solution structure determination by nmr and distance geometry calculations 1. pure protein (0.3 ml,...
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![Page 1: Solution Structure Determination by NMR and Distance Geometry Calculations 1. Pure Protein (0.3 mL, 0.5 - 1 mM; ~ 10 mg) 2. Sequence-specific resonance](https://reader034.vdocument.in/reader034/viewer/2022042616/5697c02a1a28abf838cd7e7b/html5/thumbnails/1.jpg)
Solution Structure Determination by NMR and Distance Geometry Calculations
1. Pure Protein (0.3 mL, 0.5 - 1 mM; ~ 10 mg)2. Sequence-specific resonance assignments3. Sequence-specifice distance constraints
disulfide bondsspin-spin coupling constantsinternuclear distance constraints from NOEsresidual dipolar couplingshydrogen bonds standard bond lengths; bond angles
4. Distance Geometry Calculations5. Constrained Energy Minimization; Refinement
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Basic Principles
Nuclear Spin and Magnetization
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Magnetization and Coherence
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Fourier Transform NMRErnst & AndersonRev. Scientific Instrumentation 37: 93 (1966)
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Nuclear Relaxation
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Spin-Spin Coupling
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Chemical Shift with Spin-Spin Coupling
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1D NMR Spectrum of a Protein
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2D Correlated SpectroscopY
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AV-COSY
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Nuclear Overhauser Effect (NOE)
Def: The change in the intensity of resonance i upon irradiation of resonance j due to “cross relaxation” between spins i and j through space
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2D NOESY Spectrum of a Protein
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Some Useful 2D NMR Experiments
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1H-13C Heteronuclear Correlation Spectrum
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Solution Structure Determination by NMR and Distance Geometry Calculations
1. Pure Protein (0.3 mL, 0.5 - 1 mM; ~ 10 mg)2. Sequence-specific resonance assignments3. Sequence-specifice distance constraints
disulfide bondsspin-spin coupling constantsinternuclear distance constraints from NOEsresidual dipolar couplingshydrogen bonds standard bond lengths; bond angles
4. Distance Geometry Calculations5. Constrained Energy Minimization; Refinement
![Page 22: Solution Structure Determination by NMR and Distance Geometry Calculations 1. Pure Protein (0.3 mL, 0.5 - 1 mM; ~ 10 mg) 2. Sequence-specific resonance](https://reader034.vdocument.in/reader034/viewer/2022042616/5697c02a1a28abf838cd7e7b/html5/thumbnails/22.jpg)
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WR41
Protein NMR Structures
C-TmZip
ER14
MMP-1
IL13
FGF-2
WR90
WR64
LC8
ER115
N-TmZip
JR19
ZR18
OP3
WR33
ZR31 ER75Z-domain
IR24
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ER75: Ecol YgdK (nmr)ER30: Ecol SufE (xray)IR24: Hinf IscU (nmr)SR17 Bsub IscU (nmr)
N N
C C
YgdKG. Liu et al. (Szyperski)
Gram neg IscU
IscU, SufE,YgdK Domain Families are Structurally
Similar
YgdK cf SufEA. Kuzin et al. (Hunt)
Ramelot et al, J. Mol. Biol. 2004Goldsmith et al., J. Mol. Biol. 2004Liu et al. submitted
T. Ramelot et al. (Kennedy)
Gram pos IscU
G. Kornhaber et al. (Montelione)
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