapse

-intramolecular H-bonds, Van der Waal's

2. forces that favor unfolding:

-conformational entropy

-H-bonding to solvent (water)

Front 53

molecular chaperones

Back 53

-majority fold w/o (cotranslational manner)

proteins that need help:

-chaperones bind to nascent(emerging) polypeptide and stabilize (bind -phobic residues) preventing improper intra/er -phob interactions

-many types

-some do stuff other than folding (protein assembly, transport, refolding)

Front 54

Protein misfolding diseases

Back 54

misfolded → precipitate in cross-ß structure= amyloidoses

→ athersclerosis, diabetes, Alzheimers, Parkinson's, Creutzfeld-Jacob, bovine spongiform encaphalopathy (mad cow)

Front 55

Prion diseases

Back 55

PRoteinaceous Infectious virON

-does not carry genetic material

-causes:

1. Mad cow

2. Creutzfeld-Jacob

3. Spongiform encephalopathies

-transmission: caused by abnormal isoform of synaptic glycoprotein

-spontaneous: single point mutation, majority

-results in amyloid formation → normal tissue structure disrupted

Front 56

key event in pathogenesis of Prion diseases

Back 56

conformational change in prion protein caused by injection of prion virus of PrP(SC) stimulating protein?:

PrP(C) (α-helical) → PrP(Sc) (ß-sheet→ amyloid cross formation)

-PrP(c) exists in equilibrium w/ unfolded and ß-sheet conformation

-if increase [ ]ß-sheet conformtation → oligimerization = PrP(SC) → cleavage of aggregates → → continues pulling equilibrium toward ß-sheet and oligimerization and aggregation → gain of toxic activity + loss of bio function

Front 57

PrP(C)

Back 57

cellular

-monomeric

-soluble

-protease sensitive

-predominantly α-helical

Front 58

PrP(SC)

Back 58

-multimeric

-insoluble

-protease resistant

-predominantly ß-sheet

Front 59

types of protein0misfolding diseases

Back 59

1. familial

-genetically inherited

-symptoms in childhood

-Huntington's

2. Sporadic

-patternless

-late onset (aging or incorrect lifestyle)

-no gene mutations

-Alzheimer's, Parkinson's

3. Transmissible

-prion disease

-spongiform encephalopathies

-fatal familial encephalopathies

Front 60

amyloidoses

Back 60

-main family of protein-misfolding diseases → most clinically relevant due to high ovvurrence of neurodegenerative diseases and type II diabetes

-2 types:

1. systemic:

-a lot of fibrils accummulate everywhere

2. organ-limited:

-fibrils accummulate in one organ

Front 61

cause of formation of amyloid fibrils

Back 61

1. abnormal(mutated) gene

2. post-translational events

3. increased expression

4. decreased degradation

Front 62

mechanism of formation of amyloid fibrils

Back 62

1. alignment of molecules → ß-sheets

-fastest

-H-bonding

2. cross-ß structure formation

-van der waals → interdigitation of residue side chains → steric zipper

3. fibril formation

-non-covalent bonds

-nucleated-growth process: presence of pre-formed nucleus → rapid growth (entropy barrier overcome)

-stabilized by protein concentration and steric zipper formation

Front 63

amyloid fibril aggregation rates

Back 63

depend on:

1. charge

2. secondary structure

3. hydrophobicity

4. protein length

Front 64

therapeutic solutions to amyloid fibril formation

Back 64

1. inhibit protein aggregation

2. interfere w/ post-translation peptide changes prior to misfolding/aggregation step

3. upregulate molecular chaperones or aggregate clearance mechs

Front 65

consequences of amyloid fibrils

Back 65

Alzheimers

Parkinson

Prion diseases

Type II Diabetes

Huntingotn