Tai-huang Huang
Inst. Biomedical Sciences, Academia Sinica April 12, 2016 (NTU/IAMS)
Nuclear Magnetic Resonance
– From Basic Physics to Biomedical Applications
3. Manipulation of nuclear spins -
Spin gymnastics.1. The Dawn of NMR –
It is all Physics.
Outline
2. Exploiting the power of NMR –
A party for all.Chemistry, biology, material science, and medicine.
5. Look back on a wonderful journey.
4. Biomedical applications –
Work from our lab.- Packaging of SARS CoV nucleocapsid.
- Mechanism of SUMO mediated signal transduction.
- Macromolecular dynamics in solid and solution.
1. The Dawn of NMR – A fertile ground for physicists
1924 Pauli proposed the presence of nuclear magnetic moment to explain the presence of hyperfine shift in atomic spectra.
1930 Nuclear magnetic moment was detected using the refined Stern-Gerlach experiment by Estermann.
1939 Rabi et al first detected nuclear magnetic resonance by applying rf energy to a beam of hydrogen molecules.
1946 Purcell et al at Harvard reported nuclear magnetic absorption in parafilm wax.
Bloch et al at Stanford reported nuclear magnetic resonance phenomenom in liquid water.
1940s-60s NMR theories were developed by physicists.
2. Exploiting the power of NMR –
A party for all 1949 Chemical shift phenomenon was observed.1960s
- Ernst and Anderson intrlioduced Fourier Transform technique into NMR that increased NMR sensitivity by orders of magnitude.
- Solid state NMR was revived due to efforts of Waugh at MIT.
Application to material and polymer science insoluble proteins etc.
- Biological application became possible due to the introduction of superconducting magnet and high power computers.
- NMR imaging was demonstrated (Lauterbur at Stony Brook).
1970s
- Development of multi-dimensional NMR (Jeneer, Ernest, Bax ..) - Development of methodologies for determining macromolecular
structure (Wϋthrich).
1980s and beyond – Exploding applications.
- Methods for characterizing macromolecular structure/dynamics in solution matured.
- Macromolecular structures in solid and gel states become feasible.
- Material science: Zeolites, polymers,
fuel cells
etc.(Clare Grey in Cambridge on Li-Air battery 5x more compact)
- MRI become a powerful clinical imaging modality.
- Functional MRI come to stage.
- Development of several fast NMR methodologies.
- NMR-based Metabolomics.
- ……
Non-trivial applications.
- Each become a sub-discipline by itself.
Felix Bloch Physics, 1952 Edward M. Purcell
Physics, 1952
Kurt Wὕthrich Chemistry, 2002 Isador I Rabi,
Physics 1944
Paul C. Lauterbur
Physiol. Medicine, 2003 Peter Mansfield Physiol. Medicine, 2003 Richard R. Ernst
Chemistry, 1991
Nobel Laureates in NMR
NMR Spectroscopy
B
oRadio Wave h
n
Energy
Bo= 0 Bo
E = hn
Biologically interested nuclei:
1H, 13C, 15N, 19F, 31P (S=½),2D (S=1)
Larmor Equation (I = ½):
n = B
o/ 2
n = Larmor frequency
= nuclear gyric ratio
Bo = magnetic field strength
-1/2
+1/2
Basic Nuclear Spin Interactions
Nuclear Spin i Nuclear Spin j Electrons
Phonons 3
4 4
3
5
1 2 1
6
7
H
oH
oDominant Interactions: H = HZ + HCSA+ HD + HQ + HJ + …
Hz : Zeeman Int.; HCSA : Chemical Shielding Anisotropic Int.;
HD= : Dipolar Int. HQ : Quadrupolar Int. HJ : J-Coupling
Zeeman Interaction (Hz.) (Field depend);
Interaction of nuclear spin with external magnetic field .
HQ = -γIZ • Bo
Chemical Shielding Anisotropic Interaction (HCSA) (Field dep.);
The nuclear shielding effect of an applied magnetic field, caused by an induced magnetic field resulting from circulation of surrounding electrons
HCSA = -γI • σ • Bo
Dipolar Interaction (HD) (Thru space) (Field indep):
Interaction between adjacent nuclear spins through magnetic dipolar field.
