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• Membrane Proteins are Oriented
with respect to their
environment
• Orientational Restraints are
Absolute Restraints, while
Isotropic Restraints are Relative
Restraints
• Through Unique High Resolution
Structure & Dynamics detailed
Functional Understanding of
Biological Systems can be
Achieved
• Taking Advantage of Anisotropy!!
Wang et al., 2000 JMR 144:162-167.
Marassi & Opella, 2000 JMR 144: 150-155.
From Membrane Peptide
& Protein Structures to
Biological Understanding:
Using Oriented Sample &
MAS ssNMR
Tensor Characterization:
Chemical Shift Tensor
Element Magnitudes
Mai et al., Prot. Sci. JMR 1992
11 39 22 36 ppm
22 63 51 63 ppm
33 213 197 194 ppm
Val1 Gly2 Trp11
Tensor Characterization:
Tensor Element Magnitudes:
Sample Preparation
Lazo et al., BBRC 1993
Powder Pattern:15N Ala3 gA
MAS:15N Gly215N Ala3 gA
263K
123K
203K
233K
Span = 172 ppm
Span = 172
Span = 168
Span = 159
Tensor Characterization:
Tensor Element Magnitudes
Extracted from 3D
ROCSA spectra
Wylie et al., JPC B 2006
Tensor Characterization:Tensor Element Magnitudes
Wylie et al., JPC B 2006
d = dZZ -diso
h =dyy -dxx
dzz -diso
Motional Averaging of Tensors:
Local Sidechain Dihedral
(or torsional) Motions
M. Frey Dissertation, 1984
Motional Averaging of Tensors:
u||
a = u||
s 3cos2 q -1
2
æ
èç
ö
ø÷ = 0.34u||
s
Motional Averaging of Tensors:
Librational Motions
Hu et al., Biochem 1995
Note that 11 and 33 are
effected much more than 22
11 = -75 ppm
33 = 66 ppm22 = 9 ppm
Motional Averaging of Tensors:
Librational MotionsThree models for the Trp11 gA librational motions:
A. motion about 1 only
B. motion about 2 only
C. motion about 1 and 2
The model with motion
about 2 fits best
Hu et al.,
Biochem
1995
Tensor Characterization:
Tensor Element Magnitudes – definitions:
cc - perpendicular to the CNC plane
aa - in the C1NH bond angle
bb - completes the right-handed coordinate frame
Oas et al., JACS 1987Teng et al., JACS 1992
33 ≥ 22 ≥ 11 or
|zz-iso| ≥ |xx-iso| ≥ |yy-iso|
or:
33 1122
Tensor Characterization:
Stark et al., JMR 1983
This traditional approach: crystal mounted on
a goniometer that can rotate a sample
about three orthogonal axes.
From a knowledge of:
1) the orientation of the molecular frame
in the crystalline frame of reference
(from x-ray diffraction).
2) the orientation of the crystal with
respect to the goniometer
3) the observed resonance frequencies as
a function of rotations about the
three axes.
4) It is possible to determine the tensor
element magnitudes and tensor
orientation to the molecular frame.
H2NCH2-13CO-15NHCH2CO2H•H2O•HCl
Rotation about the Z axis
Rotation about the X axis
Rotation about the Y axis
Tensor Element Orientation
Tensor Characterization:
Tensor Element Orientation
Rotation patterns are a lot of work and
require a sizeable crystal – hence -
restricted to model compounds.
It is also possible to determine the
tensor orientations from powder
pattern spectra.
The addition of the 13C-15N dipolar
interaction causes a very
significant change in shape of the
powder pattern.
Teng et al., JMR 1989
Tensor Characterization:
Tensor Element Orientation A B C
39 63 213 ppm
22 51 197
36 63 194
28±5 0±5 0±5°
106±2 98±2 106±2°
Mai et al., Prot. Sci. 1993
[13C1]formyl-[15N]Val1 gA [13C1]Val1-[15N]Gly2 gA
[13C1]Leu10-[15N]Trpl11 gA
aD
N =
bDN =
s11 =
s 33 =
s 22 =
Gramicidin A: Chemical Shift Tensor
Element Magnitudes and Tensor Orientations
Mai et al., Prot. Sci. 1992
• Tensor Element Magnitudes vary
in part because of differences in
dynamics, but also from the structure and
environment. Glycine is a clear outlier.
