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

Citation
Y. Xu et al., Automatic assignment of NOESY cross peaks and determination of the proteinstructure of a new world scorpion neurotoxin using NOAH/DIAMOD, J MAGN RES, 148(1), 2001, pp. 35-46
Citations number
38
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Chemistry & Analysis","Physical Chemistry/Chemical Physics
Journal title
JOURNAL OF MAGNETIC RESONANCE
ISSN journal
1090-7807 → ACNP
Volume
148
Issue
1
Year of publication
2001
Pages
35 - 46
Database
ISI
SICI code
1090-7807(200101)148:1<35:AAONCP>2.0.ZU;2-Z
Abstract
The 3D NMR structures of the scorpion neurotoxin, CsE-v5, were determined f rom the same NOESY spectra with NOAH/ DIAMOD, an automated assignment and 3 D structure calculation software package, and with a conventional manual as signment combined with a distance geometry/simulated annealing (X-PLOR) ref inement method. The NOESY assignments and the 3D structures obtained from t he two independent methods were compared in detail. The NOAH/DIAMOD program suite uses feedback filtering and self-correcting distance geometry method s to automatically assign NOESY spectra and to calculate the 3D structure o f a protein. NOESY cross peaks were automatically picked using a standard s oftware package and combined with 74 manually assigned NOESY peaks to start the NOAH/DIAMOD calculations. After 63 NOAH/DIAMOD cycles, using REDAC pro cedures in the last 8 cycles, and final FANTOM constrained energy minimizat ion, a bundle of 20 structures with the smallest target functions has a RMS D of 0.81 Angstrom for backbone atoms and 1.11 Angstrom 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 unambi guously assigned, 150 peaks have more than one possible assignment compatib le with the bundle structures, and only 30 peaks could not be assigned with in the given chemical shift tolerance ranges in either the D1 or the D2 dim ension. The remaining 174, mainly weak NOE peaks were not compatible with t he final 20 best bundle structures at the last NOAH/DIAMOD cycle. The autom atically determined structures agree well with the structures determined in dependently using the conventional method and the same NMR spectra, with th e mean RMSD in well-defined regions of 0.84 Angstrom for bb and 1.48 Angstr om for all heavy atoms from residues 2-5, 18-26, 32-36, and 39-45. This stu dy demonstrates the potential of the NOAH/ DIAMOD program suite to automati cally assign NMR data for proteins and determine their structure. (C) 2001 Academic Press.