Basic Nuclear Spin Interactions
Quadrupolar Interaction (HQ) : (Field indep)
Nuclei with spin > 1/2 have a asymmetric distribution of nucleons (non spherical distribution of positive electric charge)
HQ = I · V · I
J-Couplings (Thru bond connection) : ( Field indep)
Resonance splitting mediated through chemical bonds
connecting two spins. It is an indirect interaction between two
nuclear spins which arises from hyperfine interactions between the nuclei and local electrons.
1H 1H 1H
β1 β2 The resonance frequency of a nuclear spin in single crystal depends on the orientation of the tensorial interaction w.r.t. the magnet field.
Single crystal
Interaction Magnitude (Hz) (1H at 2.1T)
Zeeman 108
Quadrupole 106
Chemical shift 103
Dipole 103
J-Coupling 10
NMR spectrum of samples in solid states
Powder patterns
NMR spectra of samples in different states
Small molecules in solution
Gel state (Slow motion)
<HD> = <HQ> = 0
<HCSA> = σiso; <HJ> = Jiso Well-resolved sharp lines
Macromolecules
(Slow tumbling) Broad overlapping
Gel state
(Featureless humps)
1. NMR spectra contains rich information derived from the presence of multiple interactions.
2. Each interaction provide insights into the structure/dynamics of the spin system.
3. It is difficult to quantify the interaction when there are more than one present.
Question:
How to extract the inter-twined interactions ?
Design special pulse sequences to selectively observe/
suppress certain interaction(s)
Spin gymnastics
Features:
1. Dramatically increased spectral resolution !
2. Dramatically increased sensitivity of insensitive nuclei ! Enhancement factor ∝ (γH/γI)3
3. Opened a door for thru-bond sequential resonance assignment (Thru J-coupling).
4. The idea can be extended to higher dimension to include multiple nuclei and field gradients etc
Example: (HSQC)
(2D Heteronuclear Single Quantum Correlation Spectroscopy)
B
oRadio Wave h
n
NMR Spectroscopy Classical view
Y
X Z
MX MY MZ
RF field (B1Y)
Bo
Magnetization will be flipped around Y-axis toward X-Y plane by an angle , determined by the RF field strength and the pulse duration.
Net magnetization
M
= B
1Yτ
= 90o it is call a 90o pulse or /2 pulse (maximum signal)
= 180o it is call a 180o pulse or pulse (No signal)
Protein peptide chain
Efficiency sin(2J); Maximum transfer when 2J = /2.
Pulse sequence for
15N-HSQC expt
15N-HSQC of RC-RNase
1H
15N
Ser135 RC-RNase (12 kDa)
Each spot is a 1H-15N pair of a residue
Biomedical Applications
Molecules Cell tissue Organ Whole body
1. Chemical Identification:
A. Identification of metabolites (Metabonomics) B. Drug discovery.
2. Macromolecular structure:
3. Macromolecular Dynamics:
4. Magnetic Resonance Imaging (MRI):
2. Macromolecular structure:
3. Macromolecular Dynamics:
1. Chemical Identification:
Organic synthesis, natural product identification etc.
NMR spectrum is the finger print of a chemical
Proton spectrum of ethyl acetate
2. Metabonomics
–Metabonomics aims to measure the global, dynamic metabolic response of living systems to biological stimuli or genetic manipulation. It seeks an
analytical description of complex biological samples and to characterize and quantify all the small molecules in such a sample (Urine, blood, plasma etc).
(Nicholson and Lindon, Nature 455, 1054, 2008)
Pattern recognition
Identify metabolites
Statistical analysis Raw data (Urine, blood etc)
NMR spectrum of human urine
Very complex !
Population studies show:
Metabolic variation is much larger than genetic variation !
•
Japanese N = 1000
Americans N = 900 (Urinary Metabotypes)
Chinese N = 900
The World Phenome Center network
中研院台灣人體生物資料庫
(Taiwan Biobank)
Collect and sequencing 300k samples (200K healthy, 100K patients of various diseases).