• Amide tensor element
orientations orientations
are remarkably constant
with the exception of
Glycine and the formyl-Val
Uniformly Aligned Samples
• Hydrated lipid bilayer preparations of
membrane proteins and polypeptides
~ 50% by weight water
~ 1 to 5 mg protein per sample
~38 Slides
~5000 Lipid
Bilayers
~ 1:50 to 1:80 Molar Ratio of Protein:Lipid
6 mm
Oriented Sample Solid State NMR:
n
n =
=
=
s obs =s ||
Nicholson et al., Biochem 1987
obs = ||(cos2q11-1) + (cos2q33-1)
Oriented Sample Solid State NMR:
Photomicrograph of a single glass
slide under crossed polarizers
40x and 40°C – bar is 100µm
A) Uniformly aligned bilayers
B) Parabolic Focal Conics
C) Oily streaks
Moll et al., Biophys. J. 1990
62%
38%
52%
48%
Mosaic spread 8°
Mosaic spread 12°
37% 16%
63% 84%
Das et al., Nature Protocols, 2013
Oriented Sample Solid State NMR: 15N Gramicidin
Mai et al., Protein Sci 1993
Oriented Sample Solid State NMR: More Backbone Data
Ketchem et al., JBN 1997
• With the anisotropic 15N chemical shift and the 1H-15N and 13C-15N dipolar interactions the
peptide plane orientations can be characterized. • Separated Local Field Spectra
Oriented Sample Solid State NMR: Additional Restraints
Ketchem Dissertation 1995
High Resolution Gramicidin Structure: All Atom Structure
Ketchem et al., Science 1993
Ketchem et al., Structure 1997
8+ Restraints/Residue
Validation of the All-Atom Gramicidin Structure
Kim et al., JACS 2001
• Stereoview of the refined
structure of gramicidin A.
• 40 simulated annealing
structures superimposed.
• The root mean square
deviation of the backbone
coordinates from the
refined ensembles of
structures is 0.11Å
Quiz: Where is the error in the PNAS article?
Nicholson et al., Biochem 1987
Uniformly 15N Labeled
Gramicidin A
Powder
Pattern
Oriented
Sample
A-B
Burkhardt, Li, Langs, Pangborn, Duax, PNAS 1998
Quiz: Where is the error in the PNAS article?
Nicholson et al., Biochem 1987
Uniformly 15N Labeled
Gramicidin A
Powder
Pattern
Oriented
Sample
A-B
a) “The qNH scale was aligned with the ppm scale by using
the calibration: 198 ppm ~15°, 180 ppm ~25°, and
146 ppm ~39°. Although there is not a linear
relationship between the two scales, the appropriate
alignment using this calibration demonstrates the
excellent agreement between the ensemble of NH
angles measured in the helices (of the X-ray structure)
and the NMR data.”
c) Fit of the data to the NMR structure
nN = 3 cos2qN-H - 1
Quiz:
Kovacs et al., PNAS (1999)
Refined ssNMR structure
Burkhardt et al., structure
ssNMR: Lipids
PDB: 1MAG
X-ray: Methanol
PDB: 1AV2
X-ray: Benzene/methanol
PDB: 1ALZSoln NMR: SDS
PDB: 1GRM
15N ChemShift
15N – 13CDipolar
15N – 1HDipolar
Ca – 2HQuadrupolar
Pre
d–
Ob
s
Err
or
The Trp Residues are Functionally Important
Hu & Cross (1995) Biochem. Hu, Lazo & Cross (1995) Biochem.
0
1
2
E (kJ/mol)
Ln
Co
nd
ucta
nce (
pS
)
2 4 6 8
Na+
Z
Functional Understanding
Tian & Cross, (1999) J. Mol. Biol.
Ba2+
Cs+
K+
Na+
Li+
Functional Understanding: Stepwise Dehydration
Tian & Cross, (1999) J. Mol. Biol.
