Validation of NMR Structures Jurgen Doreleijers, Ton Rullmann, Gert Vriend, Mia Raves

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Validation of NMR StructuresJurgen Doreleijers,
Ton Rullmann, Gert Vriend, Mia Raves Rob
KapteinNMR spectroscopy, Utrecht University,
EMBL Heidelberg

• NOE Violations
• NOE Completeness
• Proton Geometry

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Validation of NMR Structures NOE Violations

• Jurgen Doreleijers, Ton Rullmann Rob Kaptein
• NMR spectroscopy, Utrecht University

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Introduction

• PROCHECK_NMR
• WHAT IF
• AQUA
• Violation analysis
• Nomenclature check
• Stereospecificity assignments
• Redundancy NOEs
• Completeness NOEs

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Validation of NMR Structures How complete is the
NOE puzzle?

• Jurgen Doreleijers, Mia Raves, Ton Rullmann Rob
  Kaptein
• NMR spectroscopy, Utrecht University

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Overview

• Introduction
• Definition
• Properties and results for 97 proteins
• Conclusion

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NOE Completeness

• No simple definition
• Used by
• Hans Vis for the HU protein
• Other groups

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Expected NOEs

• Stereospecific ? protons and all methyls
• No labile protons

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Example HU Protein

• Well-defined structure with flexible arms

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Definition of Completeness

• Completeness 100

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Definition of Completeness
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Results

• 97 Entries of previous paper
• Residue types
• Flexibility
• Secondary Structure
• Ramachandran most favoured region
• Year of publication

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Residue Types
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Flexibility
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Secondary Structure
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Completeness versus Ramachandran
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Completeness versus Year
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Conclusions

• Practical selection of atoms and averaging
• Ensemble analysis accounts for structural
  variance
• More informative than restraints per residue
• Almost independent of secondary structure
• Independent of structural variance
• Correlated with Ramachandran
• Increases over time

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Validation of NMR Structures Proton geometry and
Nomenclature

• Jurgen Doreleijers, Gert Vriend, Mia Raves,
  Rob Kaptein
• NMR spectroscopy, Utrecht University
• EMBL, Heidelberg

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Overview of Proton Checks

• 1200 Protein and nucleic-acid PDB structures
• Proton Nomenclature
• Proton Geometry
• Bond lengths
• Bond angles
• Planarity
• Tetrahedral arrangement

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PDB Nomenclature Deviations
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Proton Geometry
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Proton Distortions
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Conclusions

• 240,000 atoms (1.7 ) inverted prochiral
  labelling
• Bond length deviation Cys Sg-Hg of 0.3 Å (X-PLOR)
• Bond angle deviation Thr CbOg1Hg1 of 20
  (DSPACE)
• Tetrahedral geometry okay
• Planarity deviations severe
• Deviations can be caused by violating NOEs

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Acknowledgements
Rob Kaptein
Ton Rullmann

• Gert Vriend (EMBL)

Mia Raves