Structural biology of mitochondria Werner Khlbrandt Max Planck - - PowerPoint PPT Presentation

▶
structural biology of mitochondria
SMART_READER_LITE
LIVE PREVIEW

Structural biology of mitochondria Werner Khlbrandt Max Planck - - PowerPoint PPT Presentation

Apr 06, 2024 330 likes •774 views

Structural biology of mitochondria Werner Khlbrandt Max Planck Institute of Biophysics Frankfurt, Germany The mitochondrion Powerhouse of the eukaryotic cell Produces almost all ATP to drive cellular reactions Semi-autonomous

slide-1
SLIDE 1

Werner Kühlbrandt Max Planck Institute of Biophysics Frankfurt, Germany

Structural biology

  • f mitochondria
slide-2
SLIDE 2

The mitochondrion

  • Powerhouse of the eukaryotic cell
  • Produces almost all ATP to drive cellular reactions
  • Semi-autonomous cell organelle (division, fusion,
  • wn genetic system)
  • Imports > 99% of proteins from cytoplasm
  • Outer membrane is permeable to small molecules
  • Inner membrane is site of respiration

and ATP synthesis

  • Major role in ageing and apoptosis
slide-3
SLIDE 3
  • uter membrane

~ 2000 different proteins > 99% produced outside cristae matrix pH 7.9 inter- membrane space pH 7.35 ~500 nm inner membrane

  • uter membrane

Schematic drawing of mitochondrion

slide-4
SLIDE 4

QuickTime™ and a decompressor are needed to see this picture.

Jürgen Bereiter-Hahn, Frankfurt University

Mitochondria in a human endothelial cell

~10 µm

slide-5
SLIDE 5

Bertram Daum

Podospora anserina has smaller mitochondria with fewer cristae

cristae ridges cristae junctions

slide-6
SLIDE 6

Arrangement of the mitochondrial ATP synthase

slide-7
SLIDE 7

matrix cristae space

UQ UQ

NADH NAD+ O2 2H2O H+ H+ H+ H+ H+ H+

succinate

H+ H+ H+ H+ H+ H+ H+ H+ H+ ADP + Pi ATP H+ H+ H+ H+ H+ H+ H+ Complex I

NADH dehydrogenase

Complex III

cytochrome c reductase

Complex II

succinate dehydrogenase

Complex IV

cytochrome c oxidase

Complex V

ATP synthase

cytochrome c

H+ H+

The mitochondrial respiratory chain

drawn by Karen Davies

slide-8
SLIDE 8

Deep-etched Paramecium mitochondrion

R.D.Allen et al, J.Cell Biol. 1989

200 nm

slide-9
SLIDE 9

20 nm

rat liver: tubular cristae bovine heart: lamellar cristae

Dimer ribbons in mammalian mitochondria

Strauss et al, EMBO J 2008

slide-10
SLIDE 10

subtomogram averages

Karen Davies

Dimer rows are ubiquitous

lipolytica Polytomella

slide-11
SLIDE 11

QuickTime™ and a decompressor are needed to see this picture.

ATP synthase dimers ribosomes inner membrane Davies et al, PNAS 2011

Cryo-ET of Podospora mitochondrion

slide-12
SLIDE 12

Sub-tomogram average of yeast dimer

Davies et al, PNAS 2012

slide-13
SLIDE 13

Resolution estimate

3.7 nm average of 121 sub-tomograms

Davies et al, PNAS 2012

slide-14
SLIDE 14

Sub-tomogram average of ATP synthase dimer

F1 head rotor ring central stalk peripheral stalk

Davies et al, PNAS 2012

slide-15
SLIDE 15

Sub-tomogram average of ATP synthase dimer

beta subunits peripheral stalk

F1 head

Davies et al, PNAS 2012

slide-16
SLIDE 16

Fit of peripheral stalk

bovine F1/peripheral stalk (2WSS; Rees et al, PNAS 2009) yeast F1/Fo+bovine peripheral stalk (2CLY; Dickson et al, EMBO J 2006)

Davies et al, PNAS 2012

slide-17
SLIDE 17

ATP synthase dimers self-organize into rows

coarse-grained MD simulation by José Faraldo-Gomez, Claudio Anselmi, MPI of Biophysics

Davies et al, PNAS 2012

slide-18
SLIDE 18

Energy of elastic membrane deformation is > 6 kT per dimer For comparison: Free energy of protein-protein interaction (glycophorin A dimer) ~15 kT

Free energy of dimer association

José Faraldo-Gomez, Claudio Anselmi, MPI of Biophysics

Davies et al, PNAS 2012

slide-19
SLIDE 19

inner membrane

  • uter membrane

ATP synthase monomers stroma ~ pH 8 thylakoid lumen ~ pH 5 thylakoid membrane

Chloropla

H+ H+ H+ H+

slide-20
SLIDE 20

maximal rate ~400 ATP per synthase per second 2.5

Junesch and Gräber, FEBS Lett 1991

at a delta pH of 2.5 and a membrane potential of 55 mV

ATP synthesis in chloroplasts

slide-21
SLIDE 21

2.5

Förster, Turina, Drepper, Hähnel, Fischer, Gräber, Petersen, BBA 2010

maximal rate ~80 ATP per synthase per second at a delta pH of 2.9 and a membrane potential of 133 mV