14-15 12-13 10-11
Functional Understanding: The Binding Site
Tian & Cross, (1999) J. Mol. Biol.
14-15 12-13 10-11
• This Gramicidin A structure characterized in a
liquid crystalline lipid bilayer environment
has been challenged, but remains the high
resolution structure that is recognized as
the native-like structure.
• This high resolution structure was
characterized with orientation restraints and
the I to I+6 h-bonds that were consistent
with the data….
• And two REDOR distance restraints between
the monomers.
• The sidechains were fully characterized only
the Trp sidechain structures have any
significance for the properties of the
channel.
• Stepwise dehydration and long range dipolar
interactions influencing transport kinetics
were concepts that originated with this solid
state NMR data.
First Conclusion Slide
OS ssNMR Enhanced by PISEMA
15N Anisotropic Chemical Shift (PPM)
15N
-1H
Dip
ola
r C
ou
pli
ng
PISEMA-Class SLF Experiments
1H
15N
Wu et al., JMR (1994)
15N Anisotropic Chemical Shift (PPM)
15N Val labeled Rv1861
14 Valine residues in
this 3 TM protein
Murray et al ACR 2013
15N-1H Dipolar Couplings
N
H
Bo
θ
obs= n||/2 (3cos2θ -1)
N
H
Bo
Wang et al., 2000 JMR 144:162-167.
Marassi & Opella, 2000 JMR 144: 150-155.
Structural information from OS ssNMR
15N Anisotropic Chemical Shift Tensor
Ca
O
Ca
H
C’
Ni
σ11
σ33
σ22
q
obs= 33[sin(β)cos(α)]2 + 22[sin(β)sin(α)]2+ 11cos(β)2
Wang et al., 2000 JMR 144:162-167.
Marassi & Opella, 2000 JMR 144: 150-155.
Dipolar Coupling
Wave
Chemical Shift
Wave
Bo
Structural information from OS ssNMR
The PISA Wheel & Helical Wheel
Wang et al., 2000 JMR 144:162-167.
• Data from the transmembrane peptide of the M2 protein
PISA Wheels
• PISA Wheels:
- a set (S) of (n)
coordinates for
& , the tilt and
rotational angle
S(σ,n) = [ σ11 ( A cos sin + B sin sin – C cos )2 + σ22 (D cos sin
+ E sin sin - F cos )2 + σ33 (G cos sin - H sin sin - I cos )2,
vII/2 ( 3 (J cos sin – K sin sin - L cos )2 -1)]
Wang et al., 2000 JMR 144:162-167.
Effect of Chemical Shift Anisotropy Variation
Wang et al., 2000 JMR 144:162-167.
• Typical variation in tensor element magnitudes with the exception of Glycine
Effect of Chemical Shift Tensor Orientation
Wang et al., 2000 JMR 144:162-167.
»» Typical water soluble protein helix has a value of 12°
Wang et al., 2000 JMR 144:162-167.
Effect of Peptide Plane on PISA Wheel
LdtB or
LdtA? PonA1
PonA2?
a The elongation complex
Cytosol
Cofactor?
Hydrolases?Hydrolases?
b The divisome
Cofactor?
Wag31CwsA
PBPBPBPA
PonA1
RipARpfB
FtsX? FtsW CrgA FtsQ CwsA
FhaB
P
PknARv3660c
FtsE?FtsZ
Z Ring
?
Peptidoglycan
ChiZ
The Divisome of Mycobacterium tuberculosis
Rubin and coworkers, Nat. Rev. Microbio., 2014
Mtb elongates from the poles unlike most bacteria and therefore requires
coordination between an elongation complex and the divisome.
Only FtsZ the protein that forms the Z-ring in dividing
cells binds to as many proteins as CrgA known to be
a primary recruiter of proteins to the divisome and is
a negative regulator of cell division.
