Theory and Implementation of Techniques for Oriented Systems...
Transcript of Theory and Implementation of Techniques for Oriented Systems...
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Winter School on Biomolecular Solid State NMR
January 20 - 25, 2008
Stanley J. OpellaDepartment of Chemistry and Biochemistry
University of California, San DiegoLa Jolla, California USA
Theory and Implementation of Techniques for OrientedSystems I
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Training and Dissemination Activities of The BiotechnologyResource for NMR Molecular Imaging of Proteins
P41EB002031
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Introduction
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www.virtuallaboratory.net/biofundamentals/lecturenotes
The majority of proteins reside in membranes or othersupramolecular assemblies, and are not soluble.
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TM Phage Vpu p7 MerF MerT MerC GPCR
Membrane protein structure determination rests on four pillars.
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Solution-state NMR of membrane proteins is problematic inbilayer environments.
uniformly 15N labeled Vpu
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Basic requirements of an NMR approach to membrane proteins.
Solve the correlation time problem. High sensitivity. High resolution.
Determine protein structures. Resolve resonances. Assign resonances. Measure frequencies. Extract orientation and/or distance constraints. Calculate structures.
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Solid-state NMR spectroscopy
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1972
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1974
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Nuclear spin interactions are anisotropic.
Proteins in supramolecular assemblies, e.g. membranes,typically reside in highly anisotropic physical environmentsthat prevent rapid isotropic reorientation.
The control (attenuation and measurement) of dipole-dipole couplings is essential.
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Powder pattern.
Single crystal rotation pattern.
The dipole-dipole interaction is anisotropic.
1948
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N
H
rθ
1H - 1H spins in water in gypsum. 1H are “dilute” by space.
Δν (3cos2θ -1)
r3
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N
H
rθ
1H - 15N spins in peptide bond. 15N is “dilute” by space. 1H is“abundant” in large bath.
Δν (3cos2θ -1)
r3
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The chemical shift interaction is anisotropic. 13C is “dilute” byisotopic composition. There are no 1H.
1958
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Attenuation of dipole-dipole couplings
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1965
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WaHuHa
1968
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High resolution solid-state NMR spectra of crystals andpowders
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1972
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Solid-state 15N NMR spectra of a model peptide crystal.
15N chemical shift interaction
1H
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13C MAS NMR of proteins.
1979
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15N MAS NMR of proteins.
1982
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Measurement of dipole-dipole couplings
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1974
Dipolar oscillations during CP build-up.
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1975
Dipolar oscillations during CP build-up under Lee-Goldburgirradiation and analyzed by Fourier transformation.
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1 H-13
C D
ipol
ar C
oupl
ing
13C Chemical ShiftSeparation by: 1) chemical shifts of the dilute spins 2) homonuclear decoupling of the abundant spins 1976
Separated local field spectra of a single crystal.
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High resolution solid-state NMR spectra of aligned samples
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Separated local field spectra of a uniaxially aligned polymer.
1977
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Separated local field spectrum of a specifically 15N labeled proteinaligned and immobilized within a virus particle.
1983
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Separated local field spectra of selectively and uniformly 15Nproteins aligned and immobilized within a virus particle.
1985
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PISEMA
1994
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Three-dimensional HETCOR/PISEMA 1H/15N experiments.
1H15N
1995
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Complete resolution of a uniformly 15N labeled membrane protein.
1997
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SAMMY.
2003
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Improvements in solid-state NMR spectra of proteins.
1976 1983 2004
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Mapping of structure onto spectra.
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In aligned samples, orientationally dependent resonancefrequencies map the structure onto the spectra.
MerFm: 80 residues, 2 TMVpu TM: 36 residues, 1 TMDPPC (C16) DMPC (C14) DMPC (C14)
0.5 ppm
15N chemical shift
150 Hz
1H-15N dipolar coupling
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PISA Wheels: Polarity Index Slant Angle.
2000
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Projection down helix axis.
3.6 residues per turn.
Arc of 100o between adjacent residues.
18 possible orientations.
“wheel-like” spectrum.
Slant angle (tilt).
Polarity index (rotation).
18 possible resonances
17o
Helical Wheel spin-interactions PISA Wheel
PISA Wheels.
1
2
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PISA wheels.
Polarity Index
Slant Angle
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Structuredetermination
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H-N bond is 15°tilted away fromthe helix axis
f(θav,φav,ρ0)
α-Helix geometry and periodicity.
