TROSY, transverse relaxation-optimized spectroscopycomplexity of the NMR spectra, both of which...
Transcript of TROSY, transverse relaxation-optimized spectroscopycomplexity of the NMR spectra, both of which...
TROSY, transverse relaxation-optimized spectroscopy
Konstantin Pervushin
Laboratorium für Physikalische Chemie, Swiss Federal Institute of Technology, ETH- Hönggerberg,
CH-8093 Zürich, Switzerland.
Konstantin Pervushin: [email protected]
EMBO Practical Course, Heidelberg September 10-17, 2003
TROSY scope The general problem posed in 3D structure determination of biomolecules by NMR involves the
collection of a sufficiently dense set of experimental restraints to define the structure. Experimental
restraints can be derived from interproton NOEs [1-3], residual dipole-dipole couplings and CSA
interactions [4-9], scalar J couplings [1, 10], J couplings across hydrogen bonds [11, 12] and auto- and
cross-correlated relaxation rates [13, 14]. Currently available computer-based 3D structure
reconstruction methods require that a large number of experimental restraints are assigned to particular
atoms in the protein’s chemical structure at the outset of structure determination [15]. In large proteins
this assignment problem is aggravated by fast transverse relaxation of the spins of interest and the
complexity of the NMR spectra, both of which increase with increasing molecular size [16-19]. The use
of TROSY [20] together with uniform deuteration [21-24] reduces the transverse relaxation rates of 1HN, 15N and 13Caromatic spins. TROSY triple resonance 3-D and 4-D NMR experiments were developed
[25-28] enabling successful assignment of the backbone resonances in large biomolecules.
1
Oligomeric proteinsLarge single chain proteinsβ-barrel membrane proteins Polytopic α-helical membrane proteins
Nucleic acids and small proteins
Protein/protein and
Large supramolecular complexes
protein/nucleic acid interactions 200 kDa
100 kDa
50 kDa
800 kDa
(fine detailes of 3D structures, dynamics)
(bb and sc assignment, 3D folds, dynamics)
(chem. shift mapping, surface mapping,
(detection of individual resonances)
drug discovery)
The estimated range of molecular weights of biological systems the most effectively studied by TROSY NMR
Biological molecules studied by TROSY
- With the use of TROSY the backbone 1HN, 15N, 13Cα and side-chain 13Cβ resonances were
assigned in 81.4 kDa E. coli malate synthase G (MSG), a 723-residue monomeric enzyme, and an
isoaspartyl linkage in the protein sequence was identified [29].
- TROSY was successfully used to establish the backbone 1HN, 15N, 13Cα and side-chain 13Cβ
resonance assignment of a uniformly 2H,15N,13C labeled homooctameric S. aureus 7,8-dihydroneopterin
aldolase [30] with molecular weight of 110 kDa.
- The 44 kDa 30% randomly deuterated and uniformly 13C,15N-labeled water soluble trimeric
enzyme B. subtilis Chorismate Mutase was used to develop a set of TROSY-type experiments for
backbone assignment of large nonedeuterated or only partially deuterated proteins [31-33].
- The use of TROSY-based NMR experiments with the E. coli integral membrane proteins OmpX
and OmpA in mixed micelles with the detergent 1,2- dicaproyl-glycero-3-phosphocholine (DHPC) [34].
For OmpX, complete sequence-specific NMR assignments have been obtained for the polypeptide
backbone. The 13C chemical shifts and nuclear Overhauser effect data then resulted in the identification
of the regular secondary structure elements of OmpX/DHPC in solution, and in the collection of an
input of conformational constraints for the computation of the global fold of the protein [34]. For
OmpA, the NMR assignments are so far limited to about 80% of the polypeptide chain [35, 36],
indicating different dynamic properties of the reconstituted OmpA β-barrel from those of OmpX.
2
Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX
from E. coli and DHPC provided a detailed description of protein-detergent interactions [37].