ATP synthesis in mitochondria

matrix pH 7.9 cristae pH 5.0 ??

slide-22
SLIDE 22

ATP synthase dimers inner membrane

  • uter membrane

matrix: pH 7.9 respiratory chain proton pumps (complex I, III, IV) subunits e, g, 4 pH intermembrane space = pH cytoplasm: 7.35 H+ H+

Mitochond

H+ H+ H+ H+

slide-23
SLIDE 23

Respiratory chain supercomplex

slide-24
SLIDE 24

matrix cristae space

UQ UQ

NADH NAD+ O2 2H2O H+ H+ H+ H+ H+ H+

succinate

H+ H+ H+ H+ H+ H+ H+ H+ H+ ADP + Pi ATP H+ H+ H+ H+ H+ H+ H+ Complex I

NADH dehydrogenase

Complex III

cytochrome c reductase

Complex II

succinate dehydrogenase

Complex IV

cytochrome c oxidase

Complex V

ATP synthase

cytochrome c

H+ H+

The mitochondrial respiratory chain

drawn by Karen Davies

slide-25
SLIDE 25

QuickTime™ and a decompressor are needed to see this picture.

ATP synthase dimer row 1 ATP synthase dimer row 2 respiratory chain complexes crista membrane

Davies et al, PNAS 2011

Podospora cristae vesicle

slide-26
SLIDE 26

quantum-dot labelled complex I supercomplex next to dimer row

Supercomplex in cristae membranes

Davies et al, PNAS 2011

slide-27
SLIDE 27

class averages reprojections

  • f final volume

random conical tilt

  • n thin C film

Althoff et al, EMBO J 2011

Respiratory chain supercomplex I1II2IV1

slide-28
SLIDE 28

amphipol ring

3D cryo-EM map

Althoff et al, EMBO J 2011

slide-29
SLIDE 29

complex I (NADH UQ oxidoreductase) complex III2 (cytochrome c reductase) complex IV (cytochrome c oxidase) cytochrome c Rieske FeS

membrane

50 Å

Hunte, Zickermann et al, 2010 Hunte et al, 2000 Tsukihara et al, 1996

Respiratory chain supercomplex I1II2IV1

Althoff et al, EMBO J 2011

slide-30
SLIDE 30

10 nm

slide-31
SLIDE 31

complex I to complex III: UQ complex III to complex IV: cyt c

Electron transfer pathways

Althoff et al, EMBO J 2011

slide-32
SLIDE 32

Sites of oxygen radical production

slide-33
SLIDE 33

Protein import

slide-34
SLIDE 34

a b d e f c

Cryo-ET of chloroplast protein translocase

15 nm 15 nm

Bertram Daum with Enrico Schleiff, Frankfurt; Sommer et al, PNAS 2011

slide-35
SLIDE 35

Quantum dot labelling of TOC subunits

a b

α-75P

α-34G α-75P

15 nm 15 nm

cytoplasmic location of TOC receptor GTPase cytoplasmic location of TOC75 POTRA domain

Bertram Daum with Enrico Schleiff, Frankfurt; Sommer et al, PNAS 2011

slide-36
SLIDE 36

Ageing

slide-37
SLIDE 37

filamentous, multicellular fungus fixed lifespan of ~20 days long-lived and immortal mutants

from Scheckhuber et al, 2006

hyphae culture mitochondria

18 days (senescent) 9 days 6 days (juvenile) 18 days (senescent)

Podospora anserina: filamentous fungus with a fixed lifespan

slide-38
SLIDE 38

young (6 days)

  • ld (18 days)

Bertram Daum with Heinz Osiewacz, Frankfurt

  • P. anserina

Age-dependent change of mitochondria

slide-39
SLIDE 39

subunit g knockout wild type yeast cristae morphology ATP synthase arrangement randomly distributed monomers dimer rows along edges

Dimer-specific subunit knockouts

Davies et al, PNAS 2012

slide-40
SLIDE 40

Deryck Mills

Single-particle team

Janet Vonck Thorsten Althoff Doreen Mathies

slide-41
SLIDE 41

X-ray structure of CaiT

Bertram Daum Deryck Mills Karen Davies

Electron tomography team

Thorsten Blum

slide-42
SLIDE 42

How to fix it if it gets broken by Deryck - First & last edition Open V13? close V12? close V8? make a coffee ? fill with LN2? have breakfast? turn up HT? water plants? turn on dryer? EM? (check notes) go home?

slide-43
SLIDE 43