M P
K
S
KV R
K K N
D
FTV
SAV
SR
TPM
K VVK
GP
S SF VFW V
SL F IGL M LI G LI W L MV F
QL
A
AI
G S QA
N
PT
A L
WMA QLGP WNY AIAF AFM ITGL LLT M R
W
H L E
Membrane
Cytoplasam
TM1TM2
N terminal C terminal
37
14
28
32
45
52
32
65
93
72
87
CrgA: A regulatory protein of M. tuberculosis cell division
Full Length CrgA from Mtb – SAMPI4 Spectra15N
-1H
Dip
ola
r 15N
-1H
Dip
ola
r
MPKSKVRKKNDFTVSAVSRTPMKVKVGPSSVWFVSLFIGLMLIGLIWLMVFQL
AAIGSQAPTALNWMAQLGPWNYAIAFAFMITGLLLTMRWH
6 Met 10 Leu
6 Phe9 Ala
M e t 4 1
Das et al., 2015 PNAS
Tau: 15°
MPKSKVRKKN10 DFTVSAVSRT20 PMKVKVGPSS30 VWFVSLFIGL40
MLIGLIWLMV50 FQLAAIGSQA60 PTALNWMAQL70 GPWNYAIAFA80
FMITGLLLTM90 RWHLEHHHHH100 H
15N
-1H
Dip
ola
r C
ou
plin
g (k
Hz)
Amino Acid Labeled CrgA
Temp: 13 °CPOPC POPG
(liposome)LPR: 100:1 (Molar)
Das et al., PNAS 2015
Dipolar Waves for the Two TM helices in CrgA
Das et al., PNAS 2015
13C-13C Correlation Spectra (50 & 25 ms)
CrgA from Mtb – Distance Restraints
Structure of the
2 TM helices
Das et al., 2015 PNAS
CrgA from Mtb – 13C-13C
DARR Spectra
Blue 300 ms
Green 700ms
Red 1000ms
Reverse Labeling: excluding
Phe, Trp, Ser, Thr, Ile
G39Ca-T84Cb
L42Ca-A78Cb
M49Ca- A78Cb
M49Ca-Y75Cb
M49Ca-Y75Ce1
CrgA TM 2° and 3° Structure
A78
CrgA TM Tethered to the Lipid Interface
Refined in an all atom lipid environment the
same as that used for the experiments
Grey Ribbon: FtsQ
Cyan Ribbon: CrgA TM1
Pink Ribbon: CrgA TM2
Red Small Residues: Intra-protein contacts
Blue Small Residues: CrgA-FtsQ contacts
Green Small residues: Contacts for other proteins
CrgA recruits five other proteins to the
cell division apparatus – work in
progress
Intrinsic Disorder – Nascent Structure Characterization
MSEQVETRLT PRERLTRGLA YSAVGPVDVT RGLLELGVGL GLQSARSTAA GLRRRYREGR
LAREVAAAQE TLAQELTAAQ DVVANLPQAL QDARTQRRSK HHLWIFAGIA AAILAGGAVA
FSIVRRSSRP EPSPRPPSVE VQPRS
CwsA
MPKSKVRKKN DFTVSAVSRT PMKVKVGPSS VWFVSLFIGL MLIGLIWLMV FQLAAIGSQA
PTALNWMAQL GPWNYAIAFA FMITGLLLTM RWH
MTEHNEDPQI ERVADDAADE EAVTEPLATE SKDEPAEHPE FEGPRRRARR ERAERRAAQA
RATAIEQARR AAKRRARGQI VSEQNPAKPA ARGVVRGLKA LLATVVLAVV GIGLGLALYF
TPAMSAREIV IIGIGAVSRE EVLDAARVRP ATPLLQIDTQ QVADRVATIR RVASARVQRQ
YPSALRITIV ERVPVVVKDF SDGPHLFDRD GVDFATDPPP PALPYFDVDN PGPSDPTTKA
ALQVLTALHP EVASQVGRIA APSVASITLT LADGRVVIWG TTDRCEEKAE KLAALLTQPG
RTYDVSSPDL PTVK
MTPVRPPHTP DPLNLRGPLD GPRWRRAEPA QSRRPGRSRP GGAPLRYHRT GVGMSRTGHG
SRPVPPATTV GLALLAAAIT LWLGLVAQFG QMITGGSADG SADSTGRVPD RLAVVRVETG