- The global fold of E. coli PagP, a bacterial outer membrane enzyme which transfers a palmitate
chain from a phospholipid to lipid A, was determined in both dodecylphosphocholine (DPC) and n-
octyl-beta-D-glucoside (OG) detergent micelles using TROSY [38]. PagP consists of an eight-stranded
anti-parallel β-barrel preceded by an amphipathic α-helix. The β-barrel is well defined, whereas NMR
relaxation measurements reveal considerable mobility in the loops connecting individual β-strands.
- A model of a E. coli diacylglycerol kinase (DAGK), an α-helical polytopic membrane protein that
spans the lipid bilayer three times and which is active in some micellar systems, was built based on the
use of TROSY among other solution NMR techniques [39-41]. It was established that DAGK is
homotrimeric in decyl maltoside (DM) micelles and mixed micelles. The aggregate detergent-protein
molecular mass of DAGK in both octyl glucoside and DM micelles was determined to be in the range of
100-110 kDa.
- Some of the backbone resonances were assigned in a paradigm of all polytopic transmembrane
proteins - bacteriorhodopsin [42].
- On the surface of the NMR structure of the 23 kDa two-domain periplasmic chaperone FimC
from E. coli the contact sites with the 28 kDa mannose-binding type-1 pilus subunit FimH were
identified by 15N and 1H NMR chemical shift mapping, using TROSY [43].
- NOE steady-state cross-relaxation combined with TROSY allowed identification of the binding
surface of protein A with the Fc portion of immunoglobulin G [44].
- The interaction between the lectin chaperone calreticulin (CRT) assisting the folding and quality
control of newly synthesized glycoproteins in the endoplasmic reticulum (ER) and the thiol- disulfide
oxidoreductase (ERp57) promoting the formation of disulfide bonds in glycoproteins was studied by
TROSY [45].
- Transverse relaxation-optimized spectroscopy provided data on the thermodynamics and kinetics
of the complex formation and on the structure of this 66.5 kDa complex. Chemical shift mapping
showed that interactions with ERp57 occur exclusively through amino acid residues in the polypeptide
segment 225-251 of CRT(189-288), which forms the tip of the hairpin structure of this domain [45].
- Compared with conventional NMR correlation spectroscopy [46], [15N,1H]-TROSY [20, 47]
yielded about 70% and 30% reduction of the 15N and 1H line widths, respectively, in the signals of the
guanosine 15N1–1H and thymidine 15N3–
1H imino groups in 15N-labeled DNA [12]. The reduced TROSY
line widths then allowed the direct observation of scalar couplings across hydrogen bonds involved in
base pairing either by direct measurement in resolved multiplet fine structures [12, 48] or in more
complex coherence transfer experiments [11, 12, 48-52].
3
- In conjunction with quantum-chemical calculations [49, 53], precise measurements of scalar
couplings across hydrogen bonds can be expected to provide novel insights into the nature of hydrogen
bonds in macromolecules.
- TROSY was used to extend applicability of the conventional 15N and 13C relaxation
measurements [54] for studies of intramolecular dynamics in large nucleic acids [55] and proteins [56].
Extremely large (in NMR scale) protein complexes
The cross relaxation-enhanced polarization transfer (CRINEPT) technique in combination with
TROSY optimized for large systems promises yet another several fold increase in the molecular size
limit for NMR studies [57, 58]. These techniques prevent deterioration of the NMR spectra by the rapid
transverse relaxation of the magnetization to which large, slowly tumbling molecules are otherwise
subject. With the experimental conditions used, the line widths of the TROSY-components of the 1H-
and 15N- signals were of the order of 60 Hz at 400 kDa, whereas, for structures of size 800 kDa, the line
widths were about 75 Hz for 15N and 110 Hz for 1H [58]. The uniformly 2H,15N- labelled 72 kDa
homoheptameric co-chaperonin GroES, either free in solution or in 800 kDa complex with the
homotetradecameric chaperonin GroEL or with the 400 kDa single-ring GroEL variant SR1 were
successfully studied in solution [59]. Most amino acids of GroES showed the same resonances whether
free in solution or in complex with chaperonin; however, residues 17-32 showed large chemical shift
changes on binding. This established the utility of these techniques for solution NMR studies that
should permit the exploration of structure, dynamics and interactions in large macromolecular
complexes [59].