(Already Collected over 60k samples now.)
Perform genome sequence data of all samples for researchers performing other analyses (Data mining).
Already identified diabetes markers from genome analysis.
Hope to include NMR- and Mass-based metabonomics data.
2. Macromolecular structure/function
NMR Sample (1 mM, 0.4 ml)
2H, 13C, 15N-label
Obtain NMR spectra Assign resonances
Obtain restrains (Distances, angles,
Orientations etc) Calculate structures
Determine Protein Structure by NMR
NMR structures
(Ensemble of 20 structures)
Sequential resonance assignments
M transfer pathway for HNCA:
1H 15N 13Cα 15N
1H for Detection
Detect 1H, 13C, 15N resonances
Permit sequential correlation of backbone 1H-13C-15N resonances !!!
Heteronuclear multidimensional NMR experiments thru J-coupling
1. Build a random structure of the given sequence.
2. Energy minimization with least violation by molecular dynamics and simulated annealing to generate many structures.
Etotal = Ebond + Eangle + Eimproper + EVDW + Ecdih + ENOE + ERDC +….
Ebond = kb(b-b0)2; Eφ = kφ(φ-φ0)2; EVDW = kij[(σij/rij)12-σij/rij)6] Eimproper = kimpr(ω-ω0)2; Ecdih = kcdih(Ψ-Ψ0)2;
ENOE = kNOE(γ-γ0)2; ERDC = kRDC(θ-θ0)2;
3. Select 20 structures of least NOE violation (> 0.5 Å).
4. Criteria for good structures:
a) No NOE violation b) RMSD < 0.5 Å
c) No dihedral angle violation (Ramachandran diagram)
Structure Calculation
NMR structure of RC-Rnase
Ensemble of a set of lowest energy structures
1
H –
1H NOESY spectrum of RC-Rnase
Identify short 1H – 1H distances
1 H chemical shift (ppm)
1H chemical shift (ppm)
Tedious !
Gallery of structures determined
RC-RNase Onconase E. Coli Thioesterase
Dynamics-Fast Motion
Slow Motion
BCKD - LBD BCKD - SBD
Blo t 5 Allergen KP CoA Binding Protein
KP Feo A protein
SUMO-3
Dynamics of onconase
N248-365 of SARS CoV Telomere binding protein
Gallery of structures determined
HDGF dimer of HDGF
N248-365 of SARS CoV octamer
Model of N248-365 of SARS CoV/RNA complex PWWP-domain of HDGF
AtTRP/DNA complex HDGF/heparin complex
2.1. Packaging of SARS Coronavirus Ribonucleocapsid
Four Structural proteins:
EM Schematic
E: Envelope protein (76 a.a.) S: Spike protein (1255 a.a.);
M: Membrane protein (221)
Causative agent – SARS Coronavirus
1. A single stranded plus-sense enveloped RNA virus.
2. Genome of 29,751 nt, containing 14 ORF encoding 28 proteins
N: Nucleocapsid protein (422 a.a.)
Nucleocapsid Protein (NP)
Binds to RNA to form a helical ribonucleoprotein (RNP):
Important in virion assembly, packaging and release.
Interacts with various host proteins and implicated in functions such as replication and apoptosis etc:
The most abundant viral protein and a major antigenic determinant:
Target for detection and vaccine developments.
- Interacts with AP-1 signal transduction pathway ?
- Interacts with Smad3 and Modulates transforming Growth Factor- Signaling
- Inhibits Cell Cytokinesis and Proliferation by Interacting with Translation Elongation Factor 1
Unravel the packaging mechanism of helical ribonucleocapsid (RNP) :
1. Dissect N protein domain architecture 2. Probe N protein interaction with RNA.
3. Determine the tertiary structure of N protein.
4. Understand how RNA packs with N protein to form the helical RNP.
Goal
Dissecting Domain architecture of N protein
N181-246 N248-365 N248-422
Divide and conquer – Construct many sub-fragments and characterize their structures.
