3D Triple-Resonance Methods for Sequential Resonance Assignment of Proteins
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3D Triple-Resonance Methods for Sequential Resonance Assignment of Proteins
H2N CH C
CH2
O
C
NH2
O
N CH C
CH2
O
N
NH
N CH C
CH2
O
CH2
C
OH
O
N CH C
CH2
OH
O
OH
H H H
Strategy: Correlate Chemical Shifts of Sequentially Related Amides to the Same C (or C or CO) Chemical Shifts
C C NN
C
O HH
Intraresidue Correlation (HNCA)
Excite CRecord C frequenciesTransfer to intraresidue NRecord N frequenciesTransfer to HNRecord H frequencies
Interresidue Correlation (HN(CO)CA
Excite CRecord C frequenciesTransfer to intraresidue CO
Transfer to interresidue NRecord N frequenciesTransfer to interresidue HNRecord H frequencies
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Triple-resonance Data
Intraresidue Data(Both C & C)
Interresidue Data(Both C & C)
N CH C
R2
O
CH C
R1
O
N
H H i+1i
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Protein Chemical Shifts IndicateSecondary Structures with High Accuracy
Assign Chemical Shifts (Referencing Relative to DSS)
Compare Chemical Shifts to those in random coil peptides
-helix -sheet
CCC
H
positive negative
none positive
positive negative
negative positive
Wishart, et al., Biochemistry, 31, 1647 (1992)
Wishart, et al., J. Biomol. NMR, 4, 171 (1994)
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Identification of Close Interproton Distances
Protons separated in space by about 5 Å or less will influence the relaxation properties of one another (via dipole-dipole interactions): Known as the Nuclear Overhauser Effect, or NOE
Importantly, note that this effect is in general distinct from the interaction between nuclei via J-couplings; J-couplings are mediated by electron orbital overlap between chemically bonded nuclei and are thus observed between nuclei separated by about 4 chemical bonds, or less
NOEs instead can be observed in theory between any two possible protons within a molecule separated by 5 Å or less (irregardless of the number of chemical bonds by which the atoms are separated)
NOE (1/rIS6)f(c) rIS = internuclear distance
f(c) = statistical quantity which describes the timescale with which a molecule reorients in solution
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NOEs in Structure Determination
NOEs can be identified throughtwo-, three-, and four-dimensional spectra once the 1H resonance assignments are complete
NOESY Procedure:
1. Excite First Proton2. Record Proton Frequencies3. Transfer to Any proton 5 Å or less by NOE4. Record Proton Frequencies
N
HH3C
H2CO
NH2H
H
NH3+
COO-
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NOE Analysis - Practical Aspects
Protein of 150 residues typically has about 30 possible NOEsper residue; unambiguous identification of these can be difficultwith 2D NOE methods alone
NOE spectra can be simplified and extended into more than twodimensions by employing isotope-editing
Procedure:
Excite nitrogenRecord nitrogen frequenciesTransfer to attached proton (J-coupling)Record proton frequenciesTransfer to any proton 5 Å or less (NOE)Record Proton Frequencies
N
HH3C
H2CO
NH2H
H
NH3+
COO-
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Isotope Editing Enhances Spectral Resolution
N
HH3C
H2CO
NH2H
H
NH3+
COO-
Typically 3D 15N-edited NOESY 3D 13C-edited NOESY
4D 13C-edited, 13C-edited 4D 15N-edited, 13C-edited
Typically, recover10 - 15 interresidueNOEs per AA
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Secondary Structures Can Be Characterized
by Regular Patterns of NOEs
K. Wüthrich (1986) NMR of Proteins and Nucleic Acids, Wiley Interscience
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Angular Dependence of 3-bond J-couplings
HN
NCO(i-1)
CO(i)
HR
HHN
Bax, et al. (1994) Measurement of Homo- and Heteronuclear J-couplings from Quantitative J Correlation, Methods Enzymol., 239, 79-105
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Detection of Hydrogen Bonds
C
CON H
C
CON H
C
CON H
h3JNC’ -0.2 to -0.9
h2JHC’ -0.6 to 1.3
h3JHC 0.0 to 1.4
Ref: Grzesiek, et al. (2001) Methods Enzymol., 338, 111-133
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Anisotropic Tumbling w.r.t. to BAnisotropic Tumbling w.r.t. to Boo
Results in Residual Dipolar CouplingsResults in Residual Dipolar Couplings • Magnitude of the dipole-
dipole interaction is orientation dependent w.r.t. to the static magnetic field (Bo)
• Isotropic tumbling w.r.t. Bo normally averages dipolar couplings to zero
• Small, but non-zero, magnetic susceptibility results in residual dipolar couplings that appear as apparent J-splittings
ISθ = 90° I
S
θ = 54.7°θ = 0°I
SBdd ∝ −1 Bdd ∝ +2Bdd = 0
€
Bdd
= Dmax
AB
IAz
IBz
Bz ( 3 cos
2
θ − 1 )
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Induced Residual Alignment of Diamagnetic Induced Residual Alignment of Diamagnetic ProteinsProteins
• Lipid Bicelles LC (Tjandra & Bax, Science, 1997)• Purified Bacteriophage Particles (Pf1) LC(Hansen et al, J. Am.
Chem. Soc, 1998)• Deformed Pores in Nondenaturing Polyacrylamide Gel (Sass
et al, J. Biomol. NMR, 2000)
dimyristoyl-phos-phatidylcholine (DMPC)
dihexanoyl-phos-phatidylcholine (DHPC)
O
12
O
O
12
O
P
O
-O O
N(CH3)+
O
5
O
O
5
O
P
O
-O O
N(CH3)+
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RDC for Proteins in Solution Correlate Very Well WithPredictions from High-Resolution Crystal Structures
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NMR Structure Determination 1. Start with a peptide chain of random starting
conformation
2. Subject protein to a classical mechanical treatment (such as “simulated annealing”) that minimizes the total energy
3. Simulated annealing protocol is a common one usedTo minimize the energy. Protein is heated in the computer,which allows molecular motions to occur, and then is slowly cooled to minimize the energy (avoids local minima in the energy landscape)
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ENOE = f r(r − R)
r R
€
ETot = ENOE + EJ−coupling + EH−bond + ERDC + ...