4
ppm
7.87.98.08.18.2 ppm
124.5
125.0
125.5
126.0
126.5
8.0 2(1H) [ppm]8.2
COSY no dec.
7.707.757.807.857.907.958.008.058.108.158.20 ppm124.5125.0125.5126.0126.5 ppm
126 1(15N) [ppm] 8.0 2(1H) [ppm]8.2
125
126
1(15N)[ppm]
124
1
2
4
3S
SI
I
S34 S12 I13 I24
αα
ω ω
ω
ω
αβ
βα
ββ
Energy level diagram of a two spin 1/2 system IS showing the identification of components of the 2D multiplet with
off-diagonal density matrix elements expressed via single transition basis operators, I13, I24, S12 and S34, connecting
eigenstates j and k of the static Hamiltonian superoperator. The diagram is not drawn to scale. 2D cross-peak from the
[15N,1H]-HSQC spectrum of a backbone amide moiety of u- [15N,2H]-Aldolase, 110 kDa at 20oC measured without 1H and 15N decoupling.
TROSY techniques
1. Coherent evolution: coherence/polarization transfer by unitary rotations and design of NMR
experiments.
2. Stochastic processes: spin relaxation in a multispin system.
3. A combination of both: polarization transfer by relaxation.
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1. Coherent evolution: coherence/polarization transfer by unitary rotations and design of NMR
experiment.
Set of basis operators for a two spin ½ system.
The vector Basis forms an orthonormal, zero-trace, and by multiplication with i the skew-Hermitian
(see some useful explanations in Appendix) (or antihermitian, A† = -A, where † means adjoint or hermitian
conjugation or A† = Conjugate//Transpose//A operation) basis set for Lie Algebra su(4) special unitary
group for a 4 energy-level problem.
Each individual spin operator can be represented by a 4x4 matrix:
6
This basis set ensures that each of the individual exponentials of the form ebi is unitary.
This would not be the case if, for instance, irreducible spherical tensor or single-element
polarization/step operators were chosen as a basis, in which case bindings between the coefficients in
the exponentials are needed to ensure unitarity of the full propagator [60].)
7
However the irreducible spherical tensor T2,0 forms a unitary propagator. It corresponds to the
dipolar hamiltonian, HD = aD Sqrt[6] T2,0.
8
The single-element polarization/step operators:
The multiple quantum operators:
Design of the optimum coherent experiment
9
The conversion of one state to another can be associated with a transfer efficiency. Consider,e.g. [61],
the transfer from a quantum-mechanical state represented by an operator B to a state represented by an
operator A by a unitary transformation U (ignoring dissipative processes)
where Q is a residual operator. The higher the coefficient
the more efficient is the transfer process and thereby the experiment. Determination of amax for a given
coherence or polarization transfer process falls in the field of spin-dynamics bounds. So far, three types
of such bounds have been described for a given transfer B→A.
where ΛX is a vector with the eigenvalues of the Hermitian operator X arranged in descending order
while ΣX is a vector with the singular values of the matrix representation of the operator X also arranged
in descending order. The singular values defined as positive of a matrix M are the nonzero elements of a
diagonal matrix Σ that arise by diagonalization of M by unitary matrices T and V according to M=TΣV†.
Arbitrary matrices can be decomposed in this way and for Hermitian matrices it holds that T = V.
