Automatic assignment of NOESY cross peaks and determination of the protein structure of a new world scorpion neurotoxin using NOAH/DIAMOD

Yuan Xu, Michael J. Jablonsky, Patricia L. Jackson, Werner Braun, N. Rama Krishna

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

The 3D NMR structures of the scorpion neurotoxin, CsE-v5, were determined from the same NOESY spectra with NOAH/DIAMOD, an automated assignment and 3D structure calculation software package, and with a conventional manual assignment combined with a distance geometry/simulated annealing (X-PLOR) refinement method. The NOESY assignments and the 3D structures obtained from the two independent methods were compared in detail. The NOAH/DIAMOD program suite uses feedback filtering and self-correcting distance geometry methods to automatically assign NOESY spectra and to calculate the 3D structure of a protein. NOESY cross peaks were automatically picked using a standard software package and combined with 74 manually assigned NOESY peaks to start the NOAH/DIAMOD calculations. After 63 NOAH/DIAMOD cycles, using REDAC procedures in the last 8 cycles, and final FANTOM constrained energy minimization, a bundle of 20 structures with the smallest target functions has a RMSD of 0.81 Å for backbone atoms and 1.11 Å for all heavy atoms to the mean structure. Despite some missing chemical shifts of side chain protons, 776 (including 74 manually assigned) of 1130 NOE peaks were unambiguously assigned, 150 peaks have more than one possible assignment compatible with the bundle structures, and only 30 peaks could not be assigned within the given chemical shift tolerance ranges in either the D1 or the D2 dimension. The remaining 174, mainly weak NOE peaks were not compatible with the final 20 best bundle structures at the last NOAH/DIAMOD cycle. The automatically determined structures agree well with the structures determined independently using the conventional method and the same NMR spectra, with the mean RMSD in well-defined regions of 0.84 Å for bb and 1.48 Å for all heavy atoms from residues 2-5, 18-26, 32-36, and 39-45. This study demonstrates the potential of the NOAH/DIAMOD program suite to automatically assign NMR data for proteins and determine their structure.

Original languageEnglish (US)
Pages (from-to)35-46
Number of pages12
JournalJournal of Magnetic Resonance
Volume148
Issue number1
DOIs
StatePublished - 2001

Fingerprint

Scorpions
Neurotoxins
Nuclear magnetic resonance
Chemical shift
proteins
Software packages
Atoms
bundles
Proteins
Geometry
Simulated annealing
Software
nuclear magnetic resonance
cycles
chemical equilibrium
Protons
computer programs
Feedback
atoms
simulated annealing

Keywords

  • Automated NMR spectra assignment
  • DIAMOD
  • Neurotoxins
  • NOAH
  • Self-correcting distance geometry
  • XPLOR

ASJC Scopus subject areas

  • Molecular Biology
  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Radiology Nuclear Medicine and imaging
  • Condensed Matter Physics

Cite this

Automatic assignment of NOESY cross peaks and determination of the protein structure of a new world scorpion neurotoxin using NOAH/DIAMOD. / Xu, Yuan; Jablonsky, Michael J.; Jackson, Patricia L.; Braun, Werner; Krishna, N. Rama.

In: Journal of Magnetic Resonance, Vol. 148, No. 1, 2001, p. 35-46.

Research output: Contribution to journalArticle

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abstract = "The 3D NMR structures of the scorpion neurotoxin, CsE-v5, were determined from the same NOESY spectra with NOAH/DIAMOD, an automated assignment and 3D structure calculation software package, and with a conventional manual assignment combined with a distance geometry/simulated annealing (X-PLOR) refinement method. The NOESY assignments and the 3D structures obtained from the two independent methods were compared in detail. The NOAH/DIAMOD program suite uses feedback filtering and self-correcting distance geometry methods to automatically assign NOESY spectra and to calculate the 3D structure of a protein. NOESY cross peaks were automatically picked using a standard software package and combined with 74 manually assigned NOESY peaks to start the NOAH/DIAMOD calculations. After 63 NOAH/DIAMOD cycles, using REDAC procedures in the last 8 cycles, and final FANTOM constrained energy minimization, a bundle of 20 structures with the smallest target functions has a RMSD of 0.81 {\AA} for backbone atoms and 1.11 {\AA} for all heavy atoms to the mean structure. Despite some missing chemical shifts of side chain protons, 776 (including 74 manually assigned) of 1130 NOE peaks were unambiguously assigned, 150 peaks have more than one possible assignment compatible with the bundle structures, and only 30 peaks could not be assigned within the given chemical shift tolerance ranges in either the D1 or the D2 dimension. The remaining 174, mainly weak NOE peaks were not compatible with the final 20 best bundle structures at the last NOAH/DIAMOD cycle. The automatically determined structures agree well with the structures determined independently using the conventional method and the same NMR spectra, with the mean RMSD in well-defined regions of 0.84 {\AA} for bb and 1.48 {\AA} for all heavy atoms from residues 2-5, 18-26, 32-36, and 39-45. This study demonstrates the potential of the NOAH/DIAMOD program suite to automatically assign NMR data for proteins and determine their structure.",
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