ESLYDVAVRV APNAPTRQVA DRIRELNGLQ TPALAVGQTL IAPVG
MPLTPADVHN VAFSKPPIGK RGYNEDEVDA FLDLVENELT RLIEENSDLR QRINELDQEL
AAGGGAGVTP QATQAIPAYE PEPGKPAPAA VSAGMNEEQA LKAARVLSLA QDTADRLTNT
AKAESDKMLA DARANAEQIL GEARHTADAT VAEARQRADA MLADAQSRSE AQLRQAQEKA
DALQADAERK HSEIMGTINQ QRAVLEGRLE QLRTFEREYR TRLKTYLESQ LEELGQRGSA
APVDSNADAG GFDQFNRGKN
CrgA
FtsQ
ChiZ
Wag31
Cytoplasmic; Transmembrane Periplasmic; Intrinsic Disorder
Minimal Anisotropy: A Characteristic for Intrinsic Disorder:
Helix 1 CrgAN- Terminus Interhelical Loop
Res # DC
(kHz) ACS
(ppm)
Res # DC
(kHz) ACS
(ppm)
Ser4 0.0 110 Leu53 6.6 178.0
Val6 0.0 125 Ala54 4.2 174.0
Asn10 0.8 115 Ala55 3.3 166.0
Phe12 0.0 120 Ile56 5.8 78.0
Thr13 0.0 105 Gly57 5.2 80.0
Val14 0.8 120 Ser58 5.0 65.0-90.0
Ser15 1.6 115 Ala60 4.1 78.0
Ala16 0.2 135 Thr62 5.5 62.0
Val17 1.2 115 Ala63 4.1 78.0
Ser18 1.1 110 Leu64 5.5 65.0
Arg19 5.2 70.0 Asn65 5.0 80.0
Thr20 5.6 75.0 Trp66 5.0 85.0
Met22 3.9 105.0 Met67 5.4 88.0
Val24 5.4 70.0 Ala68 1.2 130
Val26 4.3 75.0 Leu70 0.0 105
Gly27 5.1 70.0 Gly71 0.0 110
Ser29 4.0 175.0
Ser30 8.5 225.0
Absolute vs. Relative Restraints
15N-1H Dipolar Orientational
Restraints ±0.5 kHz15N Anisotropic Chemical
Shift ±5 ppm
Backbone-Backbone
Distance Restraints
±0.5Å
Murray Dissertation, 2014
Das, Murray, Miao, Cross, 2014 Adv. Biol. SSNMR
• Absolutes restraints for secondary
structure and structural orientation
• Relative restraints are particularly
useful for tertiary and quaternary
structure
How Many Backbone Restraints does 15N Labeling Yield?
0°
90°
180°
270°
With respect to
top of helix
31: 350° 350°32: 105° 90°33: 230° 190°34: 285° 290°35: 20° 30°36: 145° 130°37: 270° 230°38: 310° 330°39: 60° 70°40: 195° 170°41: 245° 270°42: 20° 10°43: 125° 110°44: - 210°45: 340° 310°46: 30° 50°47: 190° 150°48: 290° 250°
Predicted &
Observed Pred.Obs, Helix 1
31: 350° 350° 41: 245°270°32: 105° 90° 42: 20° 10°33: 230° 190° 43: 125°110°34: 285° 290° 44: - 210°35: 20° 30° 45: 340°310°36: 145° 130° 46: 30° 50°37: 270° 230° 47: 190°
150°38: 310° 330° 48: 290°
250°39: 60° 70°40: 195° 170°
Predicted and Observed
P POO
How Many Backbone Restraints does 15N Labeling Yield?
• Instead of treating the restraints from
each peptide plane as independent
of the other planes, they are, in
fact, coupled by the Ca carbon.
• In other words knowing that residue
38 has a rotation angle relative to
residue of 31 of -40° is an
important structural restraint!