The full length protein (422 a.a.) cannot be crystallized and the NMR spectrum is bad
NTD
CTD
Linker NTD+N-term
CTD+C-term Di-domain
Characterization of protein order by 2D 15N-HSQC
1H-Chemical shift
1H-Chemical shift
15N-Chemical shift15 N-Chemical shift
Folded protein
Disordered protein
NTD NTD
NTD
CTD CTD
+ CTD
45-365
45- 181 Overlay
248-365
1 45 181 248 365 422
NTD
CTD
Domain architecture of SARS-CoV NP
Structured
(136 a.a.) Structured
(117 a.a.)
Disordered N-terminus
(44 a.a.)
Disordered Linker (67 a.a.)
Disordered C-terminus
(57 a.a.)
CTD CTD
NTD NTD
Light scattering
Analytical Ultra- Centrifugation
Size exclusion chromatography
Chemical cross linking
NMR relaxation
CTD forms a dimer
~ 50% of SARS-CoV residues exist in intrinsically disordered state.
Nucleocapsid proteins belong to a class of proteins with the most disordered residues.
Why ?
What are the advantages ?
1 45 181 248 365 422
NTD
CTD
Structured
(136 a.a.) Structured
(117 a.a.)
Disordered N-terminus
(44 a.a.)
Disordered Linker (67 a.a.)
Disordered C-terminus
(57 a.a.)
Domain architecture of SARS-CoV NP
1D 2D 1. Increase collision cross section.
2. Adapt to different shapes.
3. Coupled allosteric effect (Multi-valency effect).
Advantage of intrinsic disorder
NMR Structure Of SARS-CoV NP CTD
28 kDa homo-dimer solved by Stereo-Array Isotope Labeling (SAIL) method (M. Kainosho of Nagoya U)
A flatten rectangular domain-swapped dimer
Primary RNA binding site.
(ppm)
R320
H335
A337 Q304
Residue Number
Identification of RNA binding site in CTD
Black: Free
Red: RNA-bound
N protein binds to nucleic acid at multiple sites
cooperatively, much like an octopus clinching onto it prey.
N – Nucleic Acid Interaction
Modular nature and intrinsic disorder are keys to binding cooperativity and RNP packaging
Top view Side view
X-ray crystallography
- Structure similar to that determined by NMR.
- CTD packs as an octamer in an unit cell.
Crystal packing
Stacking of 3 octamers forms a complete turn of a left-handed twin helix.
210 Å
30 Å90 Å
DNA binding site NMR (magenta)
We propose that RNA binds to the Left-handed helix grooves.
DNA binding sites are located in the positively charged grooves
Surface Charge Potential RNA binding model
A modular protein: It consist of two structured domains and three disordered segments.
It is highly flexible: ~50% of the residues are intrinsically disordered (ID).
A sticky protein: It binds to RNA at multiple sites cooperatively.
The CTD forms a dimer and packs in helical structure in crystal.
Key features of SARS CoV N protein
Proposed model of the N/RNA complex
CTD forms the core of the left-handed twin-helix .
NTD covers the exterior and interacts with the bases.
NTD
Backbone of RNA wraps around CTD core and with bases facing outward.
Side view Top view
N/RNA complex (RNP)
This is just a model !
RNA
Helical RNP
Acknowledgements
Huang’s lab
Dr. Chungke Chang Dr. Chi-fon Chang Dr. Shih-Che Su Dr. Wen-Jing Wu
Yen-lan Hsu Yuan-hsiang Chang Fa-an Chao Tsan-Hung Yu
Hsin-I Bai Liliarty Riang
Hsin-hao Hsiao Yen-Chieh Chiang
X-ray crystallography
Dr. Chwan-Deng Hsiao Chun-Yuan Chang
Yi-Wei Chang
SAIL NMR (Nagoya U) Prof. M. Kainosho
Mitsuhiro Takeda Dr. Chungke Chang
SAXS (NSRRC, Taiwan)
Dr. Yu-shan Huang (SAXS)
NMR Structure
Prof. Peter Guetert (RIKEN)
3. Dynamics
Protein Dynamics
- Energy landscape of protein conformations
Ref. 1. Henzler-Wildman & Kern (2007) Nature 450 :964-72 2. Boehr and Wright (2006) Chem Rev. 106(8):3055-79
Measurement of Macromolecular Dynamics by NMR
NMR experiments
Biological processes
Time scale
NMR can measure a wide range of dynamic processes
N-palmitoylglactosylceramide
Characterize the restricted rotational isomerization of polymethylene chains by deuterium NMR lineshape simulation
Huang et al J. Am. Chem. Soc. 102, 7377-7379 (1980)
Deuterium quadrupole spectra were simulated with two site flipping model similar to that of the crankshaft motion.