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Periodicity in α-helical secondary structure.
2000
2002
2003
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Dipolar Waves: La Jolla Cove.
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PISA Wheels and Dipolar Waves.
17o
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Distinguishing among types of helices.
PISA Wheel Dipolar Wave Fourier Transform
3.6
4.4
3.0
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Dipolar Waves: helix distortions.
Straight Curve Kink
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Wheels, Waves and resonance assignments.
PISA Wheels Dipolar Waves
“Shotgun” effect ofselective isotopic labelingby residue type.
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Periodicity in β-sheet secondary structure.
Maha Radhakrihnan and Francesca Marassi 2001
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Orientation of β-sheet peptides in membranes through their“butterfly” patterns.
2006
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Approach to structure determination.
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Relative effort devoted to the four pillars of the Resource.
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Protein expression and purification.
1) Construct of gene fused to that of ahydrophobic protein (e.g. KSI).
2) Expression in E. coli as inclusionbodies.
3) Use Nickel column to purify fusionprotein.
4) Cleave protein from partner usingcyanogen bromide.
5) Use HPLC to purify protein.
Wu Sung Son 2005
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Samples of membrane proteins in lipids.
Micelles Isotropic Weakly aligned
Isotropic bicelles q<0.5 q=0.5 - 1.0
Magnetically aligned bicelles q=3.2 q=10 perpendicular parallel
Bilayers Mechanically aligned on glass plates Static in unoriented samples Rotationally aligned in unoriented samples
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2005
q=3
q=10
David Black
19 oC
22 oC
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The effects of lipid assemblies on protein reorientation rates.
bicelles bilayersmicelles
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DeAngelis et al, J Am ChemSoc 24, 4673 (2004)
2004
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Motional averaging of powder patterns
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Rotational averaging of chemical shift powder patterns.
CF3-C6F6
1971
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Rotational averaging of 13C chemical shift powder patterns.
C6H6
1973
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Static vs. “hop” vs. rotational diffusion.
1985
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Global rotational diffusion of a protein about the bilayer normal.
3 oC in DMPC
“...line shape can be interpreted interms of the orientation of thegroups with respect to the diffusionaxis...similar to that obtained fromoriented samples...”
30 oC in DMPC
1985
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Tilted aligned samples and rotational diffusion.
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1975
Phospholipids undergo rotational diffusion about the bilayernormal, and can be aligned on glass plates.
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15N Leu11 labeled Vpu TM in aligned bilayers on glass plates.
2006
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Parallel vs. perpendicular alignment of bilayers.
2000
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15N Leu11 labeled Vpu TM in aligned bilayers.
mechanically alignedon glass plates
magnetically aligned
2005
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2006
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15N Leu labeled membrane proteins in bilayers.
Leu11 Vpu TM Leu14/41 fd coat protein
25 oC
5 oC
unoriented
mechanicallyaligned parallel
magneticallyaligned parallel
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MerFt with two trans-membrane helices undergoes rapidrotational diffusion in DMPC bilayers.
uniformly 15Nlabeled MerFt
5 oC
40 oC
Wu Sung Son
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2007
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MAS of rotationally aligned samples provides the samefrequencies as uniaxially aligned samples using isotropic signals.
LG CP build up
fast MAS slow MAS
uniformly 15N labeled
15N Trp labeled fd coat protein
1 H-1
5 N d
ipol
ar c
plg
mechanicallyaligned bilayers
1 H-1
5 N d
ipol
ar c
plg
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Drot = 10 s-1 Drot = 104 s-1 Drot = 105 s-1
Simulated PISEMA spectra for a helix tilted 30o in perpendicularbicelles undergoing rotational diffusion about the bilayer normal.
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Trans-membrane domain of channel-forming viral membraneprotein Vpu
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Solid-state NMR spectra of membrane proteins with between 35and 350 residues.
* 15N Ile (20 sites)
2GOF2GOH1PI7
1MZT
1NH41PJF1ZN5
2H3O
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Structure Determination
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Initial structures determined by aligned sample solid-state NMR.
2003
1985
1999
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MerFt (60 aa)
2006
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back-calculated spectrum
Two orientationally dependent frequencies for each residueenable calculation of three-dimensional protein structures.
2006
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Membrane proteins structures determined in phospholipid bilayersby solid-state NMR spectroscopy.
T. A. Cross, Florida State University
F. M. Marassi, Burnham Institute
S. J. Opella, UCSD