NMR vs. Crystallography for CHEM 645. Brian Bahnson Department of Chemistry & Biochemistry University of Delaware. Distance Restraints. Through space - NOE. NOE 1/r 6 . f ( t c ). Tortional Restraints through bond J-coupling. NMR Refinement. ideal geometry. NMR term.
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Department of Chemistry & Biochemistry
University of Delaware
Through space - NOE
NOE 1/r6.f (tc)
through bond J-coupling
= wNMR distance restraint + tortional restraint + wideal Etotal
= wFwhkl (|Fo| - |Fc|)2hkl + wideal Etotal
13C, 15N labeling, homogeneity
Bigger magnet is better – 600, 750 or 900 MHz
2-D and 3-D homonuclear
and heteronuclear pulse sequences
Ikura et al., (1989) Biochemistry 29, 4659-4667., then do
NOE: Wuthrich, (1989) Science 243, 45-50. also: J-coupling ~ tortion
Pattern recognition, build 100 models, select 20 best
Minimize restraint violations, keep “good” geometry
= WN(distance restraint violation + WI (Etotal)
of closed form calmodulin
X-ray Crystal Structures
Bundle of 20 NMR models of calmodulin
Crystallography vs. NMR – advantage/disadvantages
Molecular Replacement – homology modeling
Molecular Replacement (MR) – another method to estimate phases
– use a structurally homologous protein
>25% sequence identity is sometimes possible
>50% sequence identity is a safe bet
Suppose you wanted to make a model of BSIDH
Homology Modeling Links
Homology modeling tutorial
Principles of Protein Structure, Comparative Protein Modeling and Visualization
(http://swissmodel.expasy.org//course/course-index.htm)DeepView - download a free version of this viewer. Its also for linux computers.
A tutorial for Deep View was made by Gale Rhodes, the author of CMCC.