Expt Simulated
Crankshaft motion
Huang et al J. Am. Chem. Soc. 102, 7377-7379 (1980)
Tetrahedral two site flipping model
D1
D1
Liquid state - NMR Relaxation
R1 =1/T1 = (d2/4)[J(H - N) + 3J(N) + 6J(H + N)] + c2J(N) --- (1) R2 =1/T2 = (d2/8)[4J(0) + J(H - N) + 3J(N) + 6J(H) + 6J(H + N)]
+ (c2/6)[4J(0) + 3J(N)] + Rex --- (2)
Relaxation Mechanism
Dominated by dipolar and chemical shift anisotropic interactions, and are related to the spectral density functions, J(), by the following
equations:
where d = (ohN H/82)(rNH-3), c = N(σ‖- σ)/3.
o : permeability constant of free space; h: Planck constant;
i : magnetogyric ratio of spin i; i: Larmor frequency of spin i;
rNH = 1.02 Å: length of the NH bond vector; Rex: exchange rate;
σ‖- σ = -170 ppm (size of the CSA tensor of the backbone amide nitrogen).
(Dipolar term) (Chemical shift term)
XNOE = 1 + (d2/4)(H/ N)[6J(H + N) - J(H - N)] T1 --- (3)
W
hat is J() ? -Modelfree analysis
J() = ]
)2 ( '
1
) ' 2 ( 2
)2 ( '
1
) ' 1 2
( )2
( 1 [ 2 52
s S s S f
f f S f
m S m
For a rigid macromolecule undergoing Brownian motion with a rotational
correlation time m and local internal motion with rotational correlation time s the spectral density function, J() is given by:
S2: Order parameters (Magnitude of motion)
R ex : Chemical exchange rate (Slow motion in ms or s regime)
: Correlation times (Speed of motion)
Fitting T1, T2 and NOE data to determine
S
2, and R
exRelaxation Data
Obtained in two fields:
: 500 MHz : 600 MHz
Order parameter
S2av= 0.85
S = 1 rigid S = 0 random
Mostly rigid Flexible
region
Exchange rate – Residues with low motion
Dynamics of E. coli Thioesterase I
Order parameter Exchange term
Huang, et al. (2001) J. Mol. Biol. 307, 1075-1090.
Order parameter Slow motion
Ref. Loria, Rance, and Palmer III (JACS. 1999, 121, 2331-2332)
Carr-Purcell-Meiboom-Gill (CPMG) Sequence
cp
Measuring millisecond time scale motion
In which ex = (1- 2)2p1p2; pi and i are the populations and Larmor frequencies for the nuclear spin in site i, respectively; and
ex is the lifetime of the exchanging sites.
Solve for ex for different cp (measure 0.5 – 5 ms range)
Onconase
800 MHz 600 MHz
69
Energy
Reaction coordinate ES
EI
ΔEa ~ 22 kcal/mol
pA = 99.2% pB = 0.8%
ΔG ~ 2.9 kcal/mol
𝐸 + 𝑆 ⇌ 𝐸𝑆 ⇌ 𝐸𝐼 → 𝐸 + 𝑃
Catalytic scheme:
Reflection of a Wonderful Journal
1. NMR is a prime example of the importance of basic research. The impact of basic research often takes long time to realize.
2. Science is full of surprises. It is only limited by your imagination.
Griffin “John Waugh basically invented the field of solid- state NMR when everyone else had left the field because they thought it was never going to work,"