Chapter 9. Protein Folding, Dynamics, and Structural Evolution

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1 Chapter 9 Protein Folding, Dynamics, and Structural Evolution

2 Proteins folding Self-assembly Primary sequence dictates three dimensional structure Folding accessory proteins Protein disulfide isomerases (PDIs) Peptidyl prolyl cis-trans isomerase (PPIs) Molecular chaperons

3 Protein renaturation RNAse A ~10h vs 2 min (with PDI) Theoretical chance for forming correct disulifide bonds 1 7 x 1 5 x 1 3 x 1 1 = % active (Experimental) Anfinsen (1957)

4 Not all proteins are readily renatured (acts as a linker during folding) Proinsulin

5 Determinant of protein folding Efficient space filling by helices and sheets Internal residues mainly direct protein folding Little effects on folding (or activity) by mutating surface residues Hierarchy in protein structure Domains Subdomains Sub-subdomains Protein structures are highly adaptable Secondary structure can be context-dependent Not all residues have equally important roles

6 Protein structures are highly adaptable No preferred interactions between side chains found Native fold determines the packing but packing does not determine the native fold Structural homology with little sequence homology Little overall change in structure (or activity) upon a few amino acid changes.

7 Context-dependent secondary structure B1 domain of protein G (GB1) AWTVEKAFKTF (can replace both β-hairpin and α-helix)

8 Not all residues are equally important Identical residues from Rop and GB1 Unchanged GB1 residues Non-identical residues Identical to Rop residues Change of GB1 fold to Rop fold by 50% amino acid changes (50% sequence identity to GB1, 41% sequence identity to Rop)

9 Measurements of protein folding Rapid measurement (< one millisecond or less) Stop-flow apparatus Heat pulsing of cold-denatured proteins Monitoring techniques Circular dichroism (CD) Pulsed H/D exchange

10 Stop-flow device

11 CD spectra of polypeptide

12 Pulsed H/D exchange X-H + D 2 O X-D + HOD ph pulsing (Low ph High ph Low ph) Detection by 1 H NMR No proton exchange with hydrogen bonding donor Internal residues no contact with water (no proton exchange)

13 Protein folding pathway Random or Ordered? Hydrophobic collapse (very fast, < 5ms) Subdomains Molten globule Domains ms ~ sec Tertiary structure

14 Energy-Entropy Diagram for protein Folding

15 Folding funnels

16 Folding via an ordered pathway Bovine pancreatic trypsin inhibitor (BPTI)

17 Folding in vitro is different from in vivo Protein starts folding during synthesis Folding accessory proteins Protein disulfide isomerase (PDI) Peptidy prolyl cis-trans isomerase Chaperones

18 Protein disulfide isomerase (PDI) (a) (b)

19 Molecular chaperons Prevent and reverse the formation of intramolecular and intermolecular aggregates Several different classes Heat shock protein 70 (Hsp70) Chaperonins Hsp90 Nucleoplasmins

20 GroEL (Hsp60 in E. coli) Side-view Top-view

21 GroES (Hsp10 in E. coli)

22 The GroEL/GroES Complex GroES GroEL

23 Domain movement in GroEL GroES

24 GroEL/GroES chaperonin system

25 Protein secondary structure prediction (Chou-Fasman method) P > 1 : Occurs with greater than average frequency H: Strong former h: Former I: Weak former i: Indifferent former b: Breaker B: Strong breaker

26 Protein Design Zif268 FSD-1 (Computationally designed)

27 Protein dynamics Atomic fluctuations Vibrations of individual bonds ( s, Å) Collective motions Movement of groups ( s, >5 Å) Triggered conformational changes (10-9 to 10 3 s, >10 Å)

28 Molecular dynamics simulation Myoglobin α Helix

29 Protein misfolding diseases Amyloid diseases Alzheimer s disease amyloid β-peptide (Aβ) Parkinson s disease α-synuclein Systemic amyloidosis (SSA), familial amyloid polyneuropathy (FAP) and familial amyloid cardiomopathy (FAC) transthyretin Prion diseases (Transmissible spongiform encephalopathies,tses) prion protein (PrP) Scrapies Mad cow disease Creutzfeldt-Jacob disease (CJD)

30 Picture from FEBS J. 274, 3784 (2007)

31 Amyloid β-peptide (Aβ) 39- to 43-residue peptide formed by proteolytic cleavage of APP γ-secretase β-secretase Atomic force microscopy image of Aβ fibrils

32 Amyloid fibrils Amyloid fibrils Model Isolated β sheet

33 PrP c vs PrP sc PrP c PrP sc Identical amino acid sequence and chemical composition, but different structure

34 Prion hypothesis PrP sc induces the conversion of PrP c to PrP sc PrP c PrP sc conformational change is autocatalytic and/or assisted by unknown chaperon protein PrP c is completely degraded by proteases; PrP sc is partially degraded to form a kd PrP fragment (PrP 27-30), which ultimately forms the amyloid fibrils

35 Structures are conserved rather than amino acid sequences

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