biophysical dissection of abc transporter mechanism
DESCRIPTION
Biophysical dissection of ABC Transporter mechanism. John Ramos Paul “The Man” Smith Nathan Karpowich Bo Chen Oksana Martsinkovich. Linda Millen Jonathan Moody Phillip Thomas UT Southwestern Physiology. Funding: NIH, MOD, CFF. ABC domains. ABC dimer?. - PowerPoint PPT PresentationTRANSCRIPT
Membrane Protein Roadmap 03/26/09 Slide #1 of 27
Biophysical dissection of ABC Transporter mechanism
John RamosPaul “The Man” SmithNathan KarpowichBo ChenOksana Martsinkovich
Funding: NIH, MOD, CFF
Linda Millen
Jonathan Moody
Phillip ThomasUT Southwestern Physiology
Membrane Protein Roadmap 03/26/09 Slide #2 of 27
ATP-Binding Cassette (ABC) Transporters
ABC domains ABC dimer?
Membrane Protein Roadmap 03/26/09 Slide #3 of 27
F1
F0
www.sanken.osaka-u.ac.jp
ABC domains are “F1-like” ATPases.
Walker A B
Membrane Protein Roadmap 03/26/09 Slide #4 of 27
The “A-Protein” paradigmfor (F1-like) mechanical ATPases
• ATP binds at a domain-domain interface.
• The flanking domains act as an ATP-dependent mechanical clamp.
• ATP encapsulation in the interfacial active site drives the mechanochemical “power-stroke” which is closure of the clamp formed by the flanking domains.
• Non-hydrolyzable analogues typically have much lower binding affinity than ATP … and therefore often fail to drive the powerstroke of ATPase motors.
• Same principles apply to at least some non-F1-like mechanical ATPases (definitely GroEL, DnaK/Hsp70, perhaps even myosin).
Mg++
++
+++
--
• Therefore, ATP binding (NOT HYDROLYSIS) drives the mechanochemical powerstroke.Walker A B
Membrane Protein Roadmap 03/26/09 Slide #5 of 27
ATP-Binding Cassette (ABC) Transporters
ABC domains ABC dimer?
Membrane Protein Roadmap 03/26/09 Slide #6 of 27
But the ATPase active site was not located at an interdomain interface in 5 different ABC crystal structures…
No consistent pattern of oligomerization of ABC domains!
?Completely solvent-exposed ATPase active site --
no where near an interdomain interface!
Membrane Protein Roadmap 03/26/09 Slide #7 of 27
Concluded that the problem was the inability to observe the inherently transient complex with ATP
E171
E171Q
(combined with the fact that AMP-PNP and ATP--S are lousy analogs)
Membrane Protein Roadmap 03/26/09 Slide #8 of 27
Using enzymological subterfuge to block ATP hydrolysis yields hyper-stable ABC dimerization!
MJ07962•ATP2: Rfree= 25.1% @ 1.9 Å
E171
E171Q
Membrane Protein Roadmap 03/26/09 Slide #9 of 27
The -helical subdomain rotates away from the core in the absence of the -phosphate of ATP
• Up to 20˚ rotation of -helical subdomain observed in some non-ATP-form ABC domain structures.
Membrane Protein Roadmap 03/26/09 Slide #10 of 27
ABC motor domain mechanism is fairly well understood … but how do the associated TM domains drive transport?
MJ07962•ATP2: Rfree= 25.1% @ 1.9 Å
E171
E171Q
Membrane Protein Roadmap 03/26/09 Slide #11 of 27
Divergent transmembrane domain structures within the ABC Transporter superfamily
Membrane Protein Roadmap 03/26/09 Slide #12 of 27
FRET … to vitamin B12!
B12 ABSORBANCE
- - - 488 Alexa Fluor Excitation___ 488 Alexa Fluor Emission
- - - 546 Alexa Fluor Excitation___ 546 Alexa Fluor Emission
Wavelength (nm)
BtuCD-Ftransports
vitamin B12(structures
from Locher, Rees, et al.)