Singular value decomposition is an important element of many numerical matrix algorithms. The basic
idea is to write any matrix m in the form u* mD v, where m is a diagonal matrix, D u and v are row
orthonormal matrices, and u is the Hermitian transpose of u. The function SingularValues[m]
returns a list containing the matrix
*
u, the list of diagonal elements of m , and the matrix D v. The diagonal
elements of m are known as the singular values of the matrix D m. One interpretation of the singular
values is as follows. If you take a unit sphere in n-dimensional space, and multiply each vector in it by
an män matrix m, you will get an ellipsoid in m-dimensional space. The singular values give the lengths
of the principal axes of the ellipsoid. If the matrix m is singular in some way, this will be reflected in the
shape of the ellipsoid. In fact, the ratio of the largest singular value of a matrix to the smallest one gives
a condition number of the matrix, which determines, for example, the accuracy of numerical matrix
inverses. Very small singular values are usually numerically meaningless. SingularValues removes
any singular values that are smaller than a certain tolerance multiplied by the largest singular value. The
10
Hermitian bound applies for Hermitian operators A and B and there is a guarantee that the maximum
efficiency can be achieved by a unitary transformation.
(1) Select the desired polarization transfer pathway.
For the single quantum TROSY in hermitian operators it is:
Sx[2] + 2Sx[2]**Sz[3] → Sx[3] + 2Sx[3]**Sz[2]
In raiselowering (nonhermitian) operators:
S+[2] + 2S+[2]**Sz[3] → S-[3] + 2S-[3]**S-[2]
(note, that only the “minus” operators are directly detectable [62])
(2) Determine amax.
The hermitian bound:
The hermitian bound:
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Hence, we obtain aherm = aSVD = 1.
(3) Use the energy level diagram to search for appropriate selective rotations.
Double Quantum rotations with the phases x and y.
αα
βα αβ
ββ
αα
βα αβ
ββ
For a selective Double Quantum (DQ) x phase π pulse ( πx
sel) the effective hamiltonian takes the form
with the spin functions ordered |αα>, |βα>, |αβ>, |ββ> in the Hilvert space. It follows that the rotation
in Fig must be of an angle π in order to achieve the maximum possible coherence transfer efficiency.
Explicitly, the rotation is
It corresponds to a π rotation operating selectively on the double quantum transition of the two spins
and can indeed be realized experimentally provided there resolved scalar (J) or dipolar coupling
between them.
12
By constructing the corresponding propagators one can verify achieved hermitian and SVD
bounds:
The symbol i indicates a π/2 phase shift of the detected operator.
For a selective Double Quantum (DQ) y phase π pulse ( πysel) the effective hamiltonian takes the form
with the spin functions ordered |αα>, |βα>, |αβ>, |ββ> in the Hilvert space.
Explicitly, the rotation is
13
Zero Quantum rotations with the phases x and y.
αα
βα αβ
ββ
αα
βα αβ
ββ
For a selective Zero Quantum (ZQ) x phase π pulse ( πx
sel) the effective hamiltonian takes the form
or
representing a planar mixing sequence which earlier has been proposed for the accomplishment of
the coherence order selective anti-phase transfer [63].
For a selective Zero Quantum (ZQ) y phase π pulse ( πy
sel) the effective hamiltonian takes the form
14
or
(4) Find out whether the experiment can be realized in a nonselective manner.
We start with the notion that operators Sx[2]**Sx[3] and Sy[2]**Sy[3] commute as well as the
Sx[2]**Sy[3] and Sy[2]**Sx[3] operators.
and
In general,
The propagator
may straightforwardly be converted into a practical pulse sequence using relations of the type
15
transforming the transverse bilinear rotations into mixtures of linear and longitudinal bilinear rotations
which can be realized by rf irradiation and evolution under heteronuclear JIS coupling, respectively. The
latter is typically accomplished by free precession under the unperturbed Hamiltonian
which additionally shows dependence on the isotropic chemical shifts for the two spin species.
Undesired influence from the chemical shifts may by standard means be eliminated by p-pulse
refocusing, i.e.,
resulting in
The practical pulse sequence propagator is (t = 1/(4 JIS)
where the final z rotation is irrelevant in the practical implementation [64].
t2t1
y
15N
1H-y
-y
y
y
The ZQ propagator
represents an original pulse sequence proposed by Pervushin et al. [20] and subsequently called the
SingleTrasition-to-Single Transition Polarization Transfer element (ST2-PT) [47].
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t2t1
y
15N
1Hy
y
A practical implementation of the TROSY experiment based on the ST2-PT element.
Relevant polarization transfer pasways can be represented by the diagram
When both pathways indicated are retained, two diagonally shifted signals represent two out of the four 15N–1H multiplet components in the resulting [15N, 1H]-correlation spectrum. The undesired polarization
17
transfer pathway,12 → 13, is suppressed either by 2-step cycling of the phases ψ1 and ψ5 or by
application of PFGs during t1 and at time point d. The remaining anti-echo polarization transfer
pathway, 34 → 24, connects a single transition of spin S with a single transition of spin I, and in
alternate scans with inversion of the rf-phases ψ2 and ψ4, the corresponding echo transfer, 12 → 13, is
recorded. In the experiments of Fig. 2 we used both the 1H and 15N steady-state magnetizations. The
product operator analysis accounts for this by the following density matrix at time b in the experimental
scheme
The constant factors u and v reflect the relative magnitudes of the steady-state 1H and 15N
magnetizations, respectively, which are determined by the gyromagnetic ratios, the spin–lattice
relaxation rates and the delay between individual data recordings. Since the S34 operators are transferred
to observable magnetization, both the 1H and 15N steady-state magnetizations add up to the signal
obtained with the pulse sequence, which is proportional to (u-v)/2.
Zero quantum TROSY experiment [65]
(1) The desired polarization transfer pathways are
2S+[2]**S-[3] → S-[3] + 2S-[3]**S-[2] (ZQ)
2S+[2]**S+[3] → S-[3] + 2S-[3]**S-[2] (DQ)
(2) The SVD bound is:
amax
SVD = 1.
(3) The energy level diagram to search for appropriate selective rotations.
18
αα
βα αβ
ββ
αα
βα αβ
ββ
For a selective αα−αβ x phase π pulse ( πx
sel) the effective hamiltonian takes the form
with the spin functions ordered |αα>, |βα>, |αβ>, |ββ> in the Hilvert space. The effective
hamiltonian is
(4) Implementation of the effective hamiltonian.
For the transfer process in question we first eliminate the ‘‘selective element’’ represented by the
polarization operators out of the rotations
Since involved operators commute, one obtains
The first z-rotation is immaterial, resulting in the ZQ-TROSY experimental scheme:
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t2t1
y
15N
1Hy -y
A practical implementation of the TROSY experiment based on the ZQ element.
Relevant polarization transfer pasways can be represented by the diagram
ZQ-TROSY is effectively used in the context of 3D 15N-resolved NOESY in order to suppress
strong diagonal peaks.
20
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2. Stochastic processes: spin relaxation in a multispin system
Transverse relaxation in coupled spin systems
We consider a system of two scalar coupled spins ½, I and S, with a scalar coupling constant JIS,
which is located in a protein molecule. T2 relaxation of this spin system is dominated by the DD
coupling of I and S and by CSA of each individual spin, since the stereochemistry of the polypeptide
chain restricts additional interactions of I and S to weak scalar and DD couplings with a small number
of remote protons, Ik. The relaxation rates of the individual multiplet components of spins I and S in a
single quantum spectrum may then be widely different due to the effect of interference between IS
dipolar coupling and anisotropic chemical shift on transverse relaxation [66-68]. Shimizy [69]
suggested to use the DD/CSA interference effect for determination of absolute sign of the coupling
constants by measuring the saturation or the width of each component of a NMR spectrum that gives
multiplet lines through spin-spin couplings. Detailed descriptions of the interference effects on
transverse relaxation in coupled spin systems are available [67, 70-74].
The simplest functional form of the transverse relaxation equations can be obtained by using
single-transition and zero- and double-quantum basis operators [2, 65, 67, 75]. In the slow-tumbling
limit for an isolated IS spin system in the absence of rf pulses and rf field inhomogeneities only terms in
J(0) need to be retained resulting in an uncoupled system of differential equations with the diagonal
form of the first-order relaxation matrix.
where J(ω) represents the spectral density functions at the frequencies indicated:
22
ωS and ωI are the Larmor frequencies of the spins S and I,
h is the Plank constant divided by 2π, rIS the distance between S and I, B0 the polarizing magnetic field,
and ∆σS and ∆σI are the differences between the axial and the perpendicular principal components of
the axially symmetric chemical shift tensors of spins S and I, respectively. Ckl = 0.5(3cos2Θkl-1) and Θkl
the angle between the unique tensor axes of the interactions k and l. The single-transition basis operators
To quantitatively evaluate the transverse relaxation optimization effect and contributions from
other mechanisms of relaxation we consider a specific example where I and S are identified as the 1HN
and 15N spins in a 15N–1H moiety. The internuclear distances and CSA tensors in various model
compounds including amide moieties in short peptides were extensively studied by solid state NMR, so
that we use the data obtained there: the internuclear distance r(15N−1HN) = 1.04 Å for the peptide
backbone amide moieties [76]; ∆σ(1HN) = σzz – (σxx + σyy)/2 = 15 ppm, is axially symmetric with the
angle between the zz axis and the 15N−1HN bond = 10o [77, 78]; ∆σ(15N) = σzz – (σxx + σyy)/2 = -155
ppm, is axially symmetric with the angle between zz axis and 15N− 1HN bond = 15o [79].
0
50
100
200
1000500 1500B0 (1H) [MHz]
(1HN)
[Hz]
(2)
(1)
(3)
10000
50
100
200
500 1500B0 (1H) [MHz]
(15N)
[Hz]
(2)
(1)
(3)
R M(1) 20 ns (~50 kDa)(2) 60 ns (~150 kDa)(3) 320 ns (~800 kDa)
23
The above parameters of the protein backbone amide moiety along with DD contributions from
remote protons are used to calculate dependence of the TROSY 1HN and 15N line width on the
polarizing magnetic field strength expressed in the frequency units for three hypothetical proteins with
molecular weights in the range 50 to 800 kDa. Figure 3 shows that at 1H frequencies in the range of 900
to 1100 MHz significant attenuation of transverse relaxation can be achieved simultaneously for the
TROSY component of the 1HN and 15N multiplets observed for the 15N–1H moieties. For a comparison,
predicted 1HN and 15N line width for the conventional [15N,1H]-HSQC experiment is plotted showing
that the conventional scheme is not applicable for proteins with molecular weights above 150 kDa.
The relevant relaxation rates of 15N-1HN coupled and heteronuclear decoupled resonances were
determined experimentally [80]. A comparison of decay rates for the two 15N-{1HN} doublet
components shows average ratios of 4.8 and 3.5 at 800- and 600-MHz 1H frequency, respectively, in the
perdeuterated proteins, For the protonated proteins these ratios are 3.2 (800 MHz) and 2.4 (600 MHz).
Relative to the regular HSQC experiment, the enhancement in TROSY 15N resolution is 2.6
(perdeuterated; 800 MHz), 2.0 (perdeuterated; 600 MHz), 2.1 (protonated; 800 MHz), and 1.7
(protonated; 600 MHz). For the 1HN dimension, the upheld 1HN-{15N} component on average relaxes
slower than the downfield 1HN-{15N} component by a factor of 1.8 (perdeuterated; 800 MHz) and 1.6
(perdeuterated; 600 MHz). The reported data correspond well with the rates expected on the basis of the
theoretical calculations [26].
24
Appendix
25
26
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