Proteins Domains, Motifs, and Quaternary Structure

23
1 Proteins Domains, Motifs, and Quaternary Structure Petsko & Ringe 1-5 to 1-18 Voet-Voet Chapter 8-1 to 8-3 © 2004 New Science Press Ltd new-science-press.com

Transcript of Proteins Domains, Motifs, and Quaternary Structure

Page 1: Proteins Domains, Motifs, and Quaternary Structure

1

Proteins Domains, Motifs, and Quaternary Structure

Petsko & Ringe 1-5 to 1-18Voet-Voet Chapter 8-1 to 8-3

© 2004 New Science Press Ltd new-science-press.com

Page 2: Proteins Domains, Motifs, and Quaternary Structure

2

© 2004 New Science Press Ltd new-science-press.com

© 2004 New Science Press Ltd new-science-press.com

Page 3: Proteins Domains, Motifs, and Quaternary Structure

3

© 2004 New Science Press Ltd new-science-press.com

How does the location of a Glu residue on a single α-helix would

affect its pKa?

NH2

COOH

Page 4: Proteins Domains, Motifs, and Quaternary Structure

4

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-43a The H helix of sperm whale myoglobin. (a) A helical wheel representation in which the side chain positions about the α helix are projected down the helix axis onto a plane.

Page

247

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-43b The H helix of sperm whale myoglobin.(b) A skeletal model, viewed as in Part a.

Page

247

Page 5: Proteins Domains, Motifs, and Quaternary Structure

5

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-43c The H helix of sperm whale myoglobin.(c) A space-filling model, viewed from the bottom of the page in Parts a and b and colored as in Part b.

Page

247

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-16b β pleated sheets. (b) The parallel β pleated sheets.

Page

227

Page 6: Proteins Domains, Motifs, and Quaternary Structure

6

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-16a β pleated sheets. (a) The antiparallel βpleated sheets.

Page

227

NSP In association withBioMed Central© 2004 New Science Press Ltd new-science-press.com

Page 7: Proteins Domains, Motifs, and Quaternary Structure

7

NSP In association withBioMed Central© 2004 New Science Press Ltd new-science-press.com

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-17 A two-stranded β antiparallel pleated sheet drawn to emphasize its pleated appearance.

Page

228

Side chainsalternate indirection

7 Angstrom

Page 8: Proteins Domains, Motifs, and Quaternary Structure

8

NSP In association withBioMed Central© 2004 New Science Press Ltd new-science-press.com

© 2004 New Science Press Ltd new-science-press.com

Page 9: Proteins Domains, Motifs, and Quaternary Structure

9

© 2005 New Science Press Ltd new-science-press.com

Page 10: Proteins Domains, Motifs, and Quaternary Structure

10

© 2005 New Science Press Ltd new-science-press.com

© 2004 New Science Press Ltd new-science-press.com

Page 11: Proteins Domains, Motifs, and Quaternary Structure

11

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-47b X-Ray structures of 4-helix bundle proteins.(b) Human growth hormone.

Page

250

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-48 The immunoglobulin fold.

Page

251

Page 12: Proteins Domains, Motifs, and Quaternary Structure

12

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-49 Retinol binding protein.

Page

251

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-52 left The X-ray structure of the 247-residue enzyme triose phosphate isomerase (TIM) from chicken muscle.

Page

253

Page 13: Proteins Domains, Motifs, and Quaternary Structure

13

Voet

Bio

chem

istry

3e©

2004

Joh

n W

iley

& So

ns, I

nc.

Figure 8-54b X-Ray structures of open β sheet-containing enzymes. (b) Porcine adenylate kinase (195 residues).

Page

254

© 2004 New Science Press Ltd new-science-press.com

Page 14: Proteins Domains, Motifs, and Quaternary Structure

14

© 2004 New Science Press Ltd new-science-press.com

© 2004 New Science Press Ltd new-science-press.com

Page 15: Proteins Domains, Motifs, and Quaternary Structure

15

Pore-forming toxins (PFT)

Water-soluble forms

of bacterial pore forming

toxins

Page 16: Proteins Domains, Motifs, and Quaternary Structure

16

Staphylococcal α-HemolysinThe paradigm for β-barrel pore forming toxins

7 monomers Diameter ~ 16 Å

Song et al 1996

How does an amphipathicβ-hairpin fold into a soluble protein?

α-HemolysinSong et al 1996

Luk-FOlson et al 1999

Soluble monomer

Membrane-bound

Page 17: Proteins Domains, Motifs, and Quaternary Structure

17

Perfringolysin O

© 2004 New Science Press Ltd new-science-press.com

Page 18: Proteins Domains, Motifs, and Quaternary Structure

18

© 2004 New Science Press Ltd new-science-press.com

© 2004 New Science Press Ltd new-science-press.com

Page 19: Proteins Domains, Motifs, and Quaternary Structure

19

© 2004 New Science Press Ltd new-science-press.com

© 2004 New Science Press Ltd new-science-press.com

Page 20: Proteins Domains, Motifs, and Quaternary Structure

20

© 2004 New Science Press Ltd new-science-press.com

NSP In association withBioMed Central© 2004 New Science Press Ltd new-science-press.com

Four – helix bundle

Page 21: Proteins Domains, Motifs, and Quaternary Structure

21

Quiz

• An oligomeric protein in a dilute buffer at pH 7 dissociates to its component subunits when exposed to the following agents. 1) 6M guanidinium chloride, b) 20% ethanol, c) 2M NaCl, d) temperatures below 0 oC, e) 2-mercaptoethanol, f) pH 3, g) 0.01 M SDS.

• Which of these observations would not support the contention that the quaternary structure of the protein is stabilized exclusively by hydrophobic interactions?

Main chain torsion angles

ϕ, phi: C(-1)-N─CA-C

α α α α

Page 22: Proteins Domains, Motifs, and Quaternary Structure

22

Main chain torsion angles

ψ, psi: N-CA─C-N(+1)

α α α α

Figure 8-4 The torsional degrees of freedom of the main chain

Page

221

phi

psi

Page 23: Proteins Domains, Motifs, and Quaternary Structure

23