Membrane Protein Roadmap 03/26/09 Slide #13 of 27
Purification of BtuCD & Alexa-Fluor546-labeled BtuF*
BtuF+CysBtuCD
E142QCD
29kD
Fluorescecnescan
Coomasiestain
A C-terminal cys engineered into BtuF
Membrane Protein Roadmap 03/26/09 Slide #14 of 27
FRET provides a ruler measuring B12 movement relative to a fixed point in the transporter
Membrane Protein Roadmap 03/26/09 Slide #15 of 27
Anisotropy can monitor molecular associationalthough it also (weakly) influenced by quenching/lifetime effects
Perrin Equation:
1/r = (1/r0)(1 + (/rot) = (1/r) (1 + (RT•/V) )
Membrane Protein Roadmap 03/26/09 Slide #16 of 27
Avoid topological problems by using bicelles
QuickTime™ and a decompressor
are needed to see this picture.
Monitoring Bicelle formation usingLight Scattering (Ex.:297-Em.:315nm)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 200
5.0×10 4
1.0×10 5
1.5×10 5bicellerange~1.0-2.5
SolublizedRegion
Long to Short Chain Lipid Mass Ratio(diC6PC/3Polar-1PC)
(0Intensity
o)Detector
Membrane Protein Roadmap 03/26/09 Slide #17 of 27
Model for the conformational reaction cycle of BtuCD(partially, but not fully, validated)
Membrane Protein Roadmap 03/26/09 Slide #18 of 27
FRET / anisotropy provide rich information concerning transport reaction mechanism
Membrane Protein Roadmap 03/26/09 Slide #19 of 27
Model for the conformational reaction cycle of BtuCD(partially, but not fully, validated)
Membrane Protein Roadmap 03/26/09 Slide #20 of 27
The E-to-Q active-site mutation (E142Q) in the active traps ATP in BtuD (just like in the isolated MJ0796 ABC domain)
Membrane Protein Roadmap 03/26/09 Slide #21 of 27
BtuF binds to BtuCD with higher affinity whenATP is locked in the active site
Membrane Protein Roadmap 03/26/09 Slide #22 of 27
Model for the conformational reaction cycle of BtuCD(partially, but not fully, validated)
Membrane Protein Roadmap 03/26/09 Slide #23 of 27
The E142Q mutation in BtuD traps B12 in BtuCD just like the wild-type transporter -- but does not release it
Membrane Protein Roadmap 03/26/09 Slide #24 of 27
Model for the conformational reaction cycle of BtuCD(partially, but not fully, validated)
Membrane Protein Roadmap 03/26/09 Slide #25 of 27
A non-BtuCD-interacting mutant variant of BtuF (E50R/E180R) can monitor free B12 concentration
Membrane Protein Roadmap 03/26/09 Slide #26 of 27
Model for the conformational reaction cycle of BtuCD(partially, but not fully, validated)
Membrane Protein Roadmap 03/26/09 Slide #27 of 27
Correspondence of crystal to functional states is obscure -- except for E-to-Q MalEFG-K
Membrane Protein Roadmap 03/26/09 Slide #28 of 27
Biophysical dissection of ABC Transporter mechanism
John RamosPaul “The Man” SmithNathan KarpowichBo ChenOksana Martsinkovich
Funding: NIH, MOD, CFF
Linda Millen
Jonathan Moody
Phillip ThomasUT Southwestern Physiology
Membrane Protein Roadmap 03/26/09 Slide #29 of 27
Update on E. coli IMP overexpression physiology project
• Expressed 5 IMP’s (4 ABC Transporters, 1 MFS) in MG1655 via pQE60/pRep4 plasmids; compare 2 soluble proteins (enolase & the cytoplasmic domain of one of the ABC Transporters).
• Characterize cell growth rates, morphology +/- membrane stains, transcriptome (via microarray), expression of selected reporter genes (for factors), and protein expression level / physical state.
Funding: NIH R21!
• Expressing cells suffer from “gigantism” -- when expressing either soluble or membrane proteins.
• IMP expressing cells are growth-inhibited -- & toxicity level correlates with amount of detergent solulizable IMP produced.
• Evidence of intracellular lipid-rich inclusions in overexpressing cells, whether or IMP is recoverable.
• No activation of s, E, or Cpx systems (or s32).• ~200 genes reduced in expression -- most shared by soluble proteins &
IMPs, many annotated to be related to acid stress response.• ~50 genes increased in expression -- most specific to IMPs, 45 part of
flagellar biosynthesis / chemotaxis regulon.• ~5 overexpressed genes may be specific for IMP overexpression.
Observations (conclusions?):