Automated 2D NOESY Assignment and Structure Calculation of Crambin(S22/I25) with the Self-Correcting Distance Geometry Based NOAH/DIAMOD Programs

Yuan Xu, Jian Wu, David Gorenstein, Werner Braun

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calculate an ensemble of 40 structures from these NOE distance constraints and random starting structures. The 10 structures with smallest target function values were analyzed by the structure-based filter, NOAH, and a new set of possible assignments was automatically generated based on chemical shifts and distance constraints violations. After 60 iterations and final energy minimization, the 10 structures with smallest target functions converged to 1.48 Å for backbone atoms. Despite several missing chemical shifts, 426 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously assigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOAH due to the incomplete proton chemical shifts list.

Original languageEnglish (US)
Pages (from-to)76-85
Number of pages10
JournalJournal of Magnetic Resonance
Volume136
Issue number1
StatePublished - Jan 1999

Fingerprint

Chemical shift
Noise
Protons
Geometry
geometry
Proteins
chemical equilibrium
Feedback
Atoms
Crambe abyssinica crambin protein
lists
iteration
proteins
filters
cycles
optimization
protons
atoms

Keywords

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

ASJC Scopus subject areas

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

Cite this

Automated 2D NOESY Assignment and Structure Calculation of Crambin(S22/I25) with the Self-Correcting Distance Geometry Based NOAH/DIAMOD Programs. / Xu, Yuan; Wu, Jian; Gorenstein, David; Braun, Werner.

In: Journal of Magnetic Resonance, Vol. 136, No. 1, 01.1999, p. 76-85.

Research output: Contribution to journalArticle

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