Helix 1 of CrgA
How Many Backbone Restraints does 15N Labeling Yield? A Lot
31-32: 115°32-33: 125°33-34: 55°34-35: 95°35-36: 125°36-37: 125°37-38: 40°38-39: 110°39-40: 135°40-41: 50°41-42:135°42-43: 105°45-46: 50°46-47: 160°47-48: 100°
31-33: 240°32-34: 180°33-35: 150°34-36: 220°35-37: 250°
I-I+1
I-I+2
36-38: 165°37-39: 210°38-40: 245°39-41: 185°40-42: 185°41-43: 240°43-45: 215°45-47: 210°46-48: 260°
31-34: 295°32-35: 275°33-36: 275°34-37: 345°35-38: 290°36-39: 275°37-40: 285°38-41: 295°39-42: 320°40-43: 290°42-45: 320°43-46: 265°
I-I+3
45-48: 310°
31-35: 390°32-36: 400°33-37: 400°34-38: 385°35-39: 400°36-40: 410°37-41: 335°38-42: 430°39-43: 425°41-45: 455°42-46: 370°43-47: 435°
31-36: 515°32-37: 525°33-38: 440°34-39: 495°35-40: 535°36-41: 460°
I-I+4
I-I+5
37-42: 470°38-43: 535°40-45: 505°41-46: 505°42-47: 530°43-48: 525°
31-37: 640°32-38: 565°33-39: 550°34-40: 630°35-41: 585°36-42: 595°37-43: 575°39-45: 640°40-46: 550°41-47: 665°42-48: 630°
31-38: 680°32-39: 675°
I-I+6
I-I+7
33-40: 685°34-41: 680°35-42: 720°36-43: 700°38-45: 750°38-46: 800°39-47: 850°40-48: 815°
31-39: 790°32-40: 810°33-41: 735°34-42: 815°35-43: 825°37-45: 790°38-46: 750°39-47: 850°40-48: 815°
31-40: 925°32-41: 860°
I-I+8
I-I+9
33-42: 870°34-43: 920°36-45: 915°37-46: 840°38-47: 960°39-48: 950°
31-41: 965°32-42: 995°33-43: 975°35-45: 1040°36-46: 965°37-47: 1000°38-48: 1060°
•
•
31-48: 1740°
I-I+10
I-I+17
120 additional
restraints
Second Conclusion Slide
• PISA wheels and Dipolar waves together define
precise rotation and tilt angles for the helices.
• The combination of orientational and distance
restraints is needed for high resolution structural
characterization of transmembrane helices.
• CrgA characterized by ssNMR is the first protein of
the Mycobacterium tuberculosis divisome to be
structurally characterized.
• It is possible to characterize the nascent structure of
Intrinsically Disordered Domains.
• The CrgA data for two helices fit remarkably well to a
single PISA wheel pattern implying that the helical
structures are remarkably uniform.
• Correlation Restraints provide additional restraints
between the peptide planes resulting in a high
resolution structure of the helical backbone.
Other Helices Occur - 310 Helices: Voltage Gated 2-pore channel – PDB 5E1J
Guo et al., (2015) Nature
f/y h-bond-62°/-33°-59°/-61°-48°/-49°-71°/-59°-81°/3°-112°/-42°-66°/-30°-62°/-28°-94°/35°-87°/-1°-71°/-9°-71°/-21°-94°/6°-72°/-15°-74°/-11°-72°/-14°-81°/-12°-68°/-19°-63°/-28°-67°/-19°-68°/-16°-74°/-12°
1.9
Å
2.2
Å 2.3
Å
2.3
Å
2.5
Å2.3
Å
2.2
Å
2.3
Å
3.1
Å
2.3
Å
2.0
Å
2.7
Å
3.0
Å
2.4
Å
2.3
Å
1.9
Å
2.0
Å
2.3
Å
a-helix
310-helix
Why use a 310 helix?
Helices Residues & Atoms per turn: a-Helix: 3.6 residues & 13 atoms (3.613 helix)
310-Helix: 3.2 residues & 10 atoms (3.210 helix)
-Helix: 4.4 residues & 16 atoms (4.416 helix)
Helices
Kim & Cross (2004) JMR.
310 Helix a Helix Helix
3.6 Res./turn
= 100°/res.
4.3 Res./turn
= 84°/residue
3.2 Res./turn
=
112°/residue
Helical
Wheels
= peptide
plane tilt
angle wrt
helix axis
Rhamachandran Diagram
The Rhamachandran-delta diagram
• For uniform
helical structures:
Lines of constant
peptide plane tilt
angle
Kim & Cross, JMR 2004
Helices
PISEMA Simulations
Helical Wheels
310 a
Kim & Cross, JMR 2004
Helices
310 a
Pisema Simulations
Kim & Cross, JMR 2004
PISA Wheels
as a function
of
Kim & Cross, JMR 2004
Membrane Protein Environment
Dielectric Constant: 2 to 220 80
[H2O]: ~10-6 to 55 M 55 M
Fluidity Scd: 0 - 0.4 0
Lateral Pressure: 1 to 300 atm 1 atm
Electric and Chemical potentials
across the membrane
Variable Lipid and Protein
Composition
Protein Structure and Function are
modulated by the Membrane
Environment & Lipid Composition
Membrane
Environment
Aqueous
Environment
Tamm (2011)
Nobel Laureate Christian
Anfinsen’s thermodynamic
hypothesis states “…that the
native conformation (of a protein)
is determined by the totality of
inter-atomic interactions and
hence by the amino acid sequence
in a given environment.”Science July 20, 1973
Observed PISA Wheels: = 9±4°; f=-60°, y=-45°
Page et al., Structure 2008
Helical Torsion Angles
• The difference between fy
angles of -40°, -65° and -45°, -
60°
Page et al., 2008 Structure
Dependence of PISA Wheels on Local Conformation
f= -60 ± 0°y = -45 ± 0°
f= -60 ± 4°y = -45 ± 4°
f= -60 ± 8°y = -45 ± 8°
Page et al., 2007 MRC
Torsion Angle Data for Membrane Proteins
from x-ray crystallographic structures
Page et al., 2008 Structure
• Each ellipse contains 90% of the TM helical torsion angles
• Since the crystal lattice is a not a membrane environment we expect less
torsion angle variation in structural characterizations performed on membrane
proteins in lipid environments
Bacteriorhodopsin
Structures:
1C3W: 1.55Å
1QHJ: 1.9Å
1AP9: 2.35Å
1BM1: 3.5Å
Hydrogen Bond geometryNH•••O CO•••N
Angles + H•••O dist.
• NH•••O angles are
typically ≥140°
• CO•••N angles are
typically between 140
and 160°
• H•••O distances are
typically between 2.0
and 2.4Å
Page et al., 2008 Structure
In 2007: Diacyl-Glycerol Kinase – Oriented Sample PISEMA
Spectra Published:
• 3 Met Residues all in the
predicted 3 TM helices
• 5 Trp residues 3
predicted to be in TM
helices and 2 in
Amphipathic Helices
Li et al.,2007 JACS
nn
Van Horn et al., (2009) Science
In 2009 –A Solution NMR Structure in Detergent Micelles
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M66
M63
M96
W112
W117
W47 W18
W25
Murray et al., Biophys. J. 2014
Very Poor
Agreement
with the
PISEMA Data
Obtained in
Lipid Bilayers.
nn
In 2013 X-Ray structures in Lipidic Cubic Phase: WT DgkA –A&C
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M63
M96
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Li et al (2013) Nature
Structures A and C
Are in Near Perfect
Agreement with the
PISEMA Data
nn
Li et al (2013) Nature
In 2013 X-Ray structures in Lipidic Cubic Phase: Structures A&B
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M63
W112
W47
W18W25
W117
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W117
• Structures B displays
Significant Deviations from
the Lipid Bilayer Results
• Structure B has multiple
Thermal Stabilizing
Mutations - one of these
was A41C in the TM
domain
Third and Final Set of Conclusions
• The scatter in the observed data is restricted to
± 4° in (peptide plane tilt)
± 8° in f/ytorsion angles
Modest chemical shift tensor element magnitude and orientation
variation except for Glycine.
• These OS ssNMR studies were the first studies to show the
uniformity of helical structures in lipid bilayer environments –
a feature that is now well accepted in the crystallographic
community.
• Distinction between of 310 and a-helices is clear
• This high resolution structural detail is available for validating
structures obtained by other methods and in other environments.
• Solid State NMR can Uniquely Characterize the Structural and
Dynamic Details in Membrane Proteins in a variety of model
environments and in cell membranes
Spins Up
