Happy 10th, Biowulf

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Happy 10th, Biowulf!
Protein structure from NMR chemical shifts

• Basics of protein NMR and chemical shifts
• Exploiting chemical shifts and the PDB for
  structure determination

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Chemical Shifts in NMR
? (µ/2pI)Bo(1-s)
Bo
OH CH2 CH3
Staphylococcal nuclease
Ethyl alcohol
Resonance assignment through 13C and 15N labeling
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Conventional protein structure determination
Parsons, Biochemistry 47, 3131-3142 (2008)
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Georg Kontaxis Frank Delaglio
Molecular Fragment Replacement (MFR)

• Search PDB for small fragments whose simulated
  dipolar couplings and shifts match the observed
  RDC values and chemical shifts.
• Use the fragment information to reconstitute
  larger structural elements.

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Chain building by translating oriented MFR
fragments
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• Backbone Chemical Shifts Prediction from Protein
  Structure
• Protein Structure Generation from Backbone
  Chemical Shifts

Yang Shen
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SPARTA (Shift Prediction from Analogy in Residue
type and Torsion Angle )Torsion angles gt
Chemical shifts
Query Tri-peptide (i)
R1-R2-R3
R2-R3-R4
R4-R5-R6

Rj-1-Rj-Rj1
Triplet Database (j) dDN, dDHa, dDC,dDCa,
dDCb, dDHN f,y,c1 angles sequence ring
current shifts H-bonds
Similarity Score Function
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Shift Prediction from Analogy in Residue type and
Torsion Angle SPARTA
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Accuracy of SPARTA vs SHIFTX and D(f,y)
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SPARTA knows how well it predicts the chemical
shift
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Chemical-shift-only based MFR combined with
ROSETTA
David Baker Univ Washington Monte-Carlo
combinations of N x 200 fragments
Gong et al. Prot. Sci. 161515-21 (2007) Linus
program
Cheshire
Cavalli Vendruscolo PNAS 2007
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Chemical shift Rosetta StructuresUbiquitin and
GB3
GB3
Ubiquitin
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Blind CS-Rosetta results
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No chemical shifts for given atom types
No 13C shifts
No HA shifts
No HA and CB shifts
Rosetta_ref
No 13C and HA shifts
No 13C, HA and CB shifts
csRosetta_reference
10000 models for each ubiquitin test run
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Hybrid CS-ROSETTA for proteins with missing
chemical shifts

• Paramagnetic proteins
• Conformational exchange
• Membrane proteins (?)

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Fragments quality and convergence for TM1442
missing assignments
Regular MFR
3-res fragments
9-res fragments
hybrid
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Fragments and assembly for Yb3 calbindin
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CS-Rosetta Xray of Yb3 calbindin D9K
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Christina Bodner Yang Shen Jordan Chill
Lishan Yao Alex Grishaev
Dennis Torchia
Jinfa Ying Justin Lorieau Beat
Vogeli
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Accessible space for 7-residue MFR fragments
depends on (DDd)7x6
TALOS SPARTA
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CS-Rosetta structures from solid state NMR data
backbone rmsd
regular
regular
hybrid
hybrid
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GA and GB Two designed proteins of nearly
identical sequence
Phil Bryan John Orban
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CS-Rosetta converges very well
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Rosetta without chemical shifts starts failing
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CS-Rosetta converges even when using just 13Ca or
15